Posttranscriptional regulation

Ultrabithorax and Antennapedia 5' untranslated regions promote developmentally regulated internal translation initiation. In principle, mRNAs that contain unusually long leader sequences with multiple upstream reading frames (URFs) are good candidates for initiating transcription via a cap-independent internal ribosome binding mechanism. The 5' untranslated regions (UTRs) of the Drosophila Ubx and Antp genes were tested for their ability to promote cap-independent translation initiation. The Ubx and the Antp 5' UTR were inserted between the CAT and lacZ coding sequences in a dicistronic gene and tested for internal ribosome entry site (IRES) activity in transgenic Drosophila. Predicted full-length dicistronic mRNAs were present. High CAT activity is expressed from the first cistron from all of the dicistronic constructs introduced into the fly genome. The dicistronic transgenic strains bearing the Ubx and Antp IRES elements express significant levels of beta-galactosidase (betaGAL) from the second cistron whereas little or no betaGAL is expressed in the controls lacking the IRESs. In situ analysis of betaGAL expression in the transgenic strains indicates that expression of the second cistron is spatially and temporally regulated. Although the developmental patterns of expression directed by the Antp and Ubx IRESs overlap, they exhibit several differences indicating that these IRESs are not functionally equivalent (Ye, 1997).

Alternative splicing of pre-mRNAs is a versatile regulatory mechanism that can achieve quantitative control of gene expression and functional diversification of gene products. Much progress has been made toward understanding the basic splicing reaction and recognizing exon/intron boundaries, but the mechanisms that regulate alternative splicing are only beginning to be elucidated. Recognition of the 5' splice site by U1 snRNP and of the branchpoint near the 3' splice site by U2 snRNP auxiliary factor (U2AF) are two critical early steps that are regulated in cell- or stage-specific alternative splicing. The picture emerging from biochemical and genetic studies is that splice site selection results from the combined action of conserved consensus sequences that base-pair with the U snRNAs together with protein-protein and protein-RNA interactions that stabilize snRNP binding and mediate bridging interactions between snRNPs at the 5' and 3' splice sites. These interactions involve a growing list of non-snRNP factors, some of which may be responsible for developmental regulation of splice site selection (Burnette, 1999 and references).

Members of the SR family of RNA-binding proteins are required for multiple steps of the splicing reaction in vitro and their concentration can influence splice site competition both in vitro and in overexpression assays using cultured cells. SR proteins are required for the activity of at least some splicing enhancers that stimulate the use of weak 5' or 3' splice sites, and there is evidence for distinct specificities in these interactions. Members of the hnRNP A/B family of RNA-binding proteins also influence splice site selection in a concentration-dependent manner in vitro and when overexpressed in cultured cells. In these assays the hnRNP RNA binding proteins can antagonize the action of SR proteins. These observations have suggested that SR proteins and hnRNP A/B proteins function in vivo as concentration-dependent regulators of alternative splicing. Another possibility is that members of these families serve as cofactors or targets for the actual regulators. Particular SR proteins have been proposed to interact with developmentally specific factors to promote regulation of splicing (Burnette, 1999 and references).

Although a framework of hypotheses is evolving, little is known about regulators of alternative splicing and how they function in vivo. Notable exceptions are Sex lethal and Transformer, proteins that control alternative splicing decisions during sex determination in Drosophila. Because few developmentally specific regulators of alternative splicing have been identified, it is possible that many -- if not most -- alternative splicing decisions are regulated by relatively subtle variations in the levels of general, widely distributed factors, perhaps acting cooperatively or antagonistically as proposed for SR and hnRNP A/B proteins. This is consistent with much correlative evidence and many in vitro observations, but conclusive proof that either type of protein normally regulates an alternative splicing decision in vivo has yet to be obtained. Although null alleles of the Drosophila SR protein gene B52 (homolog of human SRp55) show it to be essential for viability, examination of multiple constitutively and alternatively spliced RNAs has failed to reveal any alterations of splicing even in the absence of detectable protein (Burnette, 1999 and references).

The Ultrabithorax (Ubx) was used as a model for regulation of alternative splicing in large and complex transcription units. The six alternative Ubx mRNAs share large protein-coding 5' and 3' exons but differ in the pattern of incorporation of three elements: B is located between two alternative donor sites at the end of the first common exon, whereas mI and mII are internal cassette exons. Within the central nervous system (CNS), different neurons express distinct ratios of Ubx isoforms. The complex and quantitative nature of this regulation is unlike that of other well-studied model systems in Drosophila (e.g., sex-specific splicing in the sex determination hierarchy or germ line-specific splicing of P-element transcripts) but resembles that of many other genes in vertebrates and invertebrates. It seems most likely that this type of alternative splicing is controlled not by highly tissue- and gene-specific splicing regulators but by developmental variations in the concentration or activity of broadly distributed multifunctional factors that may act combinatorially. Hence, Ubx should be a valuable model where genetic approaches can be used to dissect this type of regulation (Burnette, 1999 and references).

Strong reductions of function for the postulated type of regulatory factors would probably cause lethal phenotypes that would be uninterpretable in terms of their effects on Ubx splicing. However, the Ubx splicing pattern should be sensitive to partial reductions in the concentration or activity of these regulatory factors. This may also be true for factors that play important accessory roles in regulation as targets or as constitutively expressed components of regulatory complexes. Two approaches were used to identify such factors. (1) First, a test was carried out to see if the Ubx alternative splicing pattern is altered in heterozygotes for strong loss-of-function mutations. Such mutations are found in a set of genes implicated in the control of alternative splicing in Sxl and P-element RNAs. (2) To identify the location of additional genes involved in regulation of Ubx splicing, a large collection of deficiencies was tested for dominant enhancement of the haploinsufficient Ubx haltere phenotype; it was then asked whether the Ubx splicing pattern is altered in heterozygotes for the interacting deficiencies, and the phenotypic interaction and effect on splicing was traced to specific genes when mutations existed in reasonable candidates. Inclusion of the cassette exons in Ubx mRNAs is reduced strongly in heterozygotes for hypomorphic alleles of hrp48, which encodes a member of the hnRNP A/B family and is implicated in control of P-element splicing. Significant reductions of mI and mII inclusion were also observed in heterozygotes for loss-of-function alleles of virilizer, fl(2)d, and crooked neck. The products of virilizer and fl(2)d are also required for Sxl autoregulation at the level of splicing; crooked neck encodes a protein with structural similarities to yeast-splicing factors Prp39p and Prp42p. Deletion of at least five other loci caused significant reductions in the inclusion of mI and/or mII (Burnette, 1999).

Coupled RT-PCR assays were used to analyze the pattern of Ubx alternative splicing in heterozygous third instar larvae and in adults. The isoform ratios in third instar larvae were in close agreement with those determined previously using nuclease protection assays. Types Ia and IIa are the predominant Ubx mRNAs and those lacking both mI and mII (isoforms IVa and b) make up only a small fraction of the total. Adults contain a significantly higher proportion of class IV mRNAs than larvae; this differs from previous reports and probably reflects the very early and narrow age distribution of the adults used in this study. It is important to note that the Ubx isoform ratios did not vary significantly between different wild-type strains nor between these and several control strains that carried different balancer chromosomes and irrelevant mutations. These results demonstrate that the mechanism that controls Ubx alternative splicing is robust, a conclusion that is consistent with the faithful conservation of Ubx isoform structure and expression among Drosophila species spanning 60 million years of evolution. The fact that the quantitative isoform pattern revealed by this assay is insensitive to considerable variation in genetic background highlights the significance of the effects described below for specific mutations and deficiencies. Although amplified Ubx cDNA fragments that contain mI but not mII (i.e., hypothetical isoforms IIIa and IIIb) should have the same length as isoforms IIa and IIb, such amplifiers would be expected to exhibit distinctly slower mobility due to the difference in nucleotide sequence (Burnette, 1999).

The products of Sxl, tra, and tra-2 are known regulators of alternative splicing decisions in Drosophila but they are not essential for processes other than sex determination (and dosage compensation, in the case of Sxl) because males that are null for these genes are viable and appear phenotypically normal. However, additional genes [fl(2)d, virilizer, and l(2)49Db] are required for correct control of alternative splicing decisions by Sxl are also essential for viability in both sexes; hence, their products may also have roles in other alternative splicing events. To determine whether these include the control of Ubx alternative splicing, it was asked whether the Ubx isoform ratios are altered in heterozygotes for mutations in these genes. In contrast to the stability described in the preceding section, the Ubx splicing pattern is altered significantly when the expression or function of virilizer or fl(2)d is reduced. The strongest effect is observed with virilizer, using a loss-of-function allele (vir3) that is recessive lethal in both sexes. In heterozygous larvae the proportion of Ubx class I mRNAs declines while that of classes II and IV increases. The proportion of class I that contains the B element is not altered. The increase in classes II and IV indicates that inclusion of both mI and mII is reduced but that the effect on mI exceeds that on mII. Inclusion of mI is also reduced in adults, although the effect was weaker than in larvae. More modest but statistically significant reductions of mI and mII inclusion are also observed in larvae heterozygous for the fl(2)d2 mutation, which is also a loss-of-function allele that is recessive lethal in both sexes (Burnette, 1999).

hrp48 plays a critical role in the inclusion of mI and mII: hrp48 is a member of the hnRNP-A/B family of RNA-binding proteins and forms part of a protein complex that regulates splicing of intron 3 (IVS3) in P-element transcripts. Although repression of IVS3 splicing in somatic tissues is dictated by PSI, which is a soma-specific component of the regulatory complex, the hrp48 protein binds specifically to sequences within the cis-acting regulatory element in the RNA. hrp48 was originally identified as a general component of heterogeneous nuclear ribonucleoprotein particles and the hrp48 gene is essential for viability, so it must perform additional functions unrelated to P-element expression; these functions might include regulation of other splicing decisions. The five known mutant alleles of hrp48 are all P-element insertions in the upstream regulatory region and are not null. Nevertheless, inclusion of mI and mII in Ubx mRNAs is reduced markedly in larvae and adults heterozygous for the strong recessive lethal allele hrp481; weaker alleles, some of which are viable as homozygotes, have similar but more modest effects. The effect of hrp48 mutations resembles that of vir and fl(2) mutations: inclusion of mII is affected more weakly than mI, and the proportion of isoform I that contains the B element is not altered. Heterozygosity for hrp481 reduces inclusion of mI by 27%; this is the strongest effect observed for any mutation or deficiency in this study, indicating that normal levels of hrp48 are critical for inclusion of the internal exons, especially mI, in Ubx mRNAs (Burnette, 1999).

One enhancer, Df(1)64c18g, deletes the genes crooked neck (crn) and kurz (kz), which are located at 2F1 and are both candidate RNA-processing factors. The crn gene encodes a protein with 16 tetratrichopeptide repeats, a motif implicated in protein-protein interactions. Although CRN protein has been proposed to function as a transcription factor involved in cell cycle control, recent data show that it is closely related to the yeast splicing factors Prp39p and Prp42p, which associate with yeast U1 snRNP and are required for splicing. The kz gene encodes a protein with extensive homology to yeast ATP-dependent splicing factors Prp2p, Prp16p, and Prp22p. These proteins define a distinct subfamily of ATP-dependent putative RNA-helicases. Because mutant alleles of these genes are available, a direct test was carried out to see if deletion of one or both might be responsible for enhancement of the Ubx haltere phenotype and whether they affect the Ubx splicing pattern. Like the deficiency, two hypomorphic, recessive lethal alleles of crn (EA130 and RC63) act as dominant zygotic enhancers of Ubx195/+ and Ubx9.22/+. RT-PCR analysis shows that inclusion of mI, but not mII, is reduced significantly in larvae heterozygous for crnEA130. The second allele, crnRC63, has similar effects on the Ubx phenotype and splicing pattern. A recessive lethal allele of kz (DF942) behaves as a weak dominant enhancer of Ubx195/+ and Ubx9.22/+, but RT-PCR analyses does not reveal a significant dominant effect on the Ubx splicing pattern (Burnette, 1999).

The inclusion of mI and mII in Ubx mRNAs is regulated by competition between 5' splice sites that flank each of these exons after they are joined to E5'. As the RNA is transcribed, mI and subsequently mII are spliced constitutively to the upstream exon but can then be removed, together with the downstream intron, using an upstream 5' splice site within E5' or at the junction with this exon. For the majority of nascent RNAs (those initially spliced using 5' splice site a in E5'), a strong 5' splice site is regenerated at the junction between E5' and mI or mII that competes with the mI or mII 5' splice site located 51 nt downstream. For a minority of nascent RNAs (those initially spliced using 5' splice site b in E5') the a site is still present in E5' and can compete with the mI or mII 5' splice site located 78 nt downstream; use of the a site then removes the B element along with mI or mII. Developmental regulation of mI and mII inclusion is achieved by modulating the competition between the upstream and downstream 5' splice sites that flank these exons (Burnette, 1999).

Reduction of function in all of the factors identified in this work leads to reduced inclusion of mI (and in most cases also mII). This suggests roles in suppression of the upstream sites (which strongly match the 5' splice site consensus) or stimulation of the downstream sites (which match the consensus more weakly). It is interesting that three of the factors identified in this study that are required for inclusion of mI and mII in Ubx mRNAs may also be required for suppression of 5' splice site utilization in other RNAs: the functions of virilizer and fl(2)d are required for Sxl to repress splicing of the male-specific exon in its own RNA, and hrp48 is implicated as part of a complex that mediates repression of a 5' splice site in P-element RNA. In addition, heterozygosity for a null allele of sans-fille (snfJ210) does not alter the Ubx splicing pattern, but the antimorphic allele snfe8H, which interferes with autoregulation of Sxl splicing, enhances the Ubx haltere phenotype and increases exclusion of mI and mII (Burnette, 1999 and references).

The products of virilizer, fl(2)d, and snf might function as parts of a complex that mediates active repression of 5' splice site utilization through interactions with U1 snRNP. Formation or stabilization of this repression complex could be directed to different target splice sites through the action of distinct factors that, like Sxl, bind to cis-acting regulatory signals and interact with components of the complex. An intriguing possibility is that hrp48 interacts (directly or indirectly) with a U1 snRnp/Snf/Vir/Fl(2)D complex to target suppression of splicing at the upstream sites that are used to remove mI. The strong reduction of mI inclusion (27%) observed in hrp481 heterozygotes suggests a critical role for hrp48 in modulating competition between the regenerated and downstream 5' splice sites that flank this exon. Although hrp48 is an hnRNP protein that probably binds nonspecifically to many RNAs, it is also known to form part of a specific complex that blocks use of the 5' splice site for the third intron of P-element RNA in somatic cells. This regulatory complex prevents U1 snRNP from binding at the 5' splice site and recruits it instead, nonproductively, to the more upstream of two overlapping pseudo-5' splice sites within the exon; hrp48 itself makes contact with the downstream pseudo-5' splice site, F2. Splicing of P-element IVS3 in a reporter transgene is partially derepressed in adult escapers homozygous for a semilethal hrp48 allele, indicating that hrp48 is necessary for efficient suppression of the 5' splice site. Hence, it may be significant that a sequence within mI that overlaps the regenerated 5' splice site matches F2 and flanking nucleotides at 8 of 10 positions; this sequence is conserved among four Drosophila species that diverged up to 60 million years but maintain identical regulation of mI inclusion. hrp48 might bind to this sequence and help to recruit U1 snRNP nonproductively to the regenerated 5' splice site at the E5'/mI junction; in intermediates where mI has been spliced to the b site of E5', this complex could also block access to the a site located 27 nt upstream. This would explain why the hrp48, vir, and fl(2)d mutations reduce mI inclusion but do not alter the proportion of class I mRNAs that contain the B element: failure to assemble the repression complex at the E5'/mI junction would allow inappropriate use of both the regenerated site (used to remove mI from E5'a/mI and E5'b/mI intermediates) and the a site (used to remove mI and the B element from E5'b/mI intermediates) (Burnette, 1999 and references).

The effect of hrp48, vir, and fl(2)d mutations on inclusion of exon mII, which does not contain an F2-like element, may not be the result of resplicing at the E5'/mII junction. The reduction of mII inclusion (detected as an increase in class IV mRNAs rather than a decrease in class II) could be explained if the repression complex must remain assembled at the E5'/mI junction to prevent subsequent removal of mI and mII together during splicing of intron 3. Intermediates from which mI is removed during splicing of intron 2 would retain mII. The net result would be an increase in both class II and class IV mRNAs, as observed. In addition, it is noted that the effect of hrp48 mutations on mI and mII inclusion is the opposite of what one would expect from the simple idea that hnRNP A/B proteins generally promote exon skipping (and use of upstream 5' splice sites), antagonizing a general effect of SR proteins that promote exon inclusion (or use of downstream 5' splice sites). The observations presented here are more consistent with a specific role for hrp48 acting through cis-regulatory elements to prevent resplicing of mI. It is more difficult to speculate on the roles of crn or the still-unidentified factors deleted by deficiencies that alter the Ubx splicing pattern. In principle, these could participate in repression of the regenerated 5' splice sites or stimulation of the competing downstream site. They could also be involved in interactions between mI and mII that seem to be required for effective use of the downstream 5' splice site located at the mI/intron 2 boundary. Although a weak homology to the homeodomain led to the proposal that the crooked neck protein functions as a transcription factor, its 16 tetratrichopeptide repeats form a distinct subfamily with those of Prp39p and Prp42p, two splicing factors from yeast that interact with U1 snRNP but appear not to bind RNA directly. A third yeast member of this group has been identified that has more extensive homology to crn ; it will be interesting to learn whether this also functions as a splicing factor (Burnette, 1999 and references).

Additional observations indicate that inclusion of mI is controlled by a complex regulatory switch employing multiple factors to balance positive and negative inputs acting on the upstream and perhaps downstream splice sites. A positive role for Rbp1 is suggested by studies of cis-acting elements within mI. Rbp1 is related to the mammalian SR proteins 9G8 and SRp20; it has been implicated in the control of dsx and fru RNA splicing as a component of exonic splicing enhancer complexes that assemble on cis-acting elements with the sex-specific factor Tra. Rbp1 is expressed widely in both sexes and is likely to play a role in the splicing of many RNAs. Mutations in mI at positions +11 and +14 downstream of the E5'/mI junction reduce the efficiency of the regenerated 5' splice site in vivo; these positions lie within a sequence that matches at 11 of 12 nucleotides a set of functionally important Rbp1-binding sites within the female-specific polypyrimidine tract of dsx RNA, suggesting that Rbp1 is required to stimulate use of the regenerated 5' splice site in Ubx. (Burnette, 1999 and references).

It is unlikely that the factors described here represent all of those with critical effects on Ubx splicing regulation. The analysis of deficiencies itself poses certain limitations: an effect on the Ubx haltere phenotype may be masked by the simultaneous deletion of a gene that encodes a negative regulator of Ubx expression or function or of two factors with opposite effect on the regulation of Ubx splicing. Furthermore, detailed molecular analyses by quantitative RT-PCR was performed only for those regions whose phenotypic interactions with Ubx were confirmed by overlapping deficiencies, but another 22 regions were tentatively identified by single deficiencies as containing strong haploinsufficient enhancers of Ubx and might harbor genes with important effects on splicing; thus the regions described above are probably only a subset of those that can be identified with this approach. Using the positional information provided by the deficiencies plus RT-PCR assays of the Ubx splicing pattern, it should be possible to identify specific mutations in the relevant gene(s) within any region of interest (Burnette, 1999).

The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings

The Drosophila Bithorax Complex encodes three well-characterized homeodomain proteins that direct segment identity, as well as several noncoding RNAs of unknown function. This study analyzes the iab-4 locus, which produces the microRNAs iab-4-5p and iab-4-3p. iab-4 is analogous to miR-196 in vertebrate Hox clusters. Previous studies demonstrated that miR-196 interacts with the Hoxb8 3' untranslated region. Evidence is presented that miR-iab-4-5p directly inhibits Ubx activity in vivo. Ectopic expression of mir-iab-4-5p attenuates endogenous Ubx protein accumulation and induces a classical homeotic mutant phenotype: the transformation of halteres into wings. These findings provide the first evidence for a noncoding homeotic gene and raise the possibility that other such genes occur within the Bithorax complex (Ronshaugen, 2005).

Computational studies have identified the Ubx 3' UTR as a likely target of regulation by iab-4-5p (Stark, 2003; Grun, 2005). Of the seven potential sites identified by Stark, five exhibit conserved and canonical seed pairing of six or more nucleotides. Of these, sites #3 and #6 are perfectly conserved among sequenced Drosophilids and have seeds of at least 7 nt, a length sufficient for efficient in vivo recognition by miRNAs; site #7 also has a 7-mer seed match that is conserved in some species (Ronshaugen, 2005).

In current target-finding approaches, greater confidence is usually ascribed to those miRNA-binding sites that are conserved in the greatest number of analyzed species. Curiously, the putative iab-4-5p target sites with the lowest free energy are not necessarily the best conserved. Instead, there appear to be compensatory changes among different iab-4-5p-binding sites in individual Ubx 3' UTRs. For example, site #4 exhibits canonical 6-mer seed pairing in four species of Drosophila, but contains a G:U base pair in Drosophila virilis and a seed mismatch in Drosophila mojavenesis and is likely nonfunctional in these two species. Conversely, site #7 is mispaired in D. melanogaster and Drosophila yakuba, but is conserved as a strong 7-mer seed-paired site in D. mojavenesis, Drosophila pseudoobscura, Drosophila ananassae, and D. virilis. These observations suggest that individual target sites may be evolutionarily labile, and in vivo regulation depends on the net complement of both high- and low-affinity sites contained in the target mRNA. These compensatory changes in strong and weak target sites are reminiscent of the evolution of individual Bicoid-binding sites in the eve stripe 2 enhancers present in divergent Drosophilids (Ronshaugen, 2005).

Direct evidence for iab-4:Ubx miRNA interactions was obtained using a tub::GFP-Ubx 3' UTR transgene (the "Ubx sensor"). This construct directs ubiquitous expression of the GFP coding sequence fused to the Ubx 3' UTR, and wing imaginal discs bearing the Ubx sensor display relatively uniform expression of GFP. Ectopic expression of UAS-DsRed under the control of ptc-Gal4, which directs expression along the anterior-posterior border of the disc, has little or no effect on the distribution of GFP staining (Ronshaugen, 2005).

The expression of the Ubx sensor was assayed in the presence of ectopic iab-4 miRNAs. For this purpose, a transgene was created that contains DsRed and 400 base pairs (bp) from iab-4 encompassing the entire 100-bp 3' hairpin sequence (UAS-DsRed-iab-4). Transgenes of this type direct the expression of biologically active miRNAs in cells that are labeled by expression of DsRed (Stark, 2003). When driven by ptc-Gal4 in wing imaginal discs, Ubx sensor levels were specifically diminished in those cells expressing the iab-4 transgene. Detailed analysis of the DsRed-iab-4 and GFP-Ubx expression profiles suggests that repression of the Ubx sensor by ectopic iab-4 miRNA is dose-sensitive. These data constitute in vivo evidence that iab-4 miRNAs specifically recognize target sequences in the Ubx 3' UTR and thereby attenuate Ubx protein synthesis (Ronshaugen, 2005).

Ubx protein is broadly distributed throughout the haltere imaginal disc, where it imposes haltere identity by repressing the expression of many genes that otherwise direct wing development. This repression is very sensitive to Ubx levels, and consequently, even partial loss of Ubx function can transform halteres into wings. Haltere discs were examined for the accumulation of Ubx protein in the absence or presence of ectopic iab-4 miRNAs. Ubx is detected at high levels in most of the cells of the presumptive pouch. Expression of DsRed alone using bx-Gal4, which is active in the presumptive dorsal region of the pouch, did not affect Ubx accumulation. In contrast, haltere discs expressing UAS-DsRed-iab-4 under the control of bx-Gal4 displayed strongly reduced levels of Ubx protein. Thus, as seen for the Ubx sensor in wing discs, ectopic iab-4 miRNA inhibits accumulation of endogenous Ubx protein (Ronshaugen, 2005).

The effect of iab-4 miRNA misexpression on adult haltere development was examined. The wild-type haltere contains small lightly pigmented sensilla but lacks the triple row of sensory bristles at the leading margin seen in wings. In contrast, halteres that developed from discs expressing UAS-DsRed-iab-4 under the control of bx-Gal4 or scalloped-Gal4 are flattened and elongated in the proximal-distal axis, and exhibit an extensive row of sensory bristles at the leading margin. All of these phenotypes are strongly indicative of a classic haltere-to-wing homeotic transformation (Ronshaugen, 2005).

The demonstration that miR-iab-4 represses the anterior Hox gene Ubx might be relevant to the phenomenon of 'posterior prevalence'. Polycomb mutant embryos have previously been observed to derepress Hox gene expression, resulting in broad misexpression of all Hox genes. Ultimately, ectopic expression of posterior Hox genes (e.g., Abd-B or Hox9-13) leads to the transcriptional repression of anterior Hox genes (e.g., Ubx or Hox8 paralogs). Polycomb mutant embryos also derepress iab-4 expression throughout the embryo. Therefore, misexpression of iab-4 miRNAs may contribute to the repression of Ubx function observed in the Polycomb mutant background. Thus, posterior prevalence may arise from the dual utilization of protein-based/transcriptional mechanisms and miRNA-based/post-transcriptional mechanisms (Ronshaugen, 2005).

MicroRNA-encoded behavior in Drosophila

The relationship between microRNA regulation and the specification of behavior is only beginning to be explored. This study finds that mutation of a single microRNA locus (miR-iab4/8 - (miR-iab4/iab8)) in Drosophila larvae affects the animal's capacity to correct its orientation if turned upside-down (self-righting). One of the microRNA targets involved in this behavior is the Hox gene Ultrabithorax whose derepression in two metameric neurons leads to self-righting defects. In vivo neural activity analysis reveals that these neurons, the self-righting node (SRN), have different activity patterns in wild type and miRNA mutants while thermogenetic manipulation of SRN activity results in changes in self-righting behavior. These data thus reveal a microRNA-encoded behavior and suggests that other microRNAs might also be involved in behavioral control in Drosophila and other species (Picao-Osorio, 2015).

The regulation of RNA expression and function is emerging as a hub for gene expression control across a variety of cellular and physiological contexts, including neural development and specification. Small RNAs such as microRNAs (miRNAs) have been shown to affect neural differentiation, but their roles in the control of behavior are only beginning to be explored (Picao-Osorio, 2015).

Previous work has focused on the mechanisms and impact of RNA regulation on the expression and neural function of the Drosophila Hox genes. These genes encode a family of evolutionarily conserved transcription factors that control specific programs of neural differentiation along the body axis, offering an opportunity to investigate how RNA regulation relates to the formation of complex tissues such as the nervous system (Picao-Osorio, 2015).

This study used the Hox gene system to investigate the roles played by a single miRNA locus (miR-iab4/iab8) on the specification of the nervous system during early Drosophila development. This miRNA locus controls the embryonic expression of posterior Hox genes. Given that no detectable differences were found in the morphological layout of the main components of the nervous system in late Drosophila embryos of wild type and miR-iab4/iab8-null mutants [herein ΔmiR], this study analyzed early larval behavior as a stratagem to probe the functional integrity of the late embryonic nervous system (Picao-Osorio, 2015).

Most behaviors in early larva were unaffected by the miRNA mutation, except self-righting (SR) behavior: miRNA mutant larvae were unable to return to their normal orientation at the same speed as their wild-type counterparts (Picao-Osorio, 2015).

By means of selective target overexpression followed by SR phenotype analyses, this study identified the Drosophila Hox gene Ultrabithorax (Ubx) as a miRNA target implicated in the genetic control of SR behavior. Overexpression of Ubx within its expression domain did not affect any larval behavior tested except SR, which is in agreement with the effects observed in miRNA mutants. Analysis of Ubx 3' untranslated region (3'UTR) fluorescent reporter constructs expressed in the Drosophila central nervous system (CNS) indicates that the interaction between miR-iab4/iab8 and Ubx is direct, which is in line with prior observations in other cellular contexts (Picao-Osorio, 2015).

To identify the cellular basis for SR control, Ubx was systematically overexpressed within subpopulations of neurons. Increased levels of Ubx within the pattern of Cha(7.4kb)-Gal4, which largely targets cholinergic sensory and interneurons, phenocopied the miRNA SR anomalies. Further overexpression analysis identified two metameric neurons as the minimal node required for the SR behavior [self-righting node (SRN)] (Picao-Osorio, 2015).

Several lines of evidence confirm the role of miRNA-dependent Ubx regulation within the SRN as a determinant of SR. First, both Ubx and miRNA transcripts (miR-iab4) derived from the miR-iab4/iab8 locus were detected within the SRN. Second, in the context of miRNA mutation, Ubx protein expression is increased within the SRN. Third, reduction of Ubx (Ubx RNAi) specifically enforced within SRN cells is able to ameliorate or even rescue the SR phenotype observed in miRNA mutants (Picao-Osorio, 2015).

Two plausible scenarios arise to explain the effects of miR-iab4/iab8 in regard to SR behavior. One is that miRNA input is required for the late embryonic development of the neural networks underlying SR, arguing for a 'developmental' role of the miRNA; another is that miRNA repression affects normal physiological/behavioral functions largely without disrupting neural development in line with a 'behavioral' role. Two independent experiments support that the primary roles of miR-iab4/8 are behavioral. First, anatomical analysis of SRN cells in wild type (wt), ΔmiR, and R54503>Ubx [SRN-driver line] show no significant differences in total numbers of SRN cells or in SRN cell body size; furthermore, analysis of wt, ΔmiR, and R54503>Ubx show indistinguishable SRN-projection patterns. Second, Gal-80ts-mediated conditional expression experiments show that SRN-specific Ubx overexpression after embryogenesis is sufficient to trigger the SR behavior (Picao-Osorio, 2015).

These results suggest that miRNA-dependent Hox regulation within the SRN must somehow modify the normal physiology of SRN cells so that when the miRNA is mutated, these neurons perform functions different from those in wild-type animals. To test this hypothesis, genetically encoded calcium sensors [GCaMP6] specifically expressed in SRN cells were used, and spontaneous profiles of neural activity were tracked down. SRN cells in miRNA mutants produce activity traces that are significantly different from those observed in wild-type SRN cells. Quantification of maximal amplitude and proportion of active cells in each genotype also reveal significant differences in SRN function across the genotypes, but no change in cell viability is observed. Neural activity differences across genotypes are significant within regions of expression of miR-iab4, suggesting that this miRNA (and not miR-iab8) might be the main contributor to SR control. Analysis of mutations that selectively affect miR-iab4 or miR-iab8 strongly suggests that miR-iab4 is the key regulator of SR (Picao-Osorio, 2015).

To demonstrate that the changes in SRN neural activity were causal to SR behavior, SRN cells were artificially activated or inhibited this was shown to trigger the aberrant SR phenotype. This suggested that activation of SRN cells in larvae placed 'right side up' might be sufficient to 'evoke' actions reminiscent of a self-righting response. An optogenetic system was developed in which SRN cells were activated by means of R54F03-driven channelrhodopsin 2 (ChR2) in trans-retinal fed larvae. Under blue light stimulation, larvae performed an atypical bending movement, frequently adopting a 'lunette' position. Neither parental line R54F03-Gal4 nor UAS-Ch2R showed similar reactions to stimulation, confirming the specificity of this effect (Picao-Osorio, 2015).

To study the links between SRN neurons and the SR movement, SRN projections were labeled with myr-GFP and SRN cells were discovered to innervate two of the lateral transverse (LT) muscles and can be colabeled antibodies against Fasciclin 2 (Fas2), demonstrating these to be motorneurons. LT muscles are innervated by Bar-H1+ motorneurons, so Bar-H1-Gal4 was used as a second driver to demonstrate that appropriate Ubx levels in these cells are required for normal SR behavior, establishing the SRN cells as the LT-MNs (Picao-Osorio, 2015).

This study has therefore shown that miRNA-dependent Hox gene repression within a distinct group of motorneurons (SRN/LT-MNs) is required for the control of a specific locomotor behavior in the early Drosophila larva. The finding that Hox gene posttranscriptional regulation is involved in SR control suggests that other RNA-based regulatory processes affecting Hox gene expression might also impinge on specific neural outputs; this possibility is currently being investigated, with special regard to the roles of the Hox genes in the specification of neural lineages with axial-specific architectures, and the roles of other miRNAs on behavior are being systematically tested (Picao-Osorio, 2015).

That no obvious neuro-anatomical changes in miRNA mutant embryos could be detected suggests that these are either very subtle or that the role of miRNA regulation may be primarily behavioral, in the sense of affecting the performance of a correctly wired neural system, rather than developmental, contributing to the development of the network. Given that miR-iab4/iab8 is involved in adult ovary innervation, it seems that miRNAs -- much like ordinary protein-coding genes -- can be involved in several distinct roles within the organism (Picao-Osorio, 2015).

The results of this study contribute to the understanding of how complex innate behaviors are represented in the genetic program. The data lead to a proposal that other miRNAs might also be involved in the control of behavior in Drosophila and other species (Picao-Osorio, 2015).

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands

MicroRNAs (miRNAs) are ~22-nucleotide RNAs that are processed from characteristic precursor hairpins and pair to sites in messages of protein-coding genes to direct post-transcriptional repression. The miRNA iab-4 locus in the Drosophila Hox cluster is transcribed convergently from both DNA strands, giving rise to two distinct functional miRNAs. Both sense and antisense miRNA products target neighboring Hox genes via highly conserved sites, leading to homeotic transformations when ectopically expressed. Sense/antisense miRNAs are also present in the mouse and antisense transcripts are found close to many miRNAs in both flies and mammals, suggesting that additional sense/antisense pairs exist (Stark, 2008).

Hox genes are highly conserved homeobox-containing transcription factors crucial for development in animals. Genetic analyses have identified them as determinants of segmental identity that specify morphological diversity along the anteroposterior body axis. A striking conserved feature of Hox complexes is the spatial colinearity between Hox gene transcription in the embryo and the order of the genes along the chromosome. Hox clusters also give rise to a variety of noncoding transcripts, including microRNAs (miRNAs) mir-10 and mir-iab-4/mir-196, which derive from analogous positions in Hox clusters in flies and vertebrates. miRNAs are ~22-nucleotide (nt) RNAs that regulate gene expression post-transcriptionally. They are transcribed as longer precursors and processed from characteristic pre-miRNA hairpins. In particular, Hox miRNAs have been shown to regulate Hox protein-coding genes by mRNA cleavage and inhibition of translation, thereby contributing to the extensive regulatory connections within Hox clusters. Several Hox transcripts overlap on opposite strands, providing evidence of extensive antisense transcription, including antisense transcripts for mir-iab-4 in flies and its mammalian equivalent mir-196. However, the function of these transcripts has been elusive. This study shows that the iab4 locus in Drosophila produces miRNAs from opposite DNA strands that can regulate neighboring Hox genes via highly conserved sites. Evidence is provided that such sense/antisense miRNA pairs are likely employed in other contexts and a wide range of species (Stark, 2008).

Examination of the antisense transcript that overlaps Drosophila mir-iab-4 revealed that the reverse complement of the mir-iab-4 hairpin folds into a hairpin reminiscent of miRNA precursors. Moreover, 17 sequencing reads from small RNA libraries of Drosophila testes and ovaries mapped uniquely to one arm of the iab-4 antisense hairpin. All reads were aligned at their 5' end, suggesting that the mir-iab-4 antisense hairpin is processed into a single mature miRNA in vivo, which is referred to as miR-iab-4AS. For comparison, six reads were found consistent with the known miR-iab-4-5p (or miR-iab-4 for short) and one read was foudn for its star sequence (miR-iab-4-3p). Interestingly, the relative abundance of mature miRNAs and star sequences for mir-iab-4AS (17:0) and mir-iab-4 (6:1) reflects the thermodynamic asymmetry of the predicted miRNA/miRNA* duplexes. Because they derived from complementary near palindromes, miR-iab-4 and miR-iab-4AS had high sequence similarity, only differing in four positions at the 3' region. However, they differed in their 5' ends, which largely determine miRNA target spectra: miR-iab-4AS was shifted by 2 nt, suggesting targeting properties distinct from those of miR-iab-4 and other known Drosophila miRNAs (Stark, 2008).

Robust transcription of mir-iab-4 sense and antisense precursors was confirmed by in situ hybridization to Drosophila embryos. Both transcripts were detected in abdominal segments in the posterior part of the embryo, but intriguingly in nonoverlapping domains. As described previously, mir-iab-4 sense was expressed highly in abdominal segments A5-A7, showing modulation in levels within the segments: abdominal-A (abd-A)-expressing cells appeared to have more mir-iab-4, whereas Ultrabithorax (Ubx)-positive cells appeared to have little or none. In contrast, mir-iab-4AS transcription was detected in the segments A8 and A9, where Abdominal-B (Abd-B) is known to be expressed. Primary transcripts for mir-iab-4 and mir-iab-4AS were also detected by strand-specific RT-PCR in larvae, pupae, and male and female adult flies, suggesting that both miRNAs are expressed throughout fly development (Stark, 2008).

To assess the possible biological roles of the two iab-4 miRNAs, fly genes were examined for potential target sites by searching for conserved matches to the seed region of the miRNAs. Highly conserved target sites were found for miR-iab-4AS in the 3' untranslated regions (UTRs) of several Hox genes that are proximal to the iab-4 locus and are expressed in the neighboring more anterior embryonic segments: abd-A, Ubx, and Antennapedia (Antp) have four, five, and two seed sites, respectively, most of which are conserved across 12 Drosophila species that diverged 40 million years ago. More than two highly conserved sites for one miRNA is exceptional for fly 3' UTRs, placing these messages among the most confidently predicted miRNA targets and suggesting that they might be particularly responsive to the presence of the miRNA. The strong predicted targeting of proximal Hox genes was reminiscent of previously characterized miR-iab-4 targeting of Ubx in flies and miR-196 targeting of HoxB8 in vertebrates (Stark, 2008 and references therein).

To test whether miR-iab4AS is functional and can directly target abd-A and Ubx, Luciferase reporters were constructed carrying the corresponding wild-type 3' UTRs and control 3' UTRs in which each seed site was disrupted by point substitutions. mir-iab-4AS potently repressed reporter activity for abd-A and Ubx. This repression was specific to the miR-iab-4AS seed sites; expression of the control reporters with mutated sites was not affected. Tested were perform to see whether mir-iab-4AS reduced expression of a Luciferase reporter with the Abd-B 3' UTR, which has no seed sites. As expected, mir-iab-4AS expression did not affect reporter activity, consistent with a model where miRNAs do not target genes that are coexpressed at high levels. In addition to demonstrating specific repression dependent on the predicted target sites, these assays confirmed the processing of the mir-iab-4AS hairpin into a functional mature miRNA (Stark, 2008).

If miR-iab-4AS were able to potently down-regulate Ubx in the fly, its misexpression should result in a Ubx loss-of-function phenotype, a line of reasoning that has often been used to study the functions and regulatory relationships of Hox genes. Ubx is expressed throughout the haltere imaginal disc, where it represses wing-specific genes and specifies haltere identity. When mir-iab-4AS was expressed in the haltere imaginal disc under bx-Gal4 control, a clear homeotic transformation of halteres to wings was observed. The halteres developed sense organs characteristic of the wing margin and their size increased severalfold, features typical of transformation to wing. Consistent with the increased number of miR-iab4AS target sites, the transformation was stronger than that reported for expression of iab-4, for which changes in morphology were confirmed wing-like growth was not found (Stark, 2008).

It is concluded that both strands of the iab-4 locus are expressed in nonoverlapping embryonic domains and that each transcript produces a functional miRNA in vivo. In particular, the novel mir-iab-4AS is able to strongly down-regulate neighboring Hox genes. Interestingly, vertebrate mir-196, which lies at an analogous position in the vertebrate Hox clusters, is transcribed in the same direction as mir-iab-4AS and most other Hox genes, and targets homologs of both abd-A and Ubx. With its shared transcriptional orientation and homologous targets, mir-iab-4AS appears to be the functional equivalent of mir-196 (Stark, 2008).

The expression patterns and regulatory connections between Hox genes and the two iab-4 miRNAs show an intriguing pattern in which the miRNAs appear to reinforce Hox gene-mediated transcriptional regulation. In particular, miR-iab-4AS would reinforce the posterior expression boundary of abd-A, Ubx, and Antp, supporting their transcriptional repression by Abd-B. mir-iab-4 appears to support abd-A- and Abd-B-mediated repression of Ubx, reinforcing the abd-A/Ubx expression domains and the posterior boundary of Ubx expression. Furthermore, both iab-4 miRNAs have conserved target sites in Antp, which is also repressed by Abd-B, abd-A, and Ubx. The iab-4 miRNAs thus appear to support the established regulatory hierarchy among Hox transcription factors, which exhibits 'posterior prevalence,' in that more posterior Hox genes repress more anterior ones and are dominant in specifying segment identity. Interestingly, Abd-B and mir-iab-4AS are expressed in the same segments, and the majority of cis-regulatory elements controlling Abd-B expression are located 3' of Abd-B. This places them near the inferred transcription start of mir-iab-4AS, where they potentially direct the coexpression of these genes. Similarly, abd-A and mir-iab-4 may be coregulated as both are transcribed divergently, potentially under the control of shared upstream elements (Stark, 2008).

These data demonstrate the transcription and processing of sense and antisense mir-iab-4 into functional miRNAs with highly conserved functional target sites in neighboring Hox genes. In an accompanying study (Bender 2008), genetic and molecular analyses in mir-iab-4 mutant Drosophila revealed that the proposed regulation of Ubx by both sense and antisense miRNAs occurs under physiological conditions and, in particular, the regulation by miR-iab-4AS is required for normal development. These lines of evidence establish miR-iab-4AS as a novel Hox gene, being expressed from within the Hox cluster and regulating Hox genes during development (Stark, 2008).

The genomic arrangement of two miRNAs that are expressed from the same locus but on different strands might provide a simple and efficient means to create nonoverlapping miRNA expression domains. Such sense/antisense miRNAs could restrict each other's transcription, either by direct transcriptional interference, as shown for overlapping convergently transcribed genes, or post-transcriptionally, possibly via RNA-RNA duplexes formed by the complementary transcripts. Sense/antisense miRNAs would usually differ at their 5' ends and thereby target distinct sets of genes, which might help define and establish sharp boundaries between expression domains. Coupled with feedback loops or coregulation of miRNAs and genes in cis or trans, this arrangement could provide a powerful regulatory switch. The iab-4 miRNAs might be a special case of tight regulatory integration in which miRNAs and proximal genes appear coregulated transcriptionally in cis and repress each other both transcriptionally and post-transcriptionally (Stark, 2008).

It is perhaps surprising that no antisense miRNA had been found previously, even though, for example, the intriguing expression pattern of the iab-4 transcripts had been reported nearly two decades ago, and iab-4 lies in one of the most extensively studied regions of the Drosophila genome. The frequent occurrence of antisense transcripts suggests that more antisense miRNAs might exist. Indeed, up to 13% of known Drosophila , 20% of mouse, and 31% of human miRNAs are located in introns of host genes transcribed on the opposite strand or are within 50 nt of antisense ESTs or cDNAs. These include an antisense transcript overlapping human mir-196. However, because of the contribution of noncanonical base pairs, particularly G:U pairs that become less favorable A:C in the antisense strand, many miRNA antisense transcripts will not fold into hairpin structures suitable for miRNA biogenesis, which explains the propensity of miRNA gene predictions to identify the correct strand. Nonetheless, in a recent prediction effort, 22 sequences reverse-complementary to known Drosophila miRNAs showed scores seemingly compatible with miRNA processing. Deep sequencing of small RNA libraries from Drosophila confirmed the processing of small RNAs from four of these high-scoring antisense candidates, and the ovary/testes libraries used here showed antisense reads for an additional Drosophila miRNA (mir-312). In addition, using high-throughput sequencing of small RNA libraries from mice, sequencing reads were found that uniquely matched the mouse genome in loci antisense to 10 annotated mouse miRNAs. Eight of the inferred antisense miRNAs were supported by multiple independent reads, and two of them had reads from both the mature miRNA and the star sequence. These results suggest that sense/antisense miRNAs could be more generally employed in diverse contexts and in species as divergent as flies and mammals (Stark, 2008).

Alternative splicing modulates Ubx protein function in Drosophila melanogaster

The Drosophila Hox gene Ultrabithorax (Ubx) produces a family of protein isoforms through alternative splicing. Isoforms differ from one another by the presence of optional segments-encoded by individual exons-that modify the distance between the homeodomain and a cofactor-interaction module termed the 'YPWM' motif. To investigate the functional implications of Ubx alternative splicing, this study analyzed the in vivo effects of the individual Ubx isoforms on the activation of a natural Ubx molecular target, the decapentaplegic (dpp) gene, within the embryonic mesoderm. These experiments show that the Ubx isoforms differ in their abilities to activate dpp in mesodermal tissues during embryogenesis. Furthermore, using a Ubx mutant that reduces the full Ubx protein repertoire to just one single isoform, specific anomalies were obtained affecting the patterning of anterior abdominal muscles, demonstrating that Ubx isoforms are not functionally interchangeable during embryonic mesoderm development. Finally, a series of experiments in vitro reveals that Ubx isoforms also vary in their capacity to bind DNA in presence of the cofactor Extradenticle (Exd). Altogether, results indicate that the structural changes produced by alternative splicing have functional implications for Ubx protein function in vivo and in vitro. Since other Hox genes also produce splicing isoforms affecting similar protein domains, it is suggested that alternative splicing may represent an underestimated regulatory system modulating Hox gene specificity during fly development (Reed, 2010).

The experiments described in this study indicate that the generation of structural differences among Ubx proteins by alternative splicing is relevant for the functional specificity of Ubx in vivo. These structural features modulate essential biochemical properties of Ubx proteins such as their DNA-binding profiles in the presence of a cofactor (Reed, 2010).

The differential effects of Ubx in vivo are apparent in the posterior visceral mesoderm, but not in the anterior. To understand this it must first be noted that the mechanism of dpp674 visceral mesoderm enhancer repression is different anterior and posterior to PS7. In the anterior visceral mesoderm, repression requires Exd, since in Exd null mutants, dpp674 is ectopically expressed anterior to PS7. But Hox genes appear to play no role in the normal repression of dpp in this region. The same Exd-dependent mechanism may also be acting in the posterior, but it is not necessary, for no posterior ectopic expression is observed in Exd null mutants. The posterior repression depends instead on the Hox protein Abd-A, which is presumably able to repress dpp674 in the absence of Exd as a cofactor (Reed, 2010).

All Ubx protein isoforms are able to induce dpp ectopically in the anterior, suggesting that they can all override the normal repression mediated by Exd. However, they exert differential effects in the posterior, where Abd-A is the controlling repressor. Abd-A has a very similar DNA-binding specificity to that of Ubx. It binds to multiple sites in the dpp674 enhancer, including those to which Ubx binds. Through some of these sites it serves as an activator, but through others it acts as a repressor. With Ubx form Ia, the repressing effect by Abd-A is dominant. The results suggest that Ubx form IVa is either able to compete more effectively as an activator with the repressing action of Abd-A bound at other sites or able to displace the binding of Abd-A at the sites where it mediates repression (Reed, 2010).

Ubx form IVa also overrides the normal specificity of the dpp-lacZ enhancer for the visceral mesoderm, activating it ectopically in the somatic mesoderm of most trunk segments. It is not known whether the activity of this enhancer is normally restricted to the visceral mesoderm by a required cofactor that is present only in the visceral mesoderm, by repressors present in other tissues, or by both mechanisms. However, UbxIVa at high levels seems able to override this normal tissue specificity. The more efficient DNA binding of this isoform (in the presence of Exd) may bypass the requirement for a cofactor or displace a repressor more effectively (Reed, 2010).

A quantitatively controlled study showed that the levels of Ubx protein are very important to determine the functional outcome of Ubx in vivo. In this context, the results show that in spite of significant variation across expression, levels of UbxIVa protein in different transgenic lines, this isoform is consistently able to produce a similar output in terms of dpp target activation in posterior regions. This suggests that for UbxIVa dpp target activation and protein concentration may relate to one another in the form of a sigmoidal function with a narrow protein concentration interval acting as a threshold that is crossed by all UbxIVa lines tested in this study. Given that UbxIa lines achieving comparable protein expression levels to UbxIVa lines, it was possible to activate dpp in posterior regions of the embryo, it is concluded that qualitative differences in Ubx protein structure as determined by alternative splicing are causal to the observed differential behavior in target activation (Reed, 2010).

The tissue-specific effects of Ubx isoform ectopic expression emphasize the likely role that the splice isoforms play in mediating specific Ubx functions in different tissues. Indeed, the isoforms have different tissue distributions in embryogenesis with UbxIa expressed predominantly in epidermis, mesoderm, and peripheral nervous system whereas UbxIVa appears to be exclusively expressed in the central nervous system. The analysis of the UbxMX17 mutation, which retains the full Ubx expression pattern but generates only isoform UbxIVa, supports the endogenous relevance of splice isoforms for tissue-specific Hox function. Although in UbxMX17 embryos UbxIVa can replace the function of Ubx isoforms I and II in the epidermis with the generation of a normal cuticle pattern, the peripheral nervous system is affected, and in this study clear defects were found in the segmental specification of somatic muscles. Tissue-specific isoform functions may be mediated by effects on cofactor interaction or may also involve effects on collaborative regulatory interactions between Hox proteins and tissue-specific regulators (Reed, 2010).

The results of in vitro binding studies of the Ubx/Exd element show that Ubx isoforms differ in their capacity to interact with DNA in the presence of the cofactor Exd. A possibility that emerges from these results is that different Ubx isoforms display differential levels of interaction with Exd (in the presence of target DNA) and, accordingly, could perform specific functions in vivo as a consequence to the distinct levels of nuclear Exd available in different regions of the embryo (Reed, 2010).

in vitro studies also show that ablation of the YPWM motif has little effect on the ability of Ubx form Ia to form a complex with Exd, but it significantly reduces complex formation by Ubx form IVa (Reed, 2010).

The observation that mutated forms of the Ubx protein lacking the hexapeptide interact with Exd at all is at first sight surprising, especially in view of the structural studies showing that the YPWM motif provides the major contact between Hox and Exd proteins bound to DNA. However, this finding is not inconsistent with earlier work. The article that originally described cooperative interactions between Ubx and Exd used Ubx proteins deleted of all sequences located amino-terminal to the homeodomain. These proteins therefore lacked the hexapeptide motif entirely. Interactions with Exd that do not require the hexapeptide have also been reported in a study focused on Ubx functions independent from Exd and Hth proteins. In addition, alanine replacement of the hexapeptide does not affect the way another Hox protein (i.e., Abd-A) interacts with Exd. Furthermore, a recent study suggests that Ubx-Exd recruitment may rely not on a single, but on several different mechanisms, some of which require a short evolutionarily conserved motif originally termed UbdA. Thus, the hexapeptide is unlikely to be the only Hox protein motif that interacts with Exd (Reed, 2010).

Crystallographic studies show that the Ubx and Exd homeodomains are closely adjacent, almost touching each other, the extent of this proximity being revealed by a significant reduction in solvent-accessible surface area within the area of putative contact. In addition, the distance between the Ubx recognition helix C terminus and the Exd recognition helix N terminus is just 9 Å, with one particular residue of Ubx (Lys58) well positioned to form hydrogen bonds with a residue of Exd (Ser48). Thus, regions within the Ubx homeodomain may be responsible for additional interactions with Exd. Sequences elsewhere in the proteins may also contribute to these interactions. A fine combination of protein mapping and crystallographic studies may be required to reveal the structural details of such interactions (Reed, 2010).

These experiments would be consistent with the possibility that the Ubx linker region itself could be a previously uncharacterized region of Ubx that makes contacts with Exd. This would be supported by experiments of protein-protein interaction in yeast, which also suggest that the Ubx linker region could affect the interaction between Ubx and Exd, and by the high evolutionary conservation of these sequences across phylogenetically distant species of flies. The results could also be accommodated in a model in which the Ubx linker region induces a conformational change elsewhere in the Ubx protein, such that the degree of interaction with Exd is affected. Alternatively, the regulatory potential of the Ubx protein could be affected. In particular, linker-dependent conformational changes may affect the behavior of critical regulatory motifs of Ubx, such as the recently studied QA motif involved in the modulation of Ubx activities in a tissue-specific manner (Hittinger, 2005) and the SSYF motif (Tour, 2005), an evolutionarily conserved motif close to the N terminus of the Ubx protein that is involved in transcriptional activation (Reed, 2010).

Other reports have also emphasized that the Hox linker regions are not just passive spacers. One such study shows that mutation of the short linker region in the Hox protein Abd-A specifically disables its capacity to activate wingless, a natural target gene, without affecting its ability to repress dpp. When comparing cofactor and DNA-binding properties of this Abd-A mutant protein with those of the wild-type Abd-A on a repressor element of the Distalless gene (DllR), no differences were seen in the interaction between the mutant form of Abd-A and Exd protein. (It is perhaps worth noting that these in vitro experiments required the presence of Homothorax protein; on this particular DNA target (DllR), the formation of complexes with Abd-A and Exd alone was below the limit of detection of the assay. Another report described Ubx isoform-specific functions for the repression of the Dll gene. These studies suggest that sequences within the Hox linker regions may modify the trans-regulatory potential of Hox proteins without necessarily affecting the DNA-binding properties of these proteins. The results extend these studies, showing that linker regions may at times affect target gene regulation and the DNA binding/cofactor interaction abilities of a Hox protein. The binding results are consistent with a recent study that integrates DNA-binding tests with computational predictions of ordered and disordered segments of the Ubx protein (Liu, 2008), proposing that sequences outside the homeodomain can reduce the DNA-binding activities of the Ubx protein by twofold (Reed, 2010).

Beyond the effects that alternative splicing may have on modulating Hox interactions with cofactors, other possibilities must also be considered. Given that in these experiments a very unstable binding of the Ubx proteins to target DNA was observed in the absence of Exd, it is difficult to advance arguments regarding the affinities of the individual Ubx isoforms for this molecular target on firm grounds. In spite of this, given that in various physiological contexts the binding of Hox proteins to target sites in the absence of cofactors has been demonstrated, it is pertinent to suggest that alternative splicing might also be influencing Hox DNA binding independently from cofactor interactions, at the level of changing DNA-binding affinities of the individual isoforms for their target DNAs. This possibility would be suitable for experimental investigation in the physiological context of Drosophila adult appendage development, as Ubx is known to act independently from cofactors during the development of these structures (Reed, 2010).

Examples from other Drosophila Hox genes further support a more general role of differential splicing in the diversification of Hox function during development, affecting protein modules outside the Ubx linker region discussed above. For instance, genetic dissection of the Abd-B gene demonstrated the existence of two distinct gene functions, originally termed morphogenetic (m) and regulatory (r). The spectrum of mRNAs derived from the Abd-B locus have been cloned, and a family of Abd-B transcripts generated by differential promoter use has been revealed , that, in turn, leads to different splicing variants affecting 5' sequences of the gene. Two proteins products, called m and r, are produced from the Abd-B transcripts; m differs from r in that it encodes an additional large glutamine-rich amino-terminal domain. Furthermore, ectopic expression of each Abd-B protein class leads to specific effects on the larval cuticle, suggesting that the isoforms have specific developmental functions (Reed, 2010).

Given that in Drosophila several Hox proteins possess alternatively spliced modules modifying the distance between the hexapeptide and the homeodomain, while others produce functionally different isoforms via differential promoter use coupled to alternative splicing, alternative splicing may truly represent a very important, yet underexplored regulatory mechanism modulating the functional specificity of Hox proteins during development (Reed, 2010).

Developmental RNA processing of 3'UTRs in Hox mRNAs as a context-dependent mechanism modulating visibility to microRNAs

The Drosophila Hox gene Ultrabithorax (Ubx) controls the development of thoracic and abdominal segments, allocating segment-specific features to different cell lineages. Recent studies have shown that Ubx expression is post-transcriptionally regulated by two microRNAs (miRNAs), miR-iab4 and miR-iab8, acting on target sites located in the 3' untranslated regions (UTRs) of Ubx mRNAs. This study shows that during embryonic development Ubx produces mRNAs with variable 3'UTRs in different regions of the embryo. Analysis of the resulting remodelled 3'UTRs shows that each species harbours different sets of miRNA target sites, converting each class of Ubx mRNA into a considerably different substrate for miRNA regulation. Furthermore, it was shown that the distinct developmental distributions of Ubx 3'UTRs are established by a mechanism that is independent of miRNA regulation and therefore are not the consequence of miR-iab4/8-mediated RNA degradation acting on those sensitive mRNA species; instead, it is proposed that this is a hard-wired 3'UTR processing system that is able to regulate target mRNA visibility to miRNAs according to developmental context. Reporter constructs that include Ubx short and long 3'UTR sequences display differential expression within the embryonic central nervous system, and mRNAs of three other Hox genes suffer similar and synchronous developmental 3'UTR processing events during embryogenesis. This work thus reveals that developmental RNA processing of 3'UTR sequences is a general molecular strategy used by a key family of developmental regulators so that their transcripts can display different levels of visibility to miRNA regulation according to developmental cues (Thomsen, 2010).

The existence of a developmentally controlled Hox 3'RNA RNA processing system is anticipated to contribute substantially to the specificity of the regulatory interactions between miRNAs and Hox gene mRNAs: in a given cell, and according to developmental cues, individual mRNA transcripts are predicted to react differently to the presence of miRNAs depending on the processing status of their 3'RNA sequences (Thomsen, 2010).

Assuming that both miRNAs and mRNA targets are co-expressed in the same cell, two alternative scenarios can be conceived for the evolution of alternative 3'RNAs. First, shorter 3'RNA forms might have evolved from an ancestral long 3'RNA state due to the need to escape miRNA detection at times when particularly high levels of Hox gene products are needed for normal development; according to this view, the pruning of an otherwise longer 3'RNA might have been positively selected as a system to eliminate crucial miRNA target sites from target mRNA transcripts, thus providing an 'miRNA avoidance' mechanism. An alternative model considers that in the ancestral state, short 3'RNA forms were produced. From such origins, the synthesis of longer, 3'RNA-extended Hox mRNAs might have evolved to provide additional regulatory surfaces that mediate interactions with miRNAs at selected spatiotemporal coordinates; this is termed the miRNA 'enhanced regulation' hypothesis. Comparative computational analysis of Hox 3'RNAs derived from different insect groups is predicted to determine ancestral and derived modes of Hox 3'RNA use, and, ultimately, resolve this issue. Nonetheless, it is argued in this study that observations during germ band extension and CNS development provide more support for the `enhanced regulation' model (Thomsen, 2010).

During germ band extension, Ubx protein and mRNA patterns and levels in the miRNA mutant are indistinguishable from those detected in wild-type embryos. This suggests that in spite of the fact that Ubx mRNAs and miR-iab4/8 show largely complementary expression patterns with some degree of overlap, these miRNAs might have no obvious involvement in controlling Ubx expression at this point in development. It would then follow that, within this context, Ubx expression is primarily controlled via canonical transcriptional regulation and not via post-transcriptional regulation by miRNAs. It is believed that the lack of interaction between Ubx and the miR-iab4/8 system at this stage is therefore primarily due to the spatial segregation of the transcriptional domains of Ubx and the miRNAs. Even in those cells positioned at the margin of these transcriptional domains, where Ubx and the miRNAs seem to coexist at a certain intermediate expression level, it is thought that interactions between these molecules is likely to be minimal or non-existent due to the fact that the only form of Ubx transcript available in this developmental context lacks the 3'RNA regions that harbour most of the miRNA target sites. As they stand, these results (1) explain why removal of miR-iab4/8 does not lead to the generation of homeotic phenotypes, and (2) are consistent with earlier work showing that lacZ reporter `enhancer-trap' constructs lacking Ubx 3'RNA sequences are able to closely recapitulate the expression pattern of Ubx during germ band extension, revealing that the cis-regulatory elements that specify Ubx expression patterns during this phase of embryogenesis are located outside Ubx 3'RNAs (Thomsen, 2010).

Within the embryonic CNS, the situation is rather different. The observed miRNA-dependent regulation of Ubx protein and mRNA levels within the embryonic CNS does indeed support a functional interaction between Ubx transcripts and the miRNA system in this developmental context, during which long Ubx transcripts are expressed at high level. Based on the expression patterns of Ubx transcripts and miR-iab4/8 and the results of 3'RNA reporter experiments, it is proposed that such extended 3'RNA Ubx mRNA forms bearing multiple miRNA target sites allow Ubx mRNAs to interact with miRNA input signals, which can be distributed in a rather complex pattern, with clear variations at the single-cell level. According to this view, the skipping of the first polyadenylation signal at stage 15 is predicted to allow active miRNA regulation during a developmental stage when Hox inputs are crucial for the normal development of the embryonic CNS. It is thus proposed that tissue-specific 3'RNA RNA processing leading to 'enhanced regulation' by miRNAs could contribute to the generation of complex and cell-specific Hox expression patterns, which cannot be explained with the current understanding of the Ubx transcriptional control regions. Further support for this idea is provided by the existence of many unique target sites for miRNAs within long 3'RNA forms of Hox mRNAs expressed in the CNS. These ideas are currently being tested, significant efforts are beind dedicated to determining the molecular mechanisms underlying Hox 3'RNA RNA processing, the effects of distinct Hox 3'RNA elements on gene expression during Drosophila CNS development, and how these 3'RNA regulatory events relate to the biological roles of Hox genes during CNS differentiation and embryonic and larval behaviour (Thomsen, 2010).

Although much remains to be learned about the subcellular and molecular mechanisms that lead to the physical contact between miRNAs and their targets, theoretically, the simple presence of a given miRNA could influence the evolution of all 3'RNAs expressed in the same cell at the same time. In certain contexts, selective pressure is anticipated to maintain miRNA target sequences unchanged, whereas in other cases, natural selection might favour the loss of miRNA sequences in mRNA 3'RNAs to ensure the lack of potentially detrimental interactions between particular miRNA species and subsets of mRNAs; such mRNAs have been defined as 'antitargets'. Earlier work has identified mRNA representatives of the miRNA antitarget classes in mammals and Drosophila; in flies, however, miRNA antitargets were primarily represented by housekeeping genes with high ubiquitous expression. This work indicates that key developmental regulators, such as the Hox genes, are able to modulate their visibility to miRNA regulation by adapting their 3'RNA regions according to information derived from developmental context, becoming what might in effect be 'conditional' miRNA antitargets (Thomsen, 2010).

In summary, the findings in the Hox system suggest that developmental 3'RNA processing of transcript mRNAs might be a powerful regulatory system that is able to modulate 'fine-grain' developmental outputs by controlling the spatiotemporal distribution of molecular contacts between target mRNAs and mRNA regulators, such as miRNAs and RNA-binding proteins (Thomsen, 2010).

Ultrabithorax: Biological Overview | Evolutionary Homologs | Transcriptional Regulation | Targets of activity | Protein Interactions | Developmental Biology | Effects of Mutation | References

Home page: The Interactive Fly © 1995, 1996 Thomas B. Brody, Ph.D.

The Interactive Fly resides on the
Society for Developmental Biology's Web server.