decapentaplegic


TRANSCRIPTIONAL REGULATION


Table of contents

cis-Regulatory Sequences and Functions

There are three major regulatory domains in the dpp gene: a downstream region of over 15 kb regulates transcription in imaginal discs; a central region including the protein coding sequences is responsible for embryonic expression in the dorsal domain, and an upstream region is responsible for wing veination (St. Johnston, 1990).

Grainyhead/NTF-1 is a cofactor in the repression of decapentaplegic and zerknüllt. Repression by Dorsal appears to require accessory proteins that bind to corepression elements in Dorsal-dependent regulatory modules called ventral repression regions (VRRs). A corepression element in dpp is located within a previously identified VRR and close to essential Dorsal-binding sites. One of the dpp response elements in the dpp VRR overlaps the binding site for a potential activator protein, suggesting that one mechanism of ventral repression may be the mutually exclusive binding of repressor and activator proteins (Huang, 1995).

Multiple regions within the second intron of dpp cooperate with one another to generate the wild-type level and pattern of dpp transcription. These regions contain both generalized enhancer elements as well as ventral-specific repressor elements. The ventral specific repression of dpp transcription is directly mediated by binding sites for the Dorsal (DL) morphogen in the repressor elements. In contrast with the zerknüllt ventral repressor element, which contains a few high-affinity DL-binding sites, dpp contains multiple relatively low-affinity sites that function together to bring about complete ventral repression. Because dpp and zerknüllt have nearly coincident early expression domains, these results indicate that the same boundary of repression can be specified by DL-binding sites of different affinity (Huang, 1993).

Several aspects of the normal dpp expression pattern appear to depend on the unique properties of the dpp core promoter, consisting of multiple independent elements in the dpp 5'-flanking region. This core promoter (extending from -22 to +6) is able to direct a phase II expression pattern, in broad longitudinal stripes, in the absence of additional upstream or downstream regulatory elements. In addition, a ventral-specific enhancer in the dpp 5'-flanking region that binds the Dorsal factor activates the heterologous hsp70 core promoter but not the dpp core promoter (Schwyter, 1995).

However, these core sequences were not sufficient to drive expression in other cells normally expressing dpp, including cells in the gnathal segments, the clypeolabrum, the ectodermal foregut, the endodermal midgut visceral mesoderm, and the ectodermal hindgut (Jackson, 1994).

dpp transcription in the midgut is regulated by homeotic proteins through a visceral mesoderm midgut enhancer. Transcription of dppin the midgut is activated by Ultrabithorax (UBX) protein and repressed by abdominal-A (ABD-A) protein. An 813 bp dpp enhancer has been identified, capable of driving expression of a lacZ gene in a correct pattern in the embryonic midgut. The enhancer is activated ectopically in the visceral mesoderm by ubiquitous expression of Ubx or Antennapedia. Ectopic expression of abd-A represses the enhancer. A candidate cofactor, the Extradenticle protein, binds to the dpp enhancer in close proximity to homeotic protein binding sites. Mutation of either this site or another conserved motif compromises enhancer function. A 45 bp fragment of DNA from within the enhancer correctly responds to both UBX and ABD-A in a largely tissue-specific manner, thus representing the smallest in vivo homeotic response element identified to date (Manak, 1994).

decapentaplegic is a direct target of dTcf repression in the Drosophila visceral mesoderm

Drosophila T cell factor (dTcf: Pangolin) mediates transcriptional activation in the presence of Wingless signaling and repression in its absence. Wingless signaling is required for the correct expression of dpp in parasegments 3 and 7 of the Drosophila visceral mesoderm. A dpp enhancer element, which directs expression of a reporter gene in the visceral mesoderm in a pattern indistinguishable from dpp, has been shown to have two functional Pangolin binding sites. Mutations that reduce or eliminate Wingless signaling abolish dpp reporter gene expression in parasegment 3 and reduce it in parasegment 7, while ectopic expression of Wingless signaling components expand reporter gene expression anteriorly in the visceral mesoderm. However, mutation of the Pangolin binding sites in the dpp enhancer results in ectopic expression of reporter gene expression throughout the visceral mesoderm, with no diminution of expression in the endogenous sites of expression. These results demonstrate that the primary function of Pangolin binding to the dpp enhancer is repression throughout the visceral mesoderm and that activation by Wingless signaling is probably not mediated via these Pangolin binding sites to facilitate correct dpp expression in the visceral mesoderm (Yang, 2000).

Expression of dpp in the VM responds to Wg signaling. wg and pan mutations eliminate BE reporter gene expression in PS3 and slightly reduce it in PS7. A similar result has been reported for Dpp protein in an arm mutant background. These result is surprising because Drosophila embryos have a large amount of maternal embryonic PAN mRNA. It was not expected that the null pan phenotype would be similar to that of wg, which is expressed only zygotically. It has been concluded that Wg signaling is required for activation of dpp in PS3 and assists in the activation in PS7. It is also suggested that the maternal contribution of pan may not play a role in this activation. Ectopic expression of Wg or the constitutively active ArmS10 throughout the mesoderm results in the expansion of BE reporter gene expression from its endogenous site in PS7 through PS2. This expansion of expression is restricted to the VM with the exception of some faint staining in the presumptive somatic muscle precursors. A similar result was reported for Dpp protein in embryos mutant for sgg, which thus exhibit ectopic Wg signaling. Levels of reporter expression appear equally intense in all staining parasegments. Therefore, either PS3 expression must be intensified relative to PS7 expression or PS7 expression must be reduced relative to PS3, since BE expression in a wild-type background is significantly higher expression in PS7 than in PS3. Furthermore, other factors must be keeping dpp off, posterior to PS7. These include Abdominal-A, a homeodomain transcription factor that binds the same sites as Ubx and prevents dpp expression. While these results clearly demonstrate that Wg signaling results in activation of dpp in the VM, they are not yet conclusive as to whether this activation is indirect (Yang, 2000).

A search of the BE enhancer element reveals two sequences with a good match to the consensus Pan binding site. These dTcf sites might be used to directly activate dpp. However, mutation of both sites does not reduce expression directed by BE in either PS7 or PS3. Strikingly, BE reporter gene expression expands throughout the VM, even overcoming repression posterior to PS7. It had previously been reported that a fragment of BE between the BamHI and MscI restriction sites could direct reporter gene expression throughout the VM. This fragment lacks both Pan sites and all of the homeodomain binding sites. It is proposed that the two Pan binding sites in BE limit expression of this element by direct repression and that this could be the primary event regulated through these sites (Yang, 2000).

Expanded expression in the double pan site mutation approaches the levels seen in PS7 and PS3 but does not completely reach these levels. This is in contrast with ectopic Wg signaling where BE reporter gene expression from PS7 through PS3 is approximately the same intensity. It is concluded that there must be additional inputs to the BE fragment that further activate BE reporter gene transcription in PS7 and PS3, but that these are not directly regulated by Wg signaling through the Pan sites in BE. The most likely candidates for this activation function are: (1) Exd, which can function as a direct activator of the BE fragment in PS7 and PS3; (2) Ubx, which has already been demonstrated to directly bind the BE fragment and activate transcription, though this latter effect can only account for PS7 expression, and (3) Wg signaling to another unknown target gene, which in turn activates dpp. As noted above, Ubx itself has already been identified as a direct target of Pan activation. These results do not preclude a role for direct activation of Wg signaling on the wild-type BE enhancer through its Pan binding sites, both in reporter gene constructs and in the endogenous dpp gene. In other words, Wg signaling might still convert Pan from a repressor to an activator directly on the BE enhancer element; however, this effect is of less consequence in regulating the BE enhancer function than was initially predicted (Yang, 2000).

Mutation of either Pan binding site alone results in partial derepression of BE reporter gene expression. Derepression is much more pronounced when site T1 is mutated than when site T2 is mutated. The ectopic expression patterns of transgenic lines for the single-site mutations are weaker and more variable than either double-site mutation. This suggests that Pan proteins might be interacting synergistically on the two binding sites to repress dpp expression in the VM. In contrast to the results using the dpp enhancer, expression of Ubx in these same cells is mediated by activation through Pan sites (Yang, 2000).

There is an interesting dichotomy in these results. In one case, mutation of the Pan binding sites in BE results in derepression of reporter gene expression throughout the VM. In the other, embryos homozygous for a null pan mutation do not show derepression of a BE reporter gene. The large maternal contribution of wild-type Pan from heterozygous mothers might be sufficient to maintain the repressed state of a BE reporter gene throughout embryogenesis. However, pan and wg mutant embryos do not express the BE reporter gene in PS3 and show slightly reduced levels in PS7. In other words, with respect to activation of the BE reporter gene via Wg signaling, a null pan mutation is behaving like a complete block to Wg activation. Maternal Pan is not sufficient to substitute for zygotic gene product in Wg signaling activation of dpp. A model is proposed to explain these results. In early embryogenesis, maternal Pan binds BE and represses expression, by binding the corepressors Gro and CBP. Pan becomes modified, possibly by acetylation, and becomes refractory to conversion to an activator. There is no Wg signal and cytoplasmic Arm is phosphorylated by Sgg and degraded. Later in development, a general VM enhancer binding protein is predicted to be present, as the BamHI-MscI fragment of BE drives reporter gene expression throughout the VM and presumably dpp expression as well. In PS3 and PS7 of the VM, Wg signaling occurs, resulting in the stabilization of cytoplasmic Arm, which then combines with newly synthesized Pan (zygotic) and displaces maternal Pan to permit transcriptional activation in combination with the putative general VM enhancer binding protein, Exd, and Ubx (specifically in PS7). Outside of PS3 and PS7, zygotic Pan can gradually replace maternal Pan but, in the absence of stable Arm, it is rapidly converted to a repressor, which blocks function of the general VM enhancer. Finally, when the Pan binding sites are mutant, the general VM enhancer binding protein can constitutively activate BE reporter genes and this level of expression is increased in PS3 and PS7 by the binding of Exd and Ubx. Additional proteins may also play a role in this regulation. One prediction of this model is that removal of maternal Pan would result in derepression of the BE reporter gene throughout the VM (Yang, 2000).

Functional dominance among Hox genes: repression dominates activation in the regulation of dpp

A 674 bp enhancer of dpp controls its expression in the second constriction domain of the visceral mesoderm (parasegment 7). Normal enhancer function requires positive regulation by Ubx and negative regulation by abd-A. This enhancer contains UBX- and ABD-A-binding sites defined in vitro. By generating complementary alterations of the binding sites and the binding specificity of UBX, it has been shown that UBX directly regulates dpp expression. These regulatory interactions are relevant to normal development, because a transgene made with this enhancer driving a dpp transcription unit rescues the second midgut constriction and larval lethality phenotype of dpp mutation (Capovilla, 1994).

An investigation was carried out into the mechanisms by which Hox genes compete for the control of positional identity. Functional dominance is often observed where different Hox genes are co-expressed, and frequently the more posteriorly expressed Hox gene is the one that prevails, a phenomenon known as posterior prevalence. To investigate functional dominance among Hox genes on a molecular basis, dpp674, a visceral mesoderm-specific enhancer of decapentaplegic was used. In the visceral mesoderm, dpp is expressed in parasegment 7 (PS7), where it is required for the formation of the second midgut constriction. Expression of dpp is positively regulated by Ubx in PS7, and negatively regulated by abd-A in PS8-12. Regulation of dpp by Ubx and abd-A takes place through a 680-bp visceral mesoderm-specific enhancer (dpp674). This enhancer contains Ubx/Abd-A protein binding sites defined by DNase I protection assays. Ubx regulation of dpp674 is direct, as shown in experiments in which expression from a mutated enhancer is reconstituted by compensatory changes in the UBX protein that alter its DNA-binding specificity (Capovilla, 1998 and references).

Posterior prevalence is not adequate to describe the regulation of dpp by Hox genes. Instead, abdominal-A dominates over the more posterior Abdominal-B and the more anterior Ultrabithorax. In the context of the dpp674 enhancer, abd-A functions as a repressor whereas Ubx and Abd-B function as activators. Thus, these results suggest that other cases of Hox competition and functional dominance may also be understood in terms of competition for target gene regulation, in which repression dominates over activation (Capovilla, 1998).

The idea that posterior prevalence is the dominance of repression over activation is supported by the observation that abd-A functions as an activator through the 5' portion of the dpp enhancer and as a repressor through its 3' portion. When these portions are fused together in the full enhancer, repression by abd-A prevails over activation. These findings suggest the possibility that other cases of functional dominance may be explained in terms of Hox proteins functioning as repressors and prevailing over Hox proteins functioning as activators. For example, in accordance with posterior prevalence, repression of Distal-less (Dll) by Ubx prevails over Dll activation by genes of the Antennapedia (Antp) complex. Similarly, apterous (ap) repression by Ubx prevails over Antp activation in the central nervous system. In contrast, and in violation of posterior prevalence, repression of centrosomin (cnn) by Antp dominates activation by Ubx in the visceral mesoderm. In another case, a phosphorylation-defective Antp protein (Antp [1,2,3,4]A ) has novel functions in addition to the wild-type Antp functions. At least some of its novel functions are a consequence of the ability of Antp [1,2,3,4]A to misregulate regulatory targets of other Hox genes. Antp [1,2,3,4]A violates posterior prevalence by repressing empty spiracles (ems) expression, which is normally activated by Abd-B. However it is interesting that the novel function of Antp [1,2,3,4]A as a dpp activator cannot overcome repression by abd-A, hence respecting the phenomenon of posterior prevalence. Thus the attractiveness of this model is that it explains the cases of posterior prevalence in which the posterior gene is the repressor, but it also explains other cases of functional dominance in which posterior prevalence is violated (Capovilla, 1998 and references).

Different Hox binding sites mediate different transcriptional activities. Repression by Abd-A is mediated only by certain binding sites. The ability of individual Abd-A binding sites to mediate repression does not correlate with their affinity for Abd-A measured in vitro. Specifically, a low-affinity site (binding site 4) is better able to mediate repression by Abd-A than a high-affinity site (binding site 2). These results suggest the existence of cofactors involved in the regulation of dpp674 by Abd-A. One candidate for such a factor is the product of extradenticle (exd); however, exd is not required for abd-A repression of dpp or dpp674lacZ (M. Capovilla and J. Botas, unpublished). Thus Hox specificity cannot be explained solely by Hox/Exd cooperative binding, and unidentified cofactors interacting differentially with Abd-A and other Hox products probably exist. These factors may alter Abd-A binding specificity and/or may function as corepressors or coactivators, altering Abd-A activity as a transcription factor. The above hypothesis on Hox functional dominance implies that in many cases posterior Hox genes function as repressors whereas anterior Hox genes function as activators of specific target genes. Posterior Hox genes would generally determine posterior body patterns by repressing target genes activated by more anterior Hox genes. However, it is of course unlikely that posterior Hox genes function exclusively as repressors. They probably also function as activators of some targets; the gene ems is a good candidate for direct activation by Abd-B. In these cases the cross-regulation between Hox genes (posterior Hox genes repress the expression of more anterior Hox genes) would ensure the dominance of posterior Hox genes. From the viewpoint of evolution, the easier way to create additional posterior patterns might be to generate ‘new’ Hox genes that repress existing targets rather than activate new targets or combinations (Capovilla, 1998).

Cubitus interruptus is necessary but not sufficient for direct activation of a wing-specific decapentaplegic enhancer

In Drosophila, the imaginal discs are the primordia for adult appendages. Their proper formation is dependent on the activation of the decapentaplegic gene in a stripe of cells just anterior to the compartment boundary. In imaginal discs, the dpp gene has been shown to be activated by Hedgehog signal transduction. However, an initial analysis of its enhancer region suggests that its regulation is complex and depends on additional factors. In order to understand how multiple factors regulate dpp expression, focus was placed on a single dpp enhancer element, the dpp heldout enhancer, from the 3' cis regulatory disc region of the dpp locus. A molecular analysis of this 358 bp wing- and haltere-specific dpp enhancer is presented that demonstrates a direct transcriptional requirement for the Cubitus interruptus (Ci) protein. The results suggest that, in addition to regulation by Ci, expression of the dpp heldout enhancer is spatially determined by Drosophila TCF (dTCF) and the Vestigial/Scalloped selector system and that temporal control is provided by dpp autoregulation. Consistent with the unexpectedly complex regulation of the dpp heldout enhancer, analysis of a Ci consensus site reporter construct suggests that Ci, a mediator of Hedgehog transcriptional activation, can only transactivate in concert with other factors (Hepker, 1999).

The dppho enhancer (so named because mutations in the region result in a 'held out' wing phenotype) was chosen for detailed analysis because this small region contains a cluster of putative transcription factor binding sites that is conserved in Drosophila virilis. The dppho enhancer is located from map position 111.9 to 112.3, approximately 18 kb from the 3' terminus of the dpp structural gene. The enhancer shares 52% sequence identity with the homologous region from D. virilis. Within the conserved sequences are found reasonable matches for the binding sites of several known transcription factors, including Engrailed, Ci, dTCF, Mothers against Decapentaplegic (Mad) and Scalloped. Of particular interest is the presence of potential Ci consensus binding sites. Gel mobility shift assays were performed with the DNA-binding domain of Ci and they demonstrated sequence-specific binding to the dppho fragment (Hepker, 1999).

The expression pattern of dppho-lacZ is consistent with this reporter being restricted by the extent of overlap between Hh and Wg signals in the wing pouch. For example, the dppho enhancer directs expression of lacZ reporter in a stripe coincident with high-level full-length Ci and endogenous dpp expression in the wing primordium of the wing imaginal disc. Furthermore, its expression is most robust in early larval stages and fades in a manner complementary to the dynamic pattern of wg expression in the wing disc. This enhancer also directs expression of a reporter ventrally in an analogous stripe in the haltere disc. Indeed ectopic expression data, together with clonal analysis, demonstrates that Ci and dTCF regulate dppho-lacZ expression, and this regulation is shown to be direct (Hepker, 1999).

Regulation of the dppho enhancer cannot be solely dependent on Wg and Hh signals since this element directs expression specifically in presumptive wing tissue. A candidate for a wing-specific factor involved in dppho regulation is the Vestigial/Scalloped transcriptional complex. The dppho sequence contains a weak match to the Sd/TEA DNA-binding site consensus, therefore a test was performed to see whether the Vg/Sd selector system is involved in restricting dppho-lacZ expression to the wing. A 30AGAL4 or an apterousGAL4 driver was used to direct expression of UAS-vg. In both cases, ectopic expression of vg induces expression of dppho-lacZ, but only near the A/P boundary. Similar experiments performed with UAS-sd result in loss of dppho-lacZ expression (Hepker, 1999).

The expression of dppho-lacZ was examined throughout larval development. Expression of the dppho-lacZ reporter diminishes with time. Expression is detected as a contiguous stripe at second larval instar but fades in intensity by mid third instar. A likely explanation for this observation is that this reporter lacks the sequences required for maintained expression. dpp autoregulation has been reported in other tissues providing a plausible mechanism for maintenance of expression. Because binding sites for downstream transducers of dpp are present in the dppho enhancer, the response of dppho-lacZ to ectopic expression of dpp was examined. A 30AGAL4 driver was used to induce expression of a UAS-dpp transgene in a dppho-lacZ background. No animals showed any response by dppho-lacZ to ectopic induction of the Dpp signal. To determine whether sequences adjacent to the dppho enhancer element were required for dpp autoregulation, expression of the dppho-lacZ reporter line was compared to a reporter containing dppho plus an additional 2.5 kb of flanking sequences (BS3.2). The BS3.2 reporter directs expression of an A stripe along the A/P boundary that extends into the notum and is robust both early (second instar) and late (late third instar). These two reporters were assayed in a heterozygous dpp hypomorphic background. Expression of dppho-lacZ is unaffected while BS3.2 is expressed at wild-type levels early but fades by the end of third larval instar, suggesting that the larger reporter is sensitive to dpp autoregulation. Consistent with this idea, the expression levels of the BS3.2 reporter increase in response to ectopic UAS-dpp driven by 30AGAL4 but only at the A/P boundary where expression of 30AGAL4 overlaps with elevated full-length Ci (Hepker, 1999).

Wingless, Decapentaplegic and EGF Receptor signaling pathways interact to specify dorso-ventral pattern in the adult abdomen of Drosophila

To understand better the regulation of dpp in the abdomen, genomic fragments from the 3' region of dpp were tested for the ability to drive lacZ expression in the pupal epidermis. dpp expression in the histoblasts and in the LEC is controlled by separate enhancer elements located between 100 to 105 kb on the standard dpp genomic map (10 kb 3' of the transcriptional termination site). Histoblast expression is regulated by two distinct regions. Fragments from between 109.5 kb and 113.5 kb on the dpp genomic map drive lacZ expression in the developing pleura, but not in the sternite or most of the tergite. Accordingly, this region is referred to as the pleural enhancer. Unlike the endogenous dpp pattern, some of the fragments from the 109.5-113.5 kb region drive persistent, rather than transient, expression in the lateral tergite. The tergite expression is controlled in part by a distinct element, located between 112.3 kb and 113.5 kb. A second enhancer region active in histoblasts (the ‘circumferential enhancer’) is located between 117.2 kb and 118.9 kb. This fragment drives expression in a stripe that extends around almost the entire segment, interrupted only at the ventral midline and near the spiracle. Presumably the activity of this enhancer is normally repressed in the tergite and sternite territories by other regulatory regions. Sequences responsible for dpp expression along the dorsal midline have not been identifed (Kopp, 1999).

Both the pleural and circumferential histoblast enhancers are responsive to hh. Expression of the BS 3.21 reporter construct, which is representative of the pleural enhancer, is strongly expanded to the anterior in the hhMir gain-of-function mutant, whereas expression of the BS 4 construct, which contains the circumferential enhancer, is duplicated. Both enhancers are repressed by wg, although to differing extents. BS 4 expression in the tergite (but not in the pleura) is completely eliminated in hs-wg pupae grown at high temperature overnight, whereas BS 3.21 expression is only weakly affected. dpp expression in the LEC is controlled by an entirely separate region. Fragments located between 98.5 kb and 106.9 kb drive expression in a correct dpp pattern in the LEC, but not in the histoblasts. Interestingly, this region is devoid of imaginal disc enhancers. The fragments BS 1.1 (98.5-100.3 kb), BS 2 (100.2-104.5 kb) and BS 2.1 (104.7-106.9 kb) produce very similar expression patterns, suggesting that dpp expression in the LEC is controlled by several redundant enhancers. Unlike the endogenous dpp gene, the BS 2 and BS 2.1 reporters are also expressed in the third instar larval epidermis (Kopp, 1999).

biniou (FoxF), a central component in a regulatory network controlling visceral mesoderm development and midgut morphogenesis in Drosophila

The subdivision of the lateral mesoderm into a visceral (splanchnic) and a somatic layer is a crucial event during early mesoderm development in both arthropod and vertebrate embryos. In Drosophila, this subdivision leads to the differential development of gut musculature versus body wall musculature. biniou, the sole Drosophila representative of the FoxF subfamily of forkhead domain genes, has a key role in the development of the visceral mesoderm and the derived gut musculature (Zaffran, 2001).

Besides tissue-specific differentiation genes that are expressed throughout the trunk visceral mesoderm, several key regulators of midgut morphogenesis are known to be expressed in a spatially restricted manner within this tissue. This type of gene product includes the homeotic factor Ubx and the secreted factor Dpp, both of which are expressed in PS7 of the visceral mesoderm. Although it has been established that Ubx and Dpp maintain their expression in PS7 through a crossregulatory loop and the action of Wg from the adjacent PS8, there is evidence that their expression requires at least one additional, visceral mesoderm-specific cofactor, for which Bin may be a candidate. To test this possibility, Ubx and dpp expression were examined in bin mutant embryos, which carried bap3-lacZ, to allow the unambiguous identification of the disrupted visceral mesoderm layer. Visceral mesoderm expression of Ubx in bin mutant embryos is similar to that of wild-type embryos until at least stage 13, although there is a low level of ectopic expression. Likewise, Ubx expression is also observed in ß-gal-positive cells in bap mutant embryos, albeit with reduced levels and an expanded domain: These conditions are comparable to those in the somatic mesoderm. These data demonstrate that the establishment of Ubx expression in the visceral mesoderm requires neither bin nor bap activity. In contrast, dpp is not expressed at any stage in PS7 in the visceral mesoderm of bin mutant embryos, indicating that Bin may serve as a critical tissue-specific cofactor for the regulation of dpp expression. The expression of wg in PS8 is also absolutely dependent on bin activity. The absence of these morphogenetic factors is likely to contribute to the defective midgut morphology in bin mutant embryos (Zaffran, 2001).

The identification of visceral mesoderm-specific enhancer elements of dpp allowed a test of the possibility that bin might be a direct upstream regulator of dpp in the visceral mesoderm. Attention was focused on two minimal enhancer elements: the 130 bp element BM and the 231 bp element. PB is able to drive reporter gene expression in PS3 and PS7 of the visceral mesoderm in a pattern that is similar to that of endogenous dpp, although PB-lacZ expression in PS7 is less robust. In contrast to PB, BM is active in a broad region extending from PS7 to PS12 in the visceral mesoderm. In addition, the combination of BM and PB results in a significant enhancement of PS7 expression compared to PB alone. Because of the broad activity of BM in the visceral mesoderm and its enhancing effect on PB (or longer versions thereof), BM has been proposed to act as a general visceral mesoderm enhancer (GVME), whereas PB is predominantly targeted by spatially restricted activities that include Ubx and Exd (Zaffran, 2001).

DNaseI protection assays were performed with recombinant Bin protein to test for the presence of Bin binding sites within BM and PB. These experiments identified two protected regions within BM, termed Bin I and Bin II, which are about 50 bp apart from one another. PB contains a third strongly protected sequence, Bin III, and two minor binding sites which overlap with the Exd binding sites e1 and e2. All three of the strongly protected sequences and the weaker e1 contain sequence motifs that perfectly match forkhead domain binding sites, including the optimal binding site of a vertebrate ortholog, HFH-8. The presence of overlapping inverted and direct repeats of this sequence motif in Bin II and Bin III, respectively, may indicate that these two sites represent dimeric binding sites. Interestingly, the sequences of the three strong and two weak Bin binding sites within PB are highly conserved between D. melanogaster and D. virilis, suggesting that they are functionally important (Zaffran, 2001).

To test whether any of the strong Bin binding sites are required for enhancer activity in vivo, nucleotide exchanges that completely abolished in vitro binding of Bin were introduced. Mutation of Bin III results in an almost complete loss of PB enhancer activity in PS7, suggesting that Bin binding to Bin III plays an important role for the activation of dpp in this parasegment. The presence of two weak Bin binding sites in the mutated PB derivative may allow residual expression in a few visceral mesoderm cells within PS7. The fact that PS3 expression is not affected significantly upon Bin III mutation may be due to the activity of Exd binding sites, of which one was previously shown to regulate PS3 expression (Zaffran, 2001).

BM enhancer activity in the visceral mesoderm is completely lost when both Bin I and Bin II are mutated. When this mutated version of BM is combined with a wild-type version of PB, there is no enhancement of PS7 expression and the same pattern observed as that with PB alone. Finally, the combination of BM and PB with mutated Bin I, II, and III binding sites does not exhibit any significant enhancer activity in PS7. These data suggest that both BM and PB contain functionally important Bin binding sites. Bin binding to Bin I and Bin II may be key to providing BM with its general visceral mesoderm enhancer activity, whereas binding to Bin III is required in concert with spatially restricted activities to provide the PB enhancer with a basal level of activity in PS7 (Zaffran, 2001).

Binding of the RING polycomb proteins to specific target genes in complex with the grainyhead-like family of developmental transcription factors

The Polycomb group (PcG) of proteins represses homeotic gene expression through the assembly of multiprotein complexes on key regulatory elements. The mechanisms mediating complex assembly have remained enigmatic since most PcG proteins fail to bind DNA. The human PcG protein dinG interacts with CP2, a mammalian member of the grainyhead-like family of transcription factors, in vitro and in vivo. The functional consequence of this interaction is repression of CP2-dependent transcription. The CP2-dinG interaction is conserved in evolution with the Drosophila factor Grainyhead binding to dring, the fly homolog of dinG. Electrophoretic mobility shift assays demonstrate that the Grh-dring complex forms on regulatory elements of genes whose expression is repressed by Grh but not on elements where Grh plays an activator role. These observations reveal a novel mechanism by which PcG proteins may be anchored to specific regulatory elements in developmental genes (Tuckfield, 2002).

Strong evolutionary conservation of amino acid sequence exists between the mammalian and Drosophila members of the Grainyhead-like family. The likelihood of a similar conservation of function led the idea of the existence of a Drosophila homolog of dinG. Database searches identified a sequence that has been termed dring (FlyBase term: Sex combs extra), which has 44% identity and 61% similarity to the dinG amino acid sequence and 50% identity and 68% similarity in the domain of the dinG protein which interacts with the GRH-like family. To determine whether the Drosophila factor Dring could interact with Grh, radiolabeled in vitro-transcribed and translated Grh was generated for GST chromatography assays. Grh was shown to be specifically retained on a GST-Dring matrix but not on GST alone, confirming the evolutionary conservation of this interaction (Tuckfield, 2002).

DinG can interact with CP2 and repress transcription from a CP2-dependent promoter. These data were generated in the context of a concatemerized consensus CP2 binding site. No physiological target genes of CP2-mediated repression have been identified in mammalian systems. In contrast, the regulatory regions in the dpp and tll genes involved in Grh-mediated repression have been clearly defined in vivo. In view of the significant homology between Grh and CP2 in the DNA binding domain, whether the CP2-dinG complex could form on the Grh-responsive element in the dpp promoter was examined. A probe containing the DRE-B region of the dpp promoter was studied in an EMSA in the presence of nuclear extract from the mammalian cell line JEG-3. Addition of this extract to the DRE-B probe resulted in the formation of a DNA-protein complex. This complex was ablated by the addition of either anti-CP2 or anti-dinG antiserum. To extend this observation, whether the GRH-DRING complex could assemble on the regulatory regions in the dpp and tll genes that are critical for GRH-mediated repression was examined. Probes containing the DRE-B region of the dpp promoter and the tor-RE element in the tll promoter were studied in an EMSA with Drosophila embryo extract in the presence and absence of anti-Grh antiserum or anti-dinG antiserum (which cross-reacts with the Drosophila DRING protein). The be2 element of the Ddc promoter (where Grh functions as a transcriptional activator) was also studied. A complex consisting of at least Grh and Dring formed on both the dpp and tll elements. In both settings, the complex was ablated (or shifted out of the gel) by anti-Grh and anti-dinG antisera. In contrast, the complex formed on the Ddc promoter was ablated by the addition of anti-Grh antiserum but remained unchanged in the presence of anti-dinG antiserum (Tuckfield, 2002).

The hexapeptide and linker regions of the AbdA hox protein regulate its activating and repressive functions

The Hox family transcription factors control diversified morphogenesis during development and evolution. They function in concert with Pbc cofactor proteins. Pbc proteins bind the Hox hexapeptide (HX) motif and are thereby thought to confer DNA binding specificity. The mutation of the AbdA HX motif as reported here does not alter its binding site selection but does modify its transregulatory properties in a gene-specific manner in vivo. A short, evolutionarily conserved motif, PFER, in the homeodomain-HX linker region acts together with the HX to control an AbdA activation/repression switch. These in vivo data thus reveal functions not previously anticipated from in vitro analyses for the hexapeptide motif in the regulation of Hox activity (Merabet, 2003).

Extensive in vitro analyses have demonstrated that the HX is responsible for the interaction with Pbc proteins, leading to the view that this motif imparts Hox DNA binding specificity and therefore assists Hox proteins in the selection of appropriate target genes. In vivo data challenge this view in several ways. (1) The unaltered capacity of AbdA(HXm) to induce A2-like identities in the thorax and to form dimeric complexes on DNA with Exd shows that the HX is not the only motif of AbdA that is able to recruit Exd. A similar situation has been shown to occur in Ubx, indicating that other residues in Hox proteins can compensate for the lack of the HX in mediating Hox/Exd interactions. (2) Mutation of the HX does not affect binding site selection by AbdA, as shown by the ability of the mutant protein to bind target sequences from Dll and dpp in vitro, and to control dpp promoter elements in vivo. Accordingly, the HX mutation does not alter target gene selection (in this case, wg and dpp in the VM) in vivo. (3) The fact that the HX mutation modifies AbdA function in the regulation of dpp, which does not depend on Exd, implies that the HX should interact with additional proteins that remain to be identified. These data thus endow the HX with unexpected functions; this does not preclude that the HX could, however, play a role in target selection in other developmental contexts. The PFER motif within the linker region was found to fulfill an important regulatory function; this was also unexpected, considering the variable length and disordered structure of this region (Merabet, 2003).

The regulation of dpp by AbdA in the VM is mediated by the dpp674 enhancer, which contains seven binding sites for AbdA. Sites 1-4 in dpp419 (the 3' portion of dpp674) mediate repression by AbdA, while sites 5-7 in dpp265 (the 5' portion of dpp674) mediate activation. Interestingly, dpp265 reveals an activating potential of AbdA on dpp transcription that is masked by the prevalence of repression over activation in the regulation of dpp674 or dpp. Exd acts in a Hox-independent manner to repress dpp in the anterior VM. Anterior expression of dpp induced by AbdA(HXm) could therefore result from an interference with the repressive function of Exd, rather than from a direct effect on dpp transcription. However, while dpp265 is not derepressed anteriorly in exd- or hth-deficient animals and, therefore, does not contain the sequences mediating repression by Exd, it is activated by AbdA(HXm). Thus, Exd and AbdA(HXm) act on different regulatory sequences to respectively repress or activate dpp in the anterior VM, which makes it unlikely that activation by AbdA(HXm) results from an interference with the Hox-independent repressive function of Exd. Considering that the HX mutation affects neither DNA binding nor target site recognition in vitro and in vivo, it is proposed that AbdA(HXm), as does AbdA, controls dpp transcription directly (Merabet, 2003).

The function of the HX and PFER motifs in switching AbdA from an activator to a repressor clearly depends on the cis-regulatory target sequence, which is illustrated by the distinct effects of the variants on dpp and wg transcription, and of AbdA(PFERm) on dpp419 and dpp265. Taking these observations together, a model is proposed that accounts for how the distinct regulatory modules, which have been identified functionally, interconnect to specify AbdA activity in the VM. According to this model, the HX plays a central dual role in repressing the function of a Q-rich activation domain and promoting that of a repression domain whose location remains to be determined. For the regulation of dpp, the HX senses dpp cis-regulatory specificity to select the repressive potential of AbdA. Conversely, in the regulation of wg, the PFER sequence senses wg cis-regulatory specificity to select the activating potential of the Hox protein. According to the functional epistatic relationship between the two motifs, suggested by the activity of the doubly mutated AbdA(HXm;PFERm) variant, the PFER sequence would not directly control repressive or activating domains of AbdA but, rather, acts upstream, as an inhibitor of HX function (Merabet, 2003).

Embryonic enhancers in the dpp disc region regulate a second round of Dpp signaling that represses Zfh-1 expression in pericardial cells

During germ band elongation, widespread dpp expression in the dorsal ectoderm patterns the underlying mesoderm. These Dpp signals specify cardial and pericardial cell fates in the developing heart. At maximum germ band extension, dpp dorsal ectoderm expression becomes restricted to the dorsal-most or leading edge cells (LE). A second round of Dpp signaling then specifies cell shape changes in ectodermal cells leading to dorsal closure. A third round of dpp dorsal ectoderm expression initiates during germ band retraction. This round of dpp expression is also restricted to LE cells but Dpp signaling specifies the repression of the transcription factor Zfh-1 in a subset of pericardial cells in the underlying mesoderm. Surprisingly, cis-regulatory sequences that activate the third round of dpp dorsal ectoderm expression are found in the dpp disc region. The activation of this round of dpp expression is dependent upon prior Dpp signals, the signal transducer Medea, and possibly release from dTCF-mediated repression. These results demonstrate that a second round of Dpp signaling from the dorsal ectoderm to the mesoderm is required to pattern the developing heart and that this round of dpp expression may be activated by combinatorial interactions between Dpp and Wingless (Johnson, 2003).

The dpp151H strain has a hobo transgene inserted into the dpp disc region. Plasmid rescue reveals a precise insertion of the transgene between nucleotides 251,529 and 251,530 of GenBank AE003583, approximately 46kb above the structural gene. dpp151H lacZ expression initiates during early germ band retraction (at roughly stage 12) in a subset of LE cells and continues through stage 17. In contrast, dpp mRNA is expressed in the LE during germ band elongation and retraction (Johnson, 2003).

The onset of dpp151H expression occurs after dpp mRNA is first detected in the LE. It was hypothesized that dpp151H expression pattern reflected a second round of Dpp LE signaling (from the dorsal ectoderm to the mesoderm. The paracentric inversions generating the alleles dppd6 and dppd5 remove varying amounts of disc region sequences from the dpp locus. dppd6 is classified as a class III disc allele. Class III mutants are missing the terminal regions of most adult appendages. dppd5 is classified as a class II disc allele. Class II mutants are milder than class III and are characterized by loss of tissue in just three adult appendages. Due to their proximity to the dpp151H insertion site, it was reasoned that the dppd6 or dppd5 inversion remove enhancers driving dpp151H expression, thus eliminating a potential second round of Dpp LE expression (Johnson, 2003).

If a second round of Dpp LE expression influences mesodermal cell fate during late stages of heart development, it would be necessary to be familiar with the wild-type expression patterns of cardial and pericardial cell markers such as Even-skipped (Eve), Seven-up, Zfh-1, and E7 3rd 63 (an enhancer trap in seven up. An unusual feature of Zfh-1 expression was noted that has not been previously described. Zfh-1 is a zinc finger and homeobox containing protein that is widely expressed in the dorsal mesoderm during early stages of heart development. Following germ band retraction, Zfh-1 becomes restricted to pericardial cells and is detected in these cells throughout the remainder of heart development. Analysis of zfh-1 loss of function mutations shows that at early stages of heart development zfh-1 is required to maintain Eve expression but that at late stages Zfh-1 and Eve are expressed in nonoverlapping sets of pericardial cells. Examination of late stage zfh-1 mutant embryos revealed morphological defects in the heart that reflect the effects of Zfh-1 on other, as yet unidentified, pericardial genes. It was noticed that the total number of pericardial cells expressing Zfh-1 decreases significantly from stage 13 to stage 17 in wild-type embryos (Johnson, 2003).

This study suggests that a second round of dpp LE expression leads to a second round of Dpp dorsal ectoderm to mesoderm signaling. The role of the second round of Dpp LE signaling appears to be the specification of a novel subset of pericardial cells by repressing the expression of the transcription factor Zfh-1. Sequences in the dpp disc region and the signal transducer Medea are required for the second round of dpp LE expression (Johnson, 2003).

Expression data reveal that a second round of dpp LE expression initiates during germ band retraction. Genetic analyses suggest that these Dpp signals influence pericardial cell fate specification by repressing Zfh-1 expression. These results provide an explanation for the observation that p-Mad is detectable in pericardial cells of germ band retracted embryos. Most likely, the second round of Dpp LE signaling stimulates p-Mad accumulation in pericardial cells during the repression of Zfh-1 expression (Johnson, 2003).

This study also extends previous studies of Zfh-1. To date, the only known function of Zfh-1 in the mesoderm is to maintain Eve expression in pericardial cells during early stages of heart development. However, late stage zfh-1 mutant embryos show heart defects not explainable by the failure to maintain Eve expression. These results led to the suggestion that Zfh-1 has additional roles during late stages of heart development. The presence of unexplained heart defects in zfh-1 mutant embryos supports the hypothesis that the second round of Dpp LE signaling functions, through repression of Zfh-1, to specify a single pericardial cell type during late stages of embryonic heart development. Perhaps the heart defects of zfh-1 mutants are due to an excess of non-Zfh-1-expressing pericardial cells (Johnson, 2003).

The second round of Dpp LE signaling shares a number of features with Dpp signaling in the embryonic midgut. For example, in both cases Dpp signals across germ layers during late stages of organogenesis to specify a single cell type via the modulation of transcription factor expression. In the midgut, Dpp signaling from the visceral mesoderm to the endoderm specifies a single cell type (copper cells) through the activation of the transcription factor labial during late stages of midgut morphogenesis (Johnson, 2003 and references therein).

Another interesting similarity between these two aspects of Dpp signaling is the unexpected location of their cis-regulatory sequences. The cis-regulatory sequences governing dpp visceral mesoderm expression are located in the shv region. However, phenotypic analyses of dpp shv mutations, including those that lack dpp visceral mesoderm expression (e.g., dpps6, a 4.5-kb deletion), reported only postembryonic lethality and adult appendage defects. Thus, the elimination of dpp visceral mesoderm expression and a subsequent loss of a single cell type (copper cells) in dpps6 individuals did not lead to embryonic lethality. As a result, early studies of dpp ascribed no embryonic function to the shv region (Johnson, 2003).

Similar circumstances apply to the dpp disc region. Phenotypic analyses show that homozygous dpp disc mutations display postembryonic lethality or adult appendage defects. Reporter gene studies show that dpp disc region sequences direct dpp expression in imaginal discs. Thus, until now, no embryonic functions have been ascribed to the disc region (Johnson, 2003).

To determine if a small percentage of embryonic lethality in dppd6 mutants may have been missed in previous studies an explicit stage of lethality study was conducted for dppd6 homozygous individuals (the genotype showing Zfh-1 repression). dppd6 homozygous embryos become larvae at exactly the same rate as individuals with a homozygous viable and fertile dpp disc mutation (dppd-ho). Thus, analogous to dpp shv mutations and copper cell specification, the absence of a single pericardial cell type in the heart in dppd6 mutants does not cause embryonic lethality (Johnson, 2003).

Genetic analysis demonstrates that some of the enhancers responsible for the second round of dpp LE expression are contained within the portion of BS3.21 that is not shared with BS3.22. An interspecific comparison shows that this region contains a stretch of 96 nucleotides that is 95% identical between two evolutionarily distant Drosophila species. An examination of this 96-base pair stretch reveals a candidate Mad/Med binding site that is 100% conserved between the species. This is consistent with results showing that BS3.21 expression requires dpp disc region sequences and that dpp151H expression requires Medea (Johnson, 2003).

Previous studies have shown that Wg signals repress dpp expression. One particularly relevant example is in the leg imaginal disc where Wg signaling represses dpp transcription within the wg expression domain. Two recent studies have been conducted to identify the factors and cis-regulatory sequences mediating Wg repression of dpp expression in leg discs. These studies show that either the expression of a dominant negative form of dTCF or the mutation of all dTCF binding sites in the reporter gene dpp-H3/Nhe eliminate Wg repression of dpp expression in leg discs. This suggests that Wg signaling represses dpp expression in leg discs via dTCF binding sites. These are the dTCF sites just outside of BS3.21 that are contained in all of the overlapping reporter genes that fail to display LE expression (Johnson, 2003).

A model is proposed for the regulation of the second round of dpp LE expression. In this model, combinatorial interactions between Dpp and Wg signals regulate the second round of dpp LE expression. It is proposed that during early stages of heart development Wg signals repress transcription from the disc region enhancers responsible for the second round of dpp LE expression via dTCF sites, just as Wg represses dpp expression in leg discs. Subsequently during germ band retraction, an as yet unidentified factor expressed in a subset of LE cells activates the second round of dpp LE expression. This factor appears to play a dual role, simultaneously disabling Wg repression and positively stimulating the second round of dpp LE expression. Once activated, Dpp autoregulation takes over to maintain the second round of dpp LE expression (Johnson, 2003).

An alternative model is suggested by studies of dpp midgut expression that showed that during early stages of midgut morphogenesis dTCF acts to repress dpp expression in the visceral mesoderm. Subsequently, Wg signaling from adjacent cells relieves dTCF repression and activates dpp expression. However, the first model is favored since it is drawn from interactions associated specifically with the disc region sequences involved in the second round of dpp LE expression (Johnson, 2003).

Interestingly, each of the three rounds of dpp dorsal ectoderm expression and Dpp signaling involve input from Wg in a different fashion. During the first round of Dpp signaling (to mesoderm), wg and dpp are independently required to maintain tinman expression. During the second round of Dpp signaling (the first from the LE but signaling within the ectoderm), Wg positively regulates dpp expression in concert with Dpp and the transcriptional cofactor Nejire. During the third round of Dpp signaling (the second round from the LE and the second round to the mesoderm), it is proposed that Wg signals repress Dpp signals in the absence of an activator (Johnson, 2003).

Is the second round of Dpp LE signaling conserved in vertebrates? The initial round of Dpp dorsal ectoderm to mesoderm signaling (the specification of heart progenitors via the maintenance of tinman expression) is conserved in vertebrate heart development. The mammalian homolog of Dpp (bone morphogenetic protein-2, BMP2) specifies cell fate in the cardiac mesoderm by regulating the expression of the tinman homolog Nkx2.5. Further, the interaction between Dpp and tinman and between BMP-2 and Nkx2.5 is via evolutionarily conserved enhancers recognized by the homologous signal transducers Medea and Smad4 (Johnson, 2003).

Two arguments are presented suggesting that the second round of Dpp dorsal ectoderm to mesoderm signaling is also conserved in vertebrate development. (1) BMP signaling represses endothelial cell fates in the cranial vasculature of zebrafish during late stages of embryonic development. Evidence for the repression of endothelial cell fate is an overabundance of endothelial cells in the cranial blood vessels of violet beauregarde (vbg) mutants. vbg encodes the BMP type I receptor similar to the Drosophila Dpp type I receptor Saxophone. The similarity of the mutant phenotypes (overabundance of Zfh-1 expressing pericardial cells in dppd6 mutants and overabundance of endothelial cells in vbg mutants) is intriguing. (2) SIP1 (Smad interacting protein) is most likely the vertebrate homolog of Zfh-1. Experiments in Xenopus show that SIP1 expression in the mesoderm is repressed by BMP overexpression and induced in the absence of BMP signaling. The similarity of the interactions and their tissue specificity (Dpp represses Zfh-1 in mesodermally derived pericardial cells and in BMP represses SIP1 in mesodermal cells) suggests evolutionary conservation (Johnson, 2003).

In summary, the role and regulation of a second round of dpp LE expression is described that corresponds to a second round of Dpp signaling from the dorsal ectoderm to the mesoderm during late stages of heart development. A second round of Dpp LE signaling represses the expression of the transcription factor Zfh-1 in a subset of pericardial cells. A subset of the enhancers driving this round of dpp LE expression are located in the dpp disc cis-regulatory region. Expression from these enhancers requires prior Dpp signaling and possibly release from dTCF-mediated repression by Wg. The continued analysis of the second round of Dpp LE signaling will provide new clues to understanding vertebrate cardiovascular development (Johnson, 2003).

Regulation of decapentaplegic expression during Drosophila wing veins pupal development

The differentiation of veins in the Drosophila wing relies on localised expression of decapentaplegic in pro-vein territories during pupal development. The expression of dpp in the pupal veins requires the integrity of the shortvein region (shv), localised 5' to the coding region. It is likely that this DNA integrates positive and negative regulatory signals directing dpp transcription during pupal development. A minimal 0.9 kb fragment has been identified giving localised expression in the vein L5 and a 0.5 kb fragment giving expression in all longitudinal veins. Using a combination of in vivo expression of reporter genes regulated by shv sequences, in vitro binding assays, and sequence comparisons between the shv region of different Drosophila species, binding sites were found for the vein-specific transciption factors Araucan, Knirps and Ventral veinless, as well as binding sites for the Dpp pathway effectors Mad and Med. It is concluded that conserved vein-specific enhancers regulated by transcription factors expressed in individual veins collaborate with general vein and intervein regulators to establish and maintain the expression of dpp confined to the veins during pupal development (Sotillos, 2006).

The expression of dpp in the wing disc is restricted to a narrow stripe of anterior cells localised at the anterior/posterior compartment boundary. This expression is regulated by sequences localised 3′ to the dpp coding region, and the function of the gene at this stage is required for the growth and patterning of the wing. The expression of dpp is still detected at the A/P boundary during the 8 h of pupal development. Later, at 14 h APF novel domains of dpp expression appear corresponding to the developing wing veins. The function of dpp during pupal development requires the integrity of the shv region, which is localised 5′ to the dpp coding region. There are two different transcripts expressed during pupal development, transcripts dpp-RA and dpp-RC, whose promoters (P5 and P3, respectively) are separated by approximately 20 kb of DNA. This DNA includes the first exon of transcript dpp-RC and corresponds to the place where all dpps alleles map. Because the strength of dpps alleles correlates with their distance to the P3 promoter, it is likely that dpp function in pupal development is mediated mainly by transcript dpp-RC. This suggests that dpps mutations affect regulatory sequences necessary to drive dpp expression in presumptive vein territories during pupal development. This possibility was confirmed by analysing the expression of a 8.5 kb construct containing most of the shv region fused to the reporter gene lacZ (shv8.5lacZ). The expression of βGal in shv8.5lacZ is detected exclusively in the pupal veins, indicating that this region includes all dpp wing veins regulatory regions (Sotillos, 2006).

Several constructs were made using different sub-fragments from the original 8.5 kb dpps DNA to identify with more precision the sequences that regulate dpp expression during pupal development. These fragments were cloned in front of a dicistronic lacZGal4 reporter gene and the activity of these constructs was analysed by looking at the expression of βGal in pupal wings from transgenic flies. In addition, to amplify the signal of the dicistronic lacZGal4 gene, the expression was monitored of a reporter gene regulated by UAS sequences. This expression should reveal all places where the Gal4 protein is present. Several regulatory regions were detected that control dpp expression in the veins during pupal development. One regulatory sequence is localised in a 1.1 kb fragment localised 6.5 kb from P3, and drives high levels of expression in most pupal veins and low levels of expression in some interveins. Additional regulatory sequences that efficiently drive expression in most veins are localised in an adjacent 0.5 kb fragment, and further vein-specific regulatory sequences for L5 are localised in the 0.9 kb SalI/KpnI fragment (Sotillos, 2006).

The expression of dpp during embryogenesis is highly dynamic and several independent regulatory regions controlling embryonic dpp expression have already been identified. The shv constructs included in the 8.5 kb EcoRI fragment drive reporter expression during embryonic development from stage 12/13 mainly in three regions of the mesoderm: the oesophagus, gastric caeca and midgut. Regulatory regions controlling dpp expression in the oesophagus appear to be duplicated, because they are localised in the 2.7 kb EcoRI/SalI fragment and also in the 3 kb KpnI/KpnI fragment. Similarly, regions controlling dpp expression in the gastric caeca are also present in the two adjacent fragments 0.9 kb SalI/KpnI and 3 kb KpnI/KpnI. The regions driving reporter expression in the gut are localised in the 3′ end of the shv region (Sotillos, 2006).

To better understand the regulation of dpp expression during vein development, the interactions were analyzed between a 2.5 kb region including wing veins pupal enhancers and several proteins involved in the regulatory network controlling the formation of veins. For this purpose, the 2.5 kb region was subdivided into overlapping fragments of 250-300 bp used as probes to detect the binding of different transcription factors by Electrophoretic Mobility-Shift Assays (EMSAs). Both prepattern specific genes that control vein development, such as Ventral veinless (Vvl) and the Araucan protein (Ara), and transcription factors belonging to the Dpp pathway (Mad and Medea) were analyzed (Sotillos, 2006).

The POU-Homeodomain protein Vvl is expressed in all vein territories throughout pupal development and is required for vein differentiation. Vvl was able to bind all the probes included in the 2.5 kb SalI/SacII region. The Vvl binding was competed by cold DNA as well as by specific oligonucleotides previously described to compete Vvl binding to the vestigial quadrant enhancer. To further characterise the binding of Vvl to the shv enhancer, focus was placed on the 0.5 kb SacII fragment, which drives expression in all longitudinal veins. This fragment was subdivided into two overlapping probes (S9 and S10) and both of them bind Vvl specifically. These bindings were competed using oligonucleotides covering these probes. Vvl-binding regions were found in S9 and in S10. Interestingly, these sequences contain previously identified consensus sequences for Vvl binding. These data suggest that Vvl participates in vein formation during pupal development through the regulation of dpp expression via the shv enhancers (Sotillos, 2006).

The Iroquois complex includes three genes, araucan (ara), caupolican (caup) and mirror, encoding highly related homeodomain-containing proteins. The genes ara and caup are expressed in the presumptive veins L3 and L5 and their activity is required for the formation of the distal region of these two veins. The activity of these genes is required during imaginal development to regulate the expression of rhomboid in the L3 and L5 veins, but it is not known whether they are also required during pupal development. The Ara homeodomain and the different probes included in the 2.5 kb SalI/SacII region were used, finding strong binding using S1, S5, S9 and S10 as probes. Only high amounts of Ara protein caused bandshift of the S2-4 and S6-8 probes. It was possible to displace these bindings using cold DNA, suggesting specific interactions between Ara and these DNA fragments. When the binding was competed with oligonucleotides included in the S9 and S10 probes, two binding regions were found in S9 and three in S10. The sequence a/t ACAnnTGT t/a has been recently defined as a binding site for the Iro-C component Mirror in random oligo-selection experiments. This sequence is specific for Mirror, although other members of the Iro-C, Ara or its homolog Irx4, also bind this sequence with a weaker affinity. Three sites were found with similar consensus sequence in the enhancer, located in the S1, S9 and S10 probes. However, in this case the palindrome is in opposite direction. Interestingly, the consensus identified included in S9 and S10 are in a highly conserved regions between D. melanogaster and D. pseudoscura and is present in oligonucleotides that compete efficiently in the binding assays, pointing to the relevance of these sequences to mediate Ara binding to the shv enhancer. The binding of Ara to the shv enhancer suggests that the Iro-C proteins participate in the development of the L3 and L5 veins acting as transcriptional activators to regulate positively the expression of dpp during pupal development (Sotillos, 2006).

The DNA-binding activity of Drosophila Smad proteins, Mad and Medea, is crucial for the expression of Dpp target genes. The expression of phosphorylated Mad (p-Mad), the activated form of the Mad protein, is restricted to the developing veins during pupal development. The efficiency of ectopic dpp expression to direct vein differentiation depends on the integrity of the shv region, suggesting that Dpp signalling is sufficient, directly or indirectly, for driving the expression of additional dpp transcription via the shv enhancer. Therefore, whether the Smads proteins can bind to the dpps enhancer was studied. Specific binding was obtained using all probes as shown by competition both with cold DNA and with specific oligonucleotides containing consensus binding sequences for Medea and for Mad and Medea. Other oligonucleotides with consensus for the transcription factor Nubbin did not compete the binding. The three main regions of competition with Mad and Medea binding included in the S9 and S10 probes correspond to GC rich sequences characteristic of Smad-response elements. However, only a single consensus sequence for Mad/Med (GCGGCTGT) in S10 is localised in a highly conserved region of different Drosophilids (see below) (Sotillos, 2006).

The pattern of four longitudinal veins is very similar in all Drosophilids despite the differences in wing size and pigmentation that exist between species. This conservation suggests that the mechanisms underlying vein pattern formation are conserved. The availability of the genomic sequence for different Drosophila species allows a direct comparison between their dpps regions. Two Drosophila species from the melanogaster group (D. melanogaster and D. ananassae), one Drosophila from the obscura group (D. pseudoobscura) and D. virilis from the virilis group were compared. It is expected that sequence similarity in non-coding regions corresponds to functional regulatory DNA. In the 2.5 kb region analysed several clusters of sequence conservation were found including most of the binding sites identified by in vitro analysis. Thus, there are four highly conserved regions corresponding to the S1, S4-5, S7-8 and S9-S10 probes containing conserved binding sequences for Vvl, Mad, Med and Ara. This conservation reinforces the importance of these regions to regulate the expression of dpp in the pupal veins. In the case of Vvl specific DNA binding to all probes was shown. However, the putative Vvl binding sequences localised in the conserved regions are only in S1, S3, S7, S8 and S10. In the case of the Dpp pathway transcription factors Mad and Med, putative binding sites are present throughout the enhancer, and accordingly binding of them to all probes was shown. However, only the S5 and S10 probes contain putative binding sites in regions of high sequence conservation. Interestingly, these conserved Mad/Med binding regions contain overlapping binding consensus for the Brinker repressor. This suggests a competition mechanism between Mad/Med and Brinker for binding to the shv enhancer. Competition mechanisms between activator and repressor also occur in several Dpp-downstream genes such as zen and omb. Four consensus binding sequences were found for the transcription factors of the Knirps-complex. The kni genes are expressed in the L2 vein, where they are required for its formation. Three Kni-binding sites were found in the 1.1 kb KpnI/SacII enhancer and one in the 0.5 SacII regions. Only two of the sequences located in the 1.1 kb KpnI/SacII enhancer present some conservation between Drosophilids. Interestingly, the 0.9 kb SalI/KpnI enhancer responsible of dpp expression in the L5 veins does not contain any putative Knirps binding sequence. Although whether Kni binds directly to the shv enhancer has not been analyzed, the presence of Kni-binding sites in conserved regions of the enhancer suggests that, in addition to its role during imaginal development, Kni might also activate dpp transcription during pupal development (Sotillos, 2006).

Therefore, regulatory sequences that drive dpp expression in the pupal veins in 2.5 kb of the dpps region have been found. This regulatory DNA can be subdivided into three fragments, a 1.1 kb fragment that recapitulates almost completely the pupal expression of dpp, a 0.9 kb upstream fragment, which drives expression in the proximal part of L5, and a 0.5 kb fragment that directs expression in all veins. Binding sites were found in these fragments for general transcription factors involved in the development of all veins (Vvl) and for the downstream activators of the dpp pathway, Mad and Medea. The regulatory region also contains binding sites for transcription factors expressed and required only in specific veins, such as Ara (L3 and L5) and Kni (L2). Most of these sequences are located in highly conserved regions of the dpp gene in different Drosophila species, indicating a general conservation of dpp regulation in the Drosophilids (Sotillos, 2006).

Analysis of the shortvein cis-regulatory region of the decapentaplegic gene

In mammals, the TGF-beta superfamily controls a variety of developmental processes. In Drosophila, by contrast, a single member of the superfamily, decapentaplegic performs most TGF-beta developmental functions. The complexity of dpp functions is reflected in the complex cis-regulatory sequences that flank the gene. Dpp is divided into three regions: (1) Hin, including the protein-coding exons; (2) disk, including 3' cis-regulatory sequences, and (3) shortvein (shv), including noncoding exons and 5' cis-regulatory sequences. This study analyzed the cis-regulatory structure of the shortvein region using a nested series of rearrangement breakpoints and rescue constructs. The molecular regions responsible for three mutant phenotypes were delimited: (1) larval lethality, (2) wing venation defects, and (3) head capsule defects. Multiple overlapping elements are responsible for larval lethality and wing venation defects. However, the area regulating head capsule formation is distinct, and resides 5' to these elements. This was demonstrated by isolating and describing two novel dpp alleles, which affect only the adult head capsule (Stultz, 2005).

Decapentaplegic head capsule mutations disrupt novel peripodial expression controlling the morphogenesis of the Drosophila ventral head

Drosophila adult structures derive from imaginal discs, consisting of sacs with apposed epithelial sheets, the disc proper (DP) and the peripodial epithelium (PE). decapentaplegic contributes to the development of adult structures through expression in all imaginal discs, driven by enhancers from the 3' cis-regulatory region of the gene. In the eye/antennal disc, there is 3' directed dpp expression in both the DP and PE associated with cell proliferation and eye formation. This study analyzes a new class of dpp cis-regulatory mutations, which specifically disrupt a previously unknown region of dpp expression, controlled by enhancers in the 5' regulatory region of the gene and limited to the PE of eye/antennal discs. These are the first described Drosophila mutations that act by solely disrupting PE gene expression. The mutants display defects in the ventral adult head and alter peripodial but not DP expression of known dpp targets. However, apoptosis is observed in the underlying DP, suggesting that this peripodial dpp signaling source supports cell survival in the DP (Stultz, 2006a).

This study describes a class of dpp mutations that specifically disrupt a previously unknown location of dpp expression within a restricted region of the PE of the eye/antennal disc. These mutants have defects in the ventral adult head capsule, indicating that this peripodial-specific expression contributes to ventral head morphogenesis. This peripodial expression is controlled by cis-regulatory elements at the 5′ end of the dpp gene, and there is a strong correlation between this expression and the position of primordia of adult structures disrupted in dpps-hc mutants. It has also been demonstrated that this lateral peripodial expression is causally responsible for the observed defect by rescuing the mutant phenotype with Dpp expression targeted to the lateral PE and phenocopying the head capsule defect by interfering with Dpp signaling in this same domain. In contrast, the dpp 3′ cis-regulatory region, which is known to mediate dpp expression in all imaginal discs, drives a different pattern of expression in the eye/antennal disc; one that correlates with the effects of dppdisk mutants on retinal formation and the proximal–distal elaboration of the antennae. There are regions of peripodial expression regulated by 3′ cis-elements, but they do not overlap with the expression caused by the 5′ cis-elements. dpps-hc and dppdisk mutations do not resemble each other in their mutant phenotypes nor do they interact genetically, suggesting two independent but parallel roles of dpp in the morphogenesis of the adult head (Stultz, 2006a).

The peripodial-specific dpp expression, mediated by the 5′ head capsule region, communicates to targets within the PE, as demonstrated by the alteration of the peripodial expression of dpp targets: dpp, Dad, and brk. However, this peropodial-specific dpp expression does not appear to communicate to these same targets within the DP as, here, expression of dpp, Dad, and brk is not altered in dpps-hc mutants. In other words, this peripodial source of the Dpp ligand does not appear to be communicating with the receptors controlling these disc-proper-specific targets. There are two possible explanations for these results. First, this peripodial-specific Dpp ligand might not be able to physically interact with the receptors in the underlying DP tissue, which are controlling these dpp targets. The Dpp ligand might be retained at the cell surface of the PE or be unable to access the receptors in the underlying DP. Second, the PE signal might not be of sufficient strength to affect these targets in the DP. The amount of Dpp available locally in the PE might be sufficient to activate PE receptors controlling these targets, but insufficient amounts might cross the lumen to activate the same targets in the DP. These results do not exclude that other dpp targets in the DP are affected by the lateral peripodial signaling. For example, it is noted that the primordia of structures altered in dpps-hc mutations, such as the palps and vibrissae, are reported to reside in the DP. This indicates that altered peripodial Dpp signaling is disrupting the morphogenesis of structures which arise from the underlying disc (Stultz, 2006a).

Some of this disruption may be caused by cell death: apoptosis was observed in the DP in dpps-hc mutants, indicating that dpp signaling in the peripodial epithelium supports cell survival in the DP, even at some distance from the lateral side of the disc. Dpp receptors are reported to be required on all DP cells for normal growth and survival, and disruption in growth factor signaling, particularly that of the dpp pathway, results in apoptotic cell death. When monitored in imaginal discs, this cell death is accompanied by basal extrusion of dying cells, similar to what was observed. Thus, the cell death observed in the DP due to loss of peripodial Dpp expression may be related to this phenomenon and could be a direct effect of BMP signal transduction, although it is formally possible that cell survival is controlled indirectly by the 5′ peripodial specific Dpp expression through a secondary signal transduction mechanism. This would suggest that the peripodial source of Dpp supports cell viability in the DP but may not be involved in the direct activation of target genes associated with patterning in this epithelial layer. It is known that different targets have different thresholds of response to Dpp and has been suggested that DP patterning targets such as omb may require higher levels of signal, while other targets, such as those that control cell proliferation and viability, may require less. In such a model, peripodial Dpp could contribute to a general pool that supports cell proliferation and viability of the DP but would have insufficient signal strength to activate patterning targets in this layer (Stultz, 2006a).

Dpp signaling thus comes from at least three sources during the development of the eye/antennal disc: the peripodial and disc proper expression caused by the 3′ cis-regulatory elements and the peripodial expression caused by the 5′ cis-regulatory head capsule elements. dpp has a well-established role in promoting the formation of the Drosophila eye and in suppressing head cuticle while other signaling molecules, such as wg and hh, have been postulated to promote head cuticle development. The discovery of another source of dpp, within the same organ primordia and with an apparent opposite function, increases the complexity of dpp signal transduction, but the existence of new head capsule mutations that remove only a peripodial signaling source should help dissect out the numerous roles that dpp plays in eye/antennal disc development and the function of the PE in this process (Stultz, 2006a).

Transcriptional activation by Extradenticle in the Drosophila visceral mesoderm

decapentaplegic is a direct target of Ultrabithorax (Ubx) in parasegment 7 (PS7) of the embryonic visceral mesoderm. This study demonstrates that extradenticle (exd) and homothorax (hth) are also required for dpp expression in this location, as well as in PS3, at the site of the developing gastric caecae. A 420 bp element from dpp contains Exd binding sites necessary for expressing a reporter gene in both these locations. Using a specificity swap, Exd was demonstrated to directly activate this element in vivo. Activation does not require Ubx, demonstrating that Exd can activate transcription independently of homeotic proteins. Restoration is restricted to the domains of endogenous dpp expression, despite ubiquitous expression of altered specificity Exd. Nuclear Exd is more extensively phosphorylated than the cytoplasmic form, suggesting that Exd is a target of signal transduction by protein kinases (Stultz, 2006b).

Previous studies (Sun, 1995) demonstrated that Ubx directly regulates dpp in PS7 of the VM using a specificity swap strategy. Subsets of six Ubx binding sites were mutated in a 420 bp reporter construct (PX) from binding sites for Q50 homeodomains to binding sites for K50 homeodomains. For example, the wild-type UBX site 5/EXD site e2 was AGGCCTATCAATTAGCACC (with the EXD site underlined) and the mutant UBX site 5/EXD site e2 was AGGCCTAGGGATTAGCACC. It was then possible to restore the expression of these constructs by changing Q50 to K50 in the Ubx protein (called Ubx K50). However, it was not possible to restore expression of a reporter in which all six Ubx sites were altered. This suggested that an additional factor was required, and it was noted that the alterations in the fully substituted PX reporter also disrupted closely apposed Exd binding sites, suggesting that Ubx and EXD may co-regulate dpp (Stultz, 2006b).

In previous work (Sun, 1995), it was not possible to restore expression of the fully substituted PX4–9 reporter using Ubx K50. This study shows that ubiquitous and simultaneous induction of Ubx K50 and Exd K50 restores expression of PX4–9 in a manner that is similar to wild-type PX. Induction of Exd K50 alone also restores PX4–9 in these domains but changes the balance of staining intensity between them, with PS7 expression appearing less prominent. This reflects a sufficiency of Exd K50 for activation of gene expression at both sites, but with an additional requirement for Ubx K50 to achieve wild-type levels in PS7. These experiments identify Exd as a direct activator of dpp's VM expression in both PS3 and PS7 (Stultz, 2006b).

No HOX proteins are expressed in PS3. Thus, Exd K50 activates gene expression independently of HOX family proteins in this location. In cases where Ubx K50 restored partially substituted PX constructs, restoration was never seen in PS3 (Sun, 1995), further indicating that dpp expression here does not require HOX proteins. In addition, in PS7, where it is clearly established that Ubx contributes to activation of dpp expression, the results demonstrate that Ubx is not absolutely required for Exd K50 to activate transcription. Ubx increases the level of dpp expression, as demonstrated by the reduced PS7 expression in Exd K50-alone restorations, but is not required for Exd function. This point is further reinforced by the ability of Exd K50 to activate PX4–9 gene expression, even in Ubx homozygous mutants. On simple Exd binding sites, PBX proteins have not demonstrated transcriptional activation, but the data suggest that Exd can participate in gene activation without a HOX gene. Other unidentified factors in PS3 or PS7 could also be involved, and one candidate would be HTH, which is genetically required for dpp's VM expression and capable of binding to the PX element in concert with Exd. Genetic evidence for the ability of Exd/HTH to act in the absence of HOX proteins has been steadily accumulating, based on mutant phenotypes that cannot be attributed to HOX genes, and both genetic and in vitro data suggest that HTH/MEIS may have transcriptional activation capabilities (Stultz, 2006b).

Two models for the role of Exd in regulating HOX targets have been proposed. The data indicate that the PX element is directly regulated by both Exd and Ubx, allowing evaluation of these two models based on the results. The 'co-selective binding' model proposes that Exd enhances the specificity and affinity of its HOX partner for a DNA binding site. This model requires that Exd and HOX proteins bind cooperatively as heterodimers to closely spaced Exd and HOX binding sites. This model predicts that the relative spacing and orientation of PBX/Exd and HOX binding sites must be tightly constrained, as has been shown by in vitro studies. Although the dpp cis-regulatory PX element contains multiple Ubx and Exd sites identified by DNA footprinting (Sun, 1995), only site e2 resembles the optimal site for binding by a PBX1/HOXB7 heterodimer. Even this site is not a perfect match, and data indicate that this site may be more likely to bind Exd/HTH in vivo. The electrophoretic mobility shift data demonstrate that Exd K50 can bind TAATCCC sites (the optimal site for HOX K50) that replace Ubx sites, as well as unaltered Exd sites. Thus, Exd K50 restores PX4–9 by binding to some or all of these sites. This demonstrates that an Exd protein altered only in its binding specificity can act in vivo through sites of altered spacing and orientation and is not necessarily constrained to act in close proximity to a HOX protein (Stultz, 2006b).

The second model, 'widespread binding', proposes that Exd determines the outcome of HOX protein action. According to this model, either Exd or HOX proteins in isolation can bind DNA and act as transcriptional repressors. When both proteins are present, a complex that activates transcription is formed. For Deformed, Exd activates an otherwise silent transcriptional activation domain within the Deformed protein. The physical association between the proteins stabilizes their binding to DNA, but they do not have to bind as heterodimers. This model is more consistent with both the spacing of Exd and HOX sites in the dpp PX element and the apparent flexibility in the location of Exd-responsive sites observed in the experiments. However, this model predicts that independent Exd action is repressive, based on a Deformed-responsive target. In contrast, the data indicate that Exd can also activate reporter gene expression without a HOX partner, suggesting that repression is not the default action of Exd in the absence of HOX proteins (Stultz, 2006b).

This study has shown that Exd is a direct activator of dpp expression in the VM. In PS3, the normal action of Exd does not require input from any homeotic protein. In PS7, input from Ubx is critical to achieving the correct level of gene expression, but the data do not support a model where Ubx is absolutely necessary for transcriptional activation. The data suggest that Exd can activate transcription in the absence of HOX proteins but that, in many cases, it also collaborates with HOX proteins, allowing the complex to achieve a more robust level of transcriptional activation. The current notion is that Exd is an essential cofactor for homeotic proteins. An equally tenable model for gene activation is that HOX proteins are the cofactors of Exd, imparting additional spatial regulation, site specificity, and activity to this transcriptional regulator (Stultz, 2006b).

The striking restriction of reporter restoration to domains influenced by kinase-mediated signaling pathways led to an examination Exd protein for evidence of phosphorylation. The primary sequence of Exd contains more than 15 potential sites for various protein kinases, including Protein Kinase A (PKA) and Casein Kinase II upstream of its NLS. Protein kinase action is required for gene activation by PBX proteins in tissue culture cells, PKA converts HOX/PBX complexes from repressors to activators on the Hoxb1 autoregulatory element, and phosphorylation by PKA induces nuclear import of PBX1 independently of the PBX/MEIS nuclear localization mechanism. While it was not possible to establish a connection between DPP signaling and Exd phosphorylation, nonetheless, Exd clearly exists in multiple phosphoprotein forms, and the increased phosphorylation is clearly correlated to subcellular localization in Drosophila as well. Thus, Exd must be a target of kinase action, although whether this activity is solely required for nuclear translocation or for activity once in the nucleus is unresolved (Stultz, 2006b).

dpp requires both its own expression and that of wg to achieve normal gene expression in the VM. These data led to a hypothesis that the spatial restriction observed in the restoration must be connected to DPP or WG signaling. However, the data do not support this hypothesis, and it is more likely that the major inputs generating dpp's localization in the VM are repressive in nature. In previous work, it was postulated that dpp's spatial regulation in the VM was the result of dual modes of regulation involving both general activation and spatially specific repression and spatially restricted activation (Sun, 1995). The general activator has been identified as biniou (bin), a member of the FoxF/forkhead family of transcription factors. This factor is capable of inducing dpp expression throughout the posterior half the VM, including PS7, when its action is not specifically repressed. This repression comes from multiple inputs. dpp is a direct target of posterior repression via Abd-A. dpp is also repressed outside of PS3 and PS7 via the action of Drosophila T Cell Factor (dTCF) in the absence of WG signaling. The ectopic PS4–6 expression of longer dpp constructs in exd or hth null embryos identifies exd and hth or a downstream target of these genes as another repressor of dpp in PS4–6. Such a downstream target could be teashirt, a known repressor whose VM expression is lost in exd null embryos and is expressed in PS4–6 (Stultz, 2006b).

To this model of multiple general activators and spatially specific repressors is added the spatially localized strong activator Ubx. Ubx directly regulates dpp and may also have indirect inputs to dpp's PS7 gene expression, as the reduced restoration in Ubx9.22 null embryos indicates. Ubx is itself repressed via chromatin factors such as Polycomb and osa in the anterior midgut and Abd-A posterior to PS7. dpp autoregulation provides additional weak activation via inputs from SMAD proteins and through DPP-mediated schnurri repression of the repressor brinker. Thus, dpp expression is the cumulative result of general activation constrained by spatially specific repression and augmented by spatially specific activation. Clearly, evolution has deemed the formation of the embryonic midgut of sufficient importance to create a highly buffered, reinforced system of gene expression (Stultz, 2006b).

The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity

Gradients of diffusible signaling proteins control precise spatial patterns of gene expression in the developing embryo. This study used quantitative expression measurements and thermodynamic modeling to uncover the cis-regulatory logic underlying spatially restricted gene expression in a Hedgehog (Hh) gradient in Drosophila. When Hh signaling is low, the Hh effector Gli, known as Cubitus interruptus (Ci) in Drosophila, acts as a transcriptional repressor; when Hh signaling is high, Gli acts as a transcriptional activator. Counterintuitively and in contrast to previous models of Gli-regulated gene expression, this study found that low-affinity binding sites for Ci were required for proper spatial expression of the Hh target gene decapentaplegic (dpp) in regions of low Hh signal. Three low-affinity Ci sites enabled expression of dpp in response to low signal; increasing the affinity of these sites restricted dpp expression to regions of maximal signaling. A model incorporating cooperative repression by Ci correctly predicted the in vivo expression of a reporter gene controlled by a single Ci site. This work clarifies how transcriptional activators and repressors, competing for common binding sites, can transmit positional information to the genome. It also provides an explanation for the widespread presence of conserved, nonconsensus Gli binding sites in Hh target genes (Parker, 2011).

The enhancers of dpp and ptc exhibit a regulatory logic opposite that predicted by the activator threshold model. ptc is regulated by Ci sites that match the optimal binding sequence (GACCACCCA), whereas dpp is regulated by nonconsensus sites of low predicted affinity. Competitive electrophoretic mobility shift assays (EMSAs) were used to measure the relative in vitro affinities of Ci sites in the ptc and dpp enhancers, and it was found that Ciptc sites in the ptc enhancer have considerably higher affinity than Cidpp sites. The predicted superior affinity of Ciptc sites, relative to Cidpp sites, is conserved across 12 Drosophila species. Thus, the regulation of dpp and ptc in the wing is opposite to that predicted by a simple activator threshold model. ptc, which is restricted to the region of highest Hh signal, is regulated by high-affinity sites. In contrast, dpp, which responds more broadly in a zone of lower Hh signaling, is regulated by low-affinity sites (Parker, 2011).

To investigate the developmental role of the low-affinity sites in the dpp enhancer, all three sites were altered to match the high-affinity Ci binding sequence found in the ptc enhancer, a change of only seven nucleotides. Transgenic lines were created containing an extra Flp-inducible copy of dpp, driven by the dpp disc (dppD) enhancer containing either wild-type low-affinity (Ciwt) or altered high-affinity (Ciptc) sites. An extra copy of dpp driven by the low-affinity dppD-Ciwt enhancer had no effect on development or survival, whereas the high-affinity Ciptc enhancer caused lethal developmental defects that resemble the effects of dpp misexpression in imaginal discs, including severe head and limb deformities and pupal lethality resulting from overgrowth fusion, and patterning defects in antenna and leg discs. These results indicate that the conserved low affinity of the dppD enhancer for Ci is functionally relevant (Parker, 2011).

A quantitative reporter gene assay was developed to further explore the role of low-affinity Ci binding sites in the dpp wing disc enhancer. Transgenic fly lines were constructed carrying two reporter genes: dppD-Ciptc-RFP, consisting of the high-affinity version of the dpp enhancer driving expression of a red fluorescent protein (RFP), and one of several dpp enhancers driving green fluorescent protein (GFP). By measuring GFP fluorescence across a transect of the wing pouch and normalizing to peak RFP expression in each disc, a quantitative readout was obtained of both the position and the intensity of GFP reporter activity (Parker, 2011).

Using this assay, the activity was compared of different versions of the dppD enhancer driving GFP expression, containing either three low-affinity sites (dppD-Ciwt) or three high-affinity sites (dppD-Ciptc). Ci-independent, 'basal' expression was also measured from a construct (dppD-CiKO) in which all three Ci sites were mutated to abolish Ci binding. This basal expression captures the effects of all factors other than Ci on dpp, including Engrailed, which directly represses dpp near the anterior/posterior boundary. This basal construct enabled direct measurement of both activation and repression by Ci, by comparing the activity of the low- or high-affinity enhancers against that of dppD-CiKO. The results show that the response of dpp to Hh cannot be explained by an activator threshold model. High-affinity Ciptc sites caused a posterior shift in stripe position toward the region of strongest Hh signal, whereas low-affinity Ciwt sites produced stronger activation in regions of moderate Hh signal. When the basal dppD-CiKO-GFP expression was subtracted from that of dppD-Ciptc-GFP and dppD-Ciwt-GFP, it was observed that within the zone of moderate Hh signal, low-affinity sites produced activation, whereas high-affinity sites conferred repression. This observation shows that CiREP plays a substantial role in the response to moderate Hh signal, a finding that directly contradicts the assumptions of the activator threshold model. Thus, an alternate biophysical model is required to explain the regulatory logic of the dpp response to Hh (Parker, 2011).

It is concluded that spatial information in the wing disc Hh gradient is interpreted by a cis-regulatory logic that relies on activator-repressor competition, which is modulated by binding site affinity and cooperative repression. In previous studies of Hh target genes, the role of the affinity of the Gli or Ci binding site has been neglected or has been assumed to play a role opposite to what the current data show. Moreover, the currently accepted activator threshold model of the transcriptional response to Hh assumes that the role of Gli and Ci repressors is limited to regions of little or no Hh signal. No previously described model of Hh response, including the activator threshold model, can account for the observations described in this study. The data show that substantial repression can occur even at moderate Hh signal and suggest that the transcriptional response in much of the Hh gradient depends on the outcome of a competition between CiACT and CiREP for enhancer binding. This new model of the cis-regulatory logic underlying Hh response integrates the effects of both CiACT and CiREP along the entire Hh gradient and explains the importance of low-affinity Gli binding sites in the positioning of gene expression (Parker, 2011).

The results suggest that the low affinity of the dpp enhancer for Ci can be explained by the need to mitigate the effects of cooperative repression in a region of the gradient where substantial amounts of CiREP are present, while still allowing activation by CiACT. Within the context of this model, repressor cooperativity is defined as any interaction that makes the binding of additional CiREP more favorable when one CiREP is already bound. Cooperativity could arise from direct interactions between CiREP or from interactions of CiREP with other transcription factors, cofactors, or histones. In principle, CiREP cooperativity at the enhancer could be attenuated by various cis-regulatory strategies besides lowering binding affinity, such as reducing the number of Ci sites or increasing their spacing. However, these alternative strategies may not be equally able to maintain activation by CiACT in regions of low Hh signaling (Parker, 2011).

The posterior-to-anterior gradient of Hh in the wing disc establishes opposing gradients of CiACT and CiREP. High amounts of CiACT are present at the anterior/posterior boundary, whereas more anterior regions feature high amounts of CiREP. Within the intermediate zone of the gradient, mixed amounts of CiACT and CiREP compete for enhancer binding, with activation and repression determined by the ratio of bound CiACT to bound CiREP. In the repressor cooperativity model, repressors outcompete activators for binding at high-affinity enhancers, but not at low-affinity enhancers, in this region of the gradient. Several morphogen signaling pathways have the potential to produce reciprocal gradients of repressors and activators competing for common binding sites. This study has presented the first detailed mechanistic model that explains how reciprocal gradients of Gli activators and repressors are transcriptionally interpreted. A similar regulatory logic may inform responses to other morphogens that control transcriptional switches, particularly those whose target genes are regulated by low-affinity sites (Parker, 2011).

The model provides an explanation for the widespread presence of evolutionarily conserved, nonconsensus Gli or Ci binding sites in the enhancers of Hh target genes. With the exception of ptc, all known direct targets of Hh in Drosophila are regulated by nonconsensus Ci sites with predicted low affinity The results indicate that low-affinity sites are necessary to position a stripe of expression in the middle of a Hh gradient, because high-affinity sites induce repression outside the zone of strongest signaling. Because mammalian Gli target genes are also regulated by nonconsensus sites, the conclusions may also apply to vertebrate Hh targets: Such targets may acquire weak-affinity Gli sites to minimize cooperative repression in a Gli cross-gradient (Parker, 2011).

In a few documented cases, low-affinity transcription factor binding sites have important spatiotemporal patterning functions. Two well-studied examples are the response to the morphogen Dorsal in Drosophila and the temporal control of developmental gene expression. In these cases, low-affinity sites set a high threshold for activator concentration, restricting activation to cells or times in which activator concentration is maximal. In the case described in this study, an opposite cis-regulatory logic applies: Low-affinity sites are specifically required for activation in cells receiving lower amounts of signal. This is a consequence of the fact that in this region of the gradient, activators and repressors compete for the same genomic binding sites (Parker, 2011).

The results suggest that most current biochemical and computational approaches to identifying Hh target genes, which typically focus on the highest-affinity Ci or Gli sites, may overlook a large proportion of important Hh target genes. More generally, transcriptional cooperativity may play an important cis-regulatory role in enhancers with conserved low-affinity binding sites (Parker, 2011).

Org-1 is required for the diversification of circular visceral muscle founder cells and normal midgut morphogenesis

The T-Box family of transcription factors plays fundamental roles in the generation of appropriate spatial and temporal gene expression profiles during cellular differentiation and organogenesis in animals. This study reports that the Drosophila Tbx1 orthologue optomotor-blind-related-gene-1 (org-1) exerts a pivotal function in the diversification of circular visceral muscle founder cell identities in Drosophila. In embryos mutant for org-1, the specification of the midgut musculature per se is not affected, but the differentiating midgut fails to form the anterior and central midgut constrictions and lacks the gastric caeca. It was demonstrate that this phenotype results from the nearly complete loss of the founder cell specific expression domains of several genes known to regulate midgut morphogenesis, including odd-paired (opa), teashirt (tsh), Ultrabithorax (Ubx), decapentaplegic (dpp) and wingless (wg). To address the mechanisms that mediate the regulatory inputs from org-1 towards Ubx, dpp, and wg in these founder cells, known visceral mesoderm specific cis-regulatory-modules (CRMs) of these genes were dissected. The analyses revealed that the activities of the dpp and wg CRMs depend on org-1, the CRMs are bound by Org-1 in vivo and their T-Box binding sites are essential for their activation in the visceral muscle founder cells. It is concluded that Org-1 acts within a well-defined signaling and transcriptional network of the trunk visceral mesoderm as a crucial founder cell-specific competence factor, in concert with the general visceral mesodermal factor Biniou. As such, it directly regulates several key genes involved in the establishment of morphogenetic centers along the anteroposterior axis of the visceral mesoderm, which subsequently organize the formation of midgut constrictions and gastric caeca and thereby determine the morphology of the midgut (Schaub, 2013).

The analysis of org-1 expression and function during visceral mesoderm development defined this gene as a new and essential lineage specific regulator of circular visceral muscle founder cell identities and midgut patterning in Drosophila. The data add new insights into the developmental regulatory mechanisms responsible for the diversification of the circular visceral muscle founder cell lineage and midgut morphogenesis (Schaub, 2013).

The initial expression of org-1 occurs in the segmented trunk visceral mesoderm (TVM), where it is coexpressed with tin, bap, bin and Alk. It has been documented that the induction of tin and bap in the dorsal mesoderm involves the combined binding of Smad proteins (Medea and Mad) and Tin to Dpp-responsive enhancers of the tin and bap genes, whereas the segmental repression of bap is mediated by binding of the sloppy paired (slp) gene product. Genetic analysis of org-1 has shown that org-1 is activated downstream of tin but independently of bap and bin, and that dpp provides the key signals for its induction. This suggests a regulatory mechanism analogous to that of bap, in which the combined binding of Smads and Tin activates a Dpp-responsive org-1 enhancer, whereas Wg activated Slp is required for its mutual segmental repression (Schaub, 2013).

The similarities in the early expression patterns of bap, bin, Alk and org-1 in the trunk visceral mesoderm primordia raise the question of the contribution of org-1 to the early development of the TVM as such. Whereas bap and bin are crucially required for the specification of the trunk visceral mesoderm and visceral musculature, loss of org-1 function, like the loss of Alk, has no obvious impact on the specification of the early TVM. Therefore, it is notable that during the subdivision of the visceral mesoderm primordia into founder and fusion-competent myoblasts (cFCs and FCMs), org-1 expression is extinguished in the FCMs and only sustained in the cFC lineage of the circular visceral musculature. This lineage-specific restriction and maintenance of org-1 expression crucially depends on Jeb mediated Alk/Ras/MAPK signaling and points toward a possible cFC lineage specific function of org-1. The genetic analysis demonstrates that org-1 is not required for cFC specification, but plays a decisive role in the induction of the visceral mesoderm specific expression of patterning genes in the founder cells of the circular musculature. Thus, org-1 is critical for the processes of cell fate diversification that provide individual fields of cells along the anteroposterior axis of the visceral mesoderm with their specific identities (Schaub, 2013).

Proper anteroposterior patterning of the trunk visceral mesoderm and the formation of localized organizer fields are prerequisites for eliciting the morphogenetic events that shape the midgut. The formation of these organizer fields depends on the appropriate spatial expression domains of the homeotic selectors Scr, Antp, Ubx and abd-A, the secreted factors dpp and wg, as well as the zinc finger proteins opa and tsh, which are required for the formation of the midgut constrictions as well as the gastric caeca. The regulatory mechanisms responsible for the establishment of the spatial, temporal and tissue-specific expression patterns of these genes in the TVM are only partially understood. Genetic and molecular analyses with the FoxF gene bin, which is expressed in all trunk visceral mesoderm precursors and their descendents, have demonstrated that bin is a direct upstream regulator of dpp in PS7 and is also required for the expression of wg in PS8 of the TVM. Thus, Bin serves as an essential TVM-specific competence factor in conjunction with the dpp/wg signaling feedback loop. The current findings have defined Org-1 as an additional tissue-specific regulator with an even broader range of downstream patterning genes in the TVM, but with a narrower spatial range of action. org-1 acts specifically within the visceral muscle founder cell lineage as a positive regulator upstream of opa, tsh, Ubx, dpp as well as wg (Schaub, 2013).

This combination of genetic data and functional enhancer analyses provides convincing evidence that both dpp and wg are direct transcriptional targets of Org-1 in the cFCs. Prior dissections of the dpp visceral mesoderm (VM) enhancer had shown that it is also regulated by the direct binding of Ubx, Exd, dTCF (a Wg effector) and Bin, and that minimal synthetic variants that contain only the binding motifs for Ubx, Exd, Bin, and dTCF within conserved sequence contexts (which happen to include the Org-1 motif) are active as VM enhancers. Likewise, the wgXC enhancer fragment integrates Org-1 with the direct regulatory inputs of Abd-A as well as CREB and Smad (Mad/Medea) proteins mediating Dpp signaling (Schaub, 2013).

Org-1 is the first transcription factor known to be required for Ubx expression in PS7 of the visceral musculature. Extensive work on an Ubx visceral mesoderm CRM (UbxRP) indicated that dpp and wg regulate Ubx through indirect autoregulation. Of note, in bin embryos, which also lack visceral mesodermal dpp and wg expression, Ubx is still expressed. Genetic data show that the UbxRP element, while requiring org-1, is not directly regulated by Org-1, since mutation of its four predicted T-Box binding sites did not have any effects. Taking into account that no UbxRP reporter activity was detected in the cFCs at pre-fusion stages, it is suggested that UbxRP represents a late enhancer element and responds to dpp and wg only after they are activated by Org-1 in the founder cells. To clarify whether the regulation of Ubx by Org-1 is direct or indirect, the identification and dissection of a founder cell specific CRM will be required (Schaub, 2013).

tsh and opa were described as homeotic target genes of Antp in PS4-6 (tsh) and PS4-5 (opa) as well as of abd-A in PS8 (tsh) and PS9-12 (opa) of the visceral musculature. The current data show that tsh and opa expression is already activated in the respective cFCs of the visceral parasegments where it requires org-1. The later activation of tsh in PS8 during muscle fusion follows the org-1 dependent founder cell specific initiation of wg in PS8, which acts upstream of tsh. Thus it was conceivable that the regulation of tsh by org-1 is indirect. However, ectopic activation of wg in an org-1 loss of function background is not able to rescue tsh expression and Antp and abd-A expression is not altered upon loss of org-1. These observations suggest that Org-1 acts directly on tsh and opa, e.g., via functional cooperation with Antp and Abd-A, respectively, during the early activation of tsh and opa in the founder cells (Schaub, 2013).

It was reported that the absence of Jeb/Alk signaling causes loss of dpp expression in the founder cells in PS7 of the visceral mesoderm. In light of the current findings that org-1 loss-of-function produces a similar phenotype, and of the previous demonstration that org-1 expression is downstream of Jeb/Alk, this observation could simply be explained by the action of a linear regulatory cascade from Jeb/Alk via org-1 towards dpp. Alternatively, Jeb/Alk may provide additional inputs towards dpp (and other patterning genes) in parallel to org-1, which could explain the slightly stronger phenotype of Alk as compared to org-1 mutations with respect to dpp. A possible candidate for an additional effector of Jeb/Alk signals in this pathway is extradenticle (exd), which is known to be required for normal dpp expression in PS7 of the visceral mesoderm, presumably through direct binding of Exd in a complex with Hox proteins and Homothorax (Hth) to a PS7-specific enhancer element (a derivative of which was used in this study). Like org-1, exd is also needed for the expression of tsh and wg in the visceral mesoderm (Additionally, it represses dpp in PS4-6 through sequences not contained in the minimal PS7 enhancer). It is thought that Exd complexed with Hox proteins and Hth increases the binding preference of these Hox complexes for specific binding sites within visceral mesodermal enhancers of their target genes (Schaub, 2013).

Since exd is expressed in both founder and fusion-competent cells in the visceral mesoderm, it is unlikely that it fulfills its roles in the regulation of dpp, wg, and tsh in the founder cells as a downstream gene of org-1. However, it is known that Exd requires nucleocytoplasmic translocation for it to be functiona and, interestingly, it has been shown that Jeb/Alk signals trigger nuclear localization of Exd specifically in the cFCs of the visceral mesoderm. Because nuclear Exd appears to be hyperphosphorylated as compared to cytoplasmic Exd, nuclear translocation of Exd may be triggered by Alk-mediated phosphorylation. Alternatively, Jeb/Alk signals may induce the expression of hth in the cFCs and Hth could then translocate Exd to the nuclei, as has been shown in other contexts. This would be compatible with the observation that Hth is upregulated in the founder cells in an org-1-independent manner (Schaub, 2013).

The combined data show that Jeb/Alk signals exert at least two parallel inputs towards patterning genes in the cFCs, which are the induction of org-1 and the nuclear translocation of Exd. Taken altogether, a model is suggested in which combinatorial binding of Org-1, nuclear Exd/Hth and the homeotic selector proteins to the corresponding visceral mesoderm specific CRMs is required for the initiation of lineage specific expression of opa, tsh, dpp, Ubx and wg in the founder cells of the respective parasegments. As shown in the examples of dpp (PS7) and wg (PS8), accessory Bin is required for the activation as a general visceral mesodermal competence factor, whereas Dpp and Wg effectors mediate autoregulatory stabilization of their expression (Schaub, 2013).

Extensive work has shown that during somatic muscle development individual founder myoblasts acquire distinct identities, which are adopted by the newly incorporated nuclei upon myoblast fusion, thus leading to the morphological and physiological diversification of the differentiating muscles. It is proposed that the same principle is active during visceral muscle development. In this view, Org-1 acts as a muscle identity factor in both the somatic and visceral mesoderm. In the visceral mesoderm, Org-1 helps diversifying founder cell identities and, after myoblast fusion, their differential identities are transmitted to the respective differentiating circular gut muscles. The activation of downstream targets of this identity factor in the developing muscles leads to the observed morphogenetic differentiation events of the midgut and the establishment of the signaling center in PS7/8 that is also required for Dpp and Wg mediated induction of labial in the endodermal germ layer. As is the case for identity factors in the somatic muscle founders, Org-1 in the visceral mesoderm acts in concert with other, spatially restricted activities such as Hox factors and signaling effectors to achieve region-specific outputs. The main difference is that, in the trunk visceral mesoderm, Org-1 is present in all founder cells whereas in the somatic mesoderm this identity factor (like others) is expressed in a particular subset of founder myoblasts. Thus, in contrast to the somatic mesoderm, the spatial expression of Org-1 does not contribute to its function in visceral muscle diversification and instead, it solely relies on spatially-restricted co-regulators during this process (Schaub, 2013).

The pool of trunk visceral mesodermal fusion-competent cells contributes to the formation of both circular and longitudinal midgut muscles, depending on whether they fuse with resident founder cells of the trunk visceral mesoderm or with founders that migrated in from the caudal visceral mesoderm. The restricted expression of the identity factor Org-1 in the founder myoblasts in the trunk visceral mesoderm and its exclusion from the FCMs represents an elegant mechanism to ensure that the respective patterning events only occur in the developing circular musculature but not in the longitudinal muscle fibers, which extend as multinucleate syncytia throughout the length of the midgut (Schaub, 2013).

Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

In the era of functional genomics, the role of transcription factor (TF)-DNA binding affinity is of increasing interest: for example, it has recently been proposed that low-affinity genomic binding events, though frequent, are functionally irrelevant. This study investigated the role of binding site affinity in the transcriptional interpretation of Hedgehog (Hh) morphogen gradients. It is noted that enhancers of several Hh-responsive Drosophila genes have low predicted affinity for Ci, the Gli family TF that transduces Hh signalling in the fly. Contrary to an initial hypothesis, improving the affinity of Ci/Gli sites in enhancers of dpp, wingless and stripe, by transplanting optimal sites from the patched gene, did not result in ectopic responses to Hh signalling. Instead, it was found that these enhancers require low-affinity binding sites for normal activation in regions of relatively low signalling. When Ci/Gli sites in these enhancers were altered to improve their binding affinity, patterning defects were observed in the transcriptional response that are consistent with a switch from Ci-mediated activation to Ci-mediated repression. Synthetic transgenic reporters containing isolated Ci/Gli sites confirmed this finding in imaginal discs. It is proposed that the requirement for gene activation by Ci in the regions of low-to-moderate Hh signalling results in evolutionary pressure favouring weak binding sites in enhancers of certain Hh target genes (Ramos, 2013).

This study present in vivo evidence corroborating previous findings that multiple tissue-specific enhancers require low-affinity Ci binding sites for optimal activation by Hh/Ci. Most of the Hh target enhancers identified up to this point in Drosophila and mouse are regulated by degenerate Ci/Gli binding sites of low predicted affinity. The prevalence of these non-consensus sites in Hh target enhancers across species demonstrates their importance in regulating the Hh response. The transcriptional relevance of low-affinity TF binding is not limited to Hh/Ci regulated enhancers. For instance, two phylogenetically conserved low-affinity binding sites in the mouse Pax6 lens enhancer have been shown to be critical to promote gene expression at the right stage of development (Ramos, 2013).

A mechanistic explanation is provided as to why these Hh/Ci-regulated elements require low-affinity sites to activate transcription in cells with moderate signalling levels. Clusters of high-affinity sites mediate a restricted response in cells with high levels of Hh signalling, most likely as a result of cooperative interactions among Ci-Rep molecules in highly occupied Ci binding sites, whereas clusters of low-affinity sites mediate a broader response by having lower occupancy by Ci. Using synthetic enhancer reporters with high- or low-affinity Ci binding sites, this effect was confirmed in the wing, but not in embryos. This tissue-specific discrepancy may imply a context-dependent function for some non-consensus Ci binding sites. As in the Pax6 lens enhancer (Rowan, 2010), it is possible that some low-affinity binding sites are required specifically during earlier stages of development to interpret overall lower levels of Hh signalling (Ramos, 2013).

Finally, clues are provided as to additional regulatory inputs into dppD by showing a requirement for conserved consensus homeodomain (HD) binding sites. Cooperation between Glis and HD proteins has been recently shown in the mouse neural tube. In this case, HD proteins are critical to repress Hh-regulated neural tube enhancers, whereas in dppD they are critical to activate gene expression (Ramos, 2013).

The limited number of known, experimentally confirmed, direct Hh/Gli target enhancers may reflect the widespread, practical tendency to search for consensus or near-consensus motifs, and to focus on the highest peaks of TF-DNA binding, when hunting for cis-regulatory sequences. From a biochemical standpoint—for example, when mining ChIP-seq data—low-affinity DNA-binding interactions are troublesome because they are much more common, by definition, than the top 1% of peaks. It is important to note that iy is not always useful to strictly equate ChIP peak height with TF binding affinity, nor to equate in vitro binding or in silico 'motif quality' with in vivo TF occupancy, though these properties may often be roughly correlated. Separating the weak but functional binding events from weak and non-functional binding events is extremely challenging, and some have proposed that low-affinity genome-binding interactions can be categorically ignored. This certainly simplifies the problem from a computational perspective, but the findings discussed here and elsewhere suggest a risk of discarding functional sequences. Similar challenges confront in silico genomic screens to identify clusters of predicted TF binding sites: these necessarily filter out binding events of low predicted affinity, because there are many more predicted low-affinity binding motifs than consensus high-affinity motifs in any given sequence. Binding site predictions have been supported by taking evolutionary sequence conservation into account, but this risks filtering out true positives: as shown in Ci motif alignments, lower-affinity binding sites seem to be less constrained with respect to sequence variation, even in cases when the presence of the site itself is highly conserved. This is presumably because, for each non-consensus binding motif, there are multiple alternative sequences with similar affinity and thus equivalent functionality. Importantly, this type of degenerate motif conservation is easily missed: for example, some of the well-conserved Ci motifs described in this study are not properly aligned in the UCSC Genome Browser, because they do not constitute contiguous blocks of perfect sequence identity. To avoid these pitfalls, it is important to use phylofootprinting approaches that account for these alignment flaws. In contrast to most of the low-affinity binding sites discussed in this study, optimal-affinity Ci motifs in the ptc enhancer have been preserved throughout the evolution of the genus Drosophila, and perhaps much farther: GACCACCCA motifs occur in promoter-proximal regions of multiple vertebrate orthologues of ptc (Ramos, 2013).

Evolutionary enhancer sequence alignments, along with limited experimental data, also suggest that, although many predicted low-affinity sites are poorly conserved, overall TF occupancy on an enhancer may be maintained despite significant sequence turnover. This may occur either through the rapid gain and loss of individual sites, or through the maintenance of relatively weak binding affinity at a site that is unstable at the level of DNA sequence. While this last idea requires further direct testing, it is consistent with the fact that Gli sites of moderate predicted affinity have many sequence variants of similar quality, whereas the highest-affinity motifs have far fewer alternatives of similar quality. In other words, there are many more ways to be a weak binding site than a strong site. For example, among all possible 9-mer sequences, there are 654 motifs with Ci matrix similarity scores between 70 and 75 (inclusive), but only 12 motifs with scores between 90 and 95, and one motif with a score above 95. Therefore, weaker binding sites, and the enhancers containing them, have a far greater volume of sequence space in which to roam without strongly impacting transcriptional output. A thermodynamics-based simulation of enhancer evolution has shown that there is a greater number of fit solutions using weak TF sites than using high-affinity sites for a given gene expression problem (Ramos, 2013).

Equally consistent with the view of TF binding site evolution is the fact that it is much easier (that is, more likely) to create a low-affinity, non-consensus binding motif with a single mutation than a high-affinity consensus motif. An enhancer-sized DNA sequence can acquire a weak Gli motif with single-nucleotide substitutions at any of a large number of positions, as demonstrated by simulations. These arguments may help to explain why sequence conservation is not a foolproof test of the functional relevance of non-consensus TF binding sites (Ramos, 2013).

While there is no simple answer to the technical challenges facing those who hunt enhancers, the findings described in this report lead to a conclusion that low-affinity TF-DNA interactions, mediated by non-consensus and often poorly conserved sequence motifs, play important and widespread roles in developmental patterning and cis-regulatory evolution, and therefore cannot be safely ignored (Ramos, 2013).

Atrophin-Rpd3 complex represses Hedgehog signaling by acting as a corepressor of CiR

The evolutionarily conserved Hedgehog (Hh) signaling pathway is transduced by the Cubitus interruptus (Ci)/Gli family of transcription factors that exist in two distinct repressor (CiR/GliR) and activator (CiA/GliA) forms. Aberrant activation of Hh signaling is associated with various human cancers, but the mechanism through which CiRGliR properly represses target gene expression is poorly understood. This study used Drosophila and zebrafish models to define a repressor function of Atrophin (Atro) in Hh signaling. Atro directly binds to Ci through its C terminus. The N terminus of Atro interacts with a histone deacetylase, Rpd3, to recruit it to a Ci-binding site at the decapentaplegic (dpp) locus and reduce dpp transcription through histone acetylation regulation. The repressor function of Atro in Hh signaling is dependent on Ci. Furthermore, Rerea, a homologue of Atro in zebrafish, represses the expression of Hh-responsive genes. It is proposed that the Atro-Rpd3 complex plays a conserved role to function as a CiR corepressor (Zhang, 2013).


Table of contents


decapentaplegic: Biological Overview | Evolutionary Homologs | Targets of activity | Protein Interactions | Post-transcriptional Regulation | Developmental Biology | Effect of mutation | References

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