trithorax
The Drosophila gene trithorax is required for the normal expression of a number of the homeotic
genes in the bithorax complex (BX-C) and the Antennapedia complex (ANT-C). Flies homozygous for
trx mutations exhibit segmental identity transformations similar to those caused by loss-of-function
mutations in the homeotic genes Sex combs reduced, Ultrabithorax, abdominal-A,
and Abdominal-B. A molecular characterization of the trx locus is presented and shown to be
necessary for normal levels of Antennapedia, Ubx, and abd-A protein accumulation.
Interestingly, the loss of trx function differentially affects the expression of these proteins; Ubx protein
levels are greatly reduced, Abd-A protein levels are reduced to a lesser extent, and Antp protein levels
are only slightly reduced. P-element mediated transformation using 34 kb of genomic DNA containing
the 25 kb trx transcription unit identifies all sequences necessary for normal trx function and limits to relatively small regions the
5' and 3' flanking sequences that could be used in a regulatory capacity. The
primary transcription unit is differentially spliced to produce two large transcripts of 12 and 15 kb that
have different developmental profiles (Breen, 1991).
The regulatory control of trx has not been analyzed. It seems likely however that early zygotic expression is under control of the dorsal-ventral system, perhaps repressed by Dorsal.
trithorax regulates the Antennapedia and Bithorax complexes.
trx is required for normal expression of multiple homeotic genes of the bithorax and Antennapedia complexes (BX-C and ANTP-C). The expression of the BX-C genes Ultrabithorax, abdominal-A, Abdominal-B and the ANTP-C genes Antennapedia, Sex combs reduced and Deformed are all influenced by trx . Each of the BX-C and ANTP-C genes exhibits different tissue-specific, parasegment-specific and promoter-specific reductions in their expression. Each of these genes appear to have different requirements for trx in different spatial contexts in order to achieve normal expression levels. Those components of homeotic gene expression patterns for which trx is dispensable require other
factors, possibly those encoded by other trithorax group genes (Breen, 1993).
Sex combs reduced
DNA fragments in the Scr regulatory region are important for regulation of Scr by Polycomb and trithorax group gene products. When DNA fragments containing these regulatory sequences are subcloned into P-element vectors containing a white minigene, transformants containing these constructs exhibit mosaic patterns of pigmentation in the adult eye, indicating that white minigene expression is repressed in a clonally heritable manner. The amount of white minigene repression is reduced in some Polycomb group mutants, whereas repression is enhanced in flies mutant for a subset of trithorax group loci (Gindhart, 1995).
A regulatory element in the Ubx gene responds to Pc-G and TRX-G genes. Transposons, genetically engineered pieces of DNA carrying the regulatory element to new ectopic sites, create new binding sites for Pc-G products in the new sites in which they integrate. The transposons carry Pc-G maintenance elements (PRE), DNA regions responsive to the repressive affect of Pc-G genes. PREs and Pc-G proteins establish a repressive complex that keeps itself and other distal enhancers repressed in cells where they were first active and then repressed, and maintains this repressed state for many cell divisions. PRE functions to silence these remote enhancers or to maintain expression regulated by TRX-group products. Hunchback mediates repression at the PRE. The TRX-G products stimulate the expression of separate and distinct enhancers, active in imaginal discs (Chan, 1994).
The Fab-7 boundary functions to ensure the autonomous activity of
the iab-6 and iab-7 cis-regulatory domains in the
Drosophila Bithorax Complex from early embryogenesis through to the
adult stage. Although Fab-7 is required only for the proper
development of a single posterior parasegment, it is active in all tissues and
stages of development that have been examined. In this respect, Fab-7
resembles conventional constitutive boundaries in flies and other eukaryotes
that act through ubiquitous cis-elements and trans-acting factors.
Surprisingly, however, the constitutive activity of
Fab-7 is generated by combining sub-elements with developmentally restricted boundary function. In vivo evidence is provided that the
Fab-7 boundary contains separable regions that function at different
stages of development. These findings suggest that the units (domains) of
genetic regulation that boundaries delimit can expand or contract by switching
insulator function off or on in a temporally regulated fashion (Schweinsberg, 2004).
The minimal Fab-7 boundary defined in the ftz:hsp70-lacZ
and wEN:mini-white enhancer blocking assays is 1.2 kb in
length. It
extends from the minor nuclease hypersensitive site on the
proximal side to the iab-7 PRE (which corresponds HS3) on the
distal side and includes two major chromatin-specific nuclease hypersensitive
regions, HS1 and HS2. The largest hypersensitive region, HS1, contains six
consensus GAGA factor binding sites arranged in three pairs, 1-2, 3-4 and 5-6.
The ubiquitously expressed GAGA factor is encoded by the
Trithorax-like (Trl) gene, and it
is thought to function in the formation and/or maintenance of the nucleosome
free regions of chromatin associated with a variety of cis-acting
elements in flies, including enhancers, promoters, Polycomb Response Elements
(PRES) and boundaries. Chromatin immunoprecipitation experiments demonstrate that
GAGA is associated with the Fab-7 boundary in vivo.
Moreover, the GAGA-binding sites in HS1 are important for boundary function.
The enhancer blocking activity of the
minimal 1.2 kb boundary is compromised in both the embryo and adult when GAGA
sites 1-5 are mutated. Although this finding indicates that GAGA (or another
protein that recognizes the GAGA consensus) is required for Fab-7
boundary activity throughout development, the GAGA sites are not functionally
equivalent. When only the centromere proximal pair, 1-2, are
mutated, blocking of the ftz UPS stripe enhancer in the ectoderm of
early embryos by the minimal Fab-7 boundary is weakened, but there is
no apparent effect on the blocking of either the ftz NE enhancer in
the CNS of older embryos or the w enhancer in adults. By contrast,
mutation of the central pair, 3-4, weakens blocking of the w enhancer
in the eye, but has little effect on the blocking of the ftz
enhancers in embryos (Schweinsberg, 2004 and references therein).
One interpretation of these results is that the constitutive boundary
activity of the Fab-7 element is generated by sub-elements whose
activities are developmentally restricted. In the studies reported here, this hypothesis was tested. Unlike other well characterized
boundaries, the constitutive activity of Fab-7 is generated by
combining a series of subelements that function at different stages of
development. This unexpected finding indicates that chromatin domains are not
always static units, but instead may be redefined by inactivating or
activating a boundary element such that the chromatin domain can expand to
include new genes or regulatory sequences, or alternatively contract
eliminating genes or regulatory sequences (Schweinsberg, 2004).
Ultrabithorax
To identify cis-acting sequences for functional reconstruction of regulation by both trithorax and Polycomb, the expression patterns have been examined in several Ubx-lacZ transgenes that carry upstream fragments (corresponding to a region of approximately 50 kb). A 14.5-kb fragment from the postbithorax/bithoraxoid region of Ultrabithorax exhibits proper regulation by both trithorax and Polycomb in the embryonic central nervous system. Trithorax or Polycomb can function independently through this upstream fragment to activate or repress the Ultrabithorax promoter, respectively. Deletion analysis of this fragment demonstrates that a 440-bp fragment contains response elements for both Trithorax and Polycomb. The integrity of the proximal promoter region is essential for trithorax-dependent activation, implicating a long-range interaction for promoter activation (Chang, 1995).
bithorax complex Transcription of bithorax complex genes (abd-A, Abd-B and Ubx) in the mesoderm and ectoderm is altered in strong trithorax mutants during germ band elongation, while the anteriorly expressed Antennapedia complex is affected only at later stages in embryonic development. In another mutant allele, expression of bithorax genes is normal, while expression of Antennapedia complex genes is reduced. Thus anterior and posterior trx effects are independently regulated (Sedkov, 1995). The earlier effect of trithorax represents a distinct expression domain of trithorax in the posterior region of the embryo, one required to maintain expression of the BX-C genes. At cellular blastoderm, Trithorax mRNA expression in D. virilis embryos is also confined to the posterior portion of the presumptive mesoderm. This
supports the idea that the specific BX-C-related expression domain is an essential and independent feature of the trithorax gene (Tillib, 1995).
In Drosophila, two classes of genes, the
trithorax group and the Polycomb group, are
required in concert to maintain gene expression by regulating chromatin
structure. Trithorax protein (Trx) binding elements have been identified
within the bithorax complex. Within the
bxd/pbx regulatory region these elements are functionally
relevant for normal expression patterns in embryos and they confer Trx
binding in vivo. Trx binding elements have been localized to three closely situated sites
within a 3-kb chromatin maintenance unit with a modular structure.
Results of an in vivo analysis have shown that these DNA fragments (each
~400 bp) contain both Trx- and Polycomb-group response elements (TREs
and PREs) and that in the context of the endogenous
Ultrabithorax gene, all of these elements are essential for
proper maintenance of expression in embryos. Dissection of one of these
maintenance modules has shown that Trx- and Polycomb-group responsiveness
is conferred by neighboring but separable DNA sequences, suggesting
that independent protein complexes are formed at their respective
response elements. The activity of this
TRE requires a sequence (~90 bp) that maps to within several tens of
base pairs from the closest neighboring PRE and the PRE activity
in one of the elements may require a binding site for Pho, the protein
product of the Polycomb-group gene
pleiohomeotic. These results show that long-range maintenance
of Ultrabithorax expression requires a complex element
composed of cooperating modules, each capable of interacting with both
positive and negative chromatin regulators (Tillib, 1999).
A PCR-linked immunoprecipitation procedure has been developed in order to discover Trx specific DNA binding sites. This procedure involves PCR amplification of DNA fragments retained in a pellet after immunoprecipitation of TRX-DNA complexes from embryonic nuclear
extracts using Trx-specific antibody.
Trx protein
localizes to 10 discrete fragments of the BX-C. The identification of
TRX binding regions within the regulatory DNA of all three genes of the
BX-C, (Ubx, abdominal-A [abd-A], and
Abdominal-B [Abd-B]), is striking because trx is required to maintain the expression levels of all
three genes in embryos. Next,
high-resolution mapping of the Trx binding sites was carried out. Since the sequence of the
entire BX-C is now available, the identified Trx binding sites were mapped to DNA fragments from
200 bp to 2,000 bp in size. Trx binding sites are found in several regulatory regions of the BX-C: abx,
bxd/pbx, iab-2, iab-3,
iab-4, iab-7, and iab-8. A
number of studies have defined PREs and
Pc protein binding sites in the BX-C. Comparison of
the data in this study with those of previous studies has shown that six Trx binding sites in
bxd/pbx, iab-3, iab-4, and
iab-7 regulatory regions are either within or very close to minimal PREs or PC binding sites identified previously. Interestingly, several signals are detected in the bxd/pbx
region, suggesting that there are multiple TRX binding sequences within this regulatory region (Tillib, 1999).
Two criteria
identify TRE and PRE activities within the reporter constructs:
maintenance of lacZ reporter expression patterns in embryos,
and trx- and PcG-dependent maintenance of white gene expression in the eyes of adult flies, including
their effects on pairing-sensitive repression of white.
Ultimately the results obtained with both reporter genes led to similar
conclusions, and the TRE and PRE activities of one module, fragment C of the Ubx promoter, were shown to
be conferred by neighboring but separable DNA sequences. An essential TRE and two distinct PREs were detected in this
central C module. Further analysis has shown that the TRE activity and TRX binding require a 90-bp region, which, based on its length, is
likely to bind more than just a single protein. This suggests that a
number of primary DNA proteins may be associated with the TRE in the C1
fragment. A gel-shift analysis of the protein binding properties of
this 90-bp TRE fragment suggests that this fragment contains two core
binding sequences that are required for apparent cooperative binding
by several nuclear proteins. These core sequences,
which are located on the boundary of the C1-B and C1-C fragments and in
the C1-D fragment appear to contribute to the formation of a large
multiprotein complex. [Note: The fragments referred to have the following locations in the bxd region of Ubx: C1 (nt 218,835 to 218,959); C2 (nt 218,960 to 219,088); C3 (nt 219,089 to 219,249). DeltaBC1-A, DeltaBC1-B, and DeltaBC1-C are deletions of nt 1 to 27, 28 to 61, and 86 to 122, respectively]. There is a direct correlation between
the sequences that are required to form this protein complex and those that are required for the Trx binding and TRE activity. Most
strikingly, the AACAA repeat in an addition fragment, the C1-D fragment, seems to be crucial
for forming this complex: it has been shown to be crucial for the TRE
activity, since complex formation is virtually abolished when the AC
residues are changed to TG. Since direct Trx
protein binding to DNA has not been established by using a number of
DNA binding assays and since the DNA binding protein complex in the C1
fragment does not contain Trx, it is suggested that Trx
binds to this TRE through interactions with a complex of primary DNA
binding proteins. At present, the identity of the
proteins that associate with these TREs is unknown. While it would not be
surprising to find that some are products of the trxG, it is
unlikely that the Gaga factor or the Zeste protein are the primary binding
proteins in this case, since the C1 element does not contain consensus binding sites for either of these proteins (Tillib, 1999).
This analysis suggested that the C2 and C3 fragments each contain a PRE.
Each of these elements, C2 and C3, is required to confer
pairing-sensitive repression on a white reporter gene. These
elements may be functionally different because their activities require
different sets of PcG proteins and because there is no
significant sequence similarity between them. Both PREs are apparently
also required, in concert, to provide full maintenance function in
embryos. This follows from the fact that while very strong anterior
overexpression occurs in embryos when the entire C fragment is deleted,
only moderate overexpression in PS5 results from the deletion of a
single PRE. In addition, one of these PREs, C3, may
contain a functionally important binding site for the PcG protein Pleiohomeotic (Pho), since deletion of this binding site abrogates both
pairing-sensitive repression and responsiveness of the white
reporter gene to three PcG mutations: pho,
Pcl, and Scm. Therefore, it is suggested
that the protein products of these three PcG genes may be
components of a putative PcG protein complex that is formed at the C3
PRE. In addition to the Pho binding sites, the C2 and C3 DNA fragments contain three consensus binding sites for the GAGA protein (Trithorax-like).
Further analysis is required to determine whether the deletion of GAGA
sites has an effect on PRE function. It is likely, however, that Pho
and GAGA are not the only primary DNA binding proteins in these PREs,
since the C2 PRE does not contain consensus Pho binding sites. These
proteins may be DNA-interacting components of particular subsets of PcG
complexes (Tillib, 1999).
The TREs and PREs in the bxd region of Ubx
are clustered in three closely situated maintenance modules, each
approximately 400 bp. Each module contains elements for both of these
opposing activities. The analysis has been focused on the Trx protein,
although it is possible that there are other positive maintenance
elements in this region that require the products of other
trxG genes. Similarly, since PRE function was analyzed only
in Trx binding regions, some PREs may have gone undetected. Despite
these limitations, several TRE- and PRE-containing modules were discovered in the bxd region of Ubx that are all
essential for proper Ubx expression, since deletion of any
one of the three modules leads to a significant loss of maintenance
activity in embryos. In the context of a natural Ubx
promoter and a large part of its regulatory region, these modules are
all essential in embryos with respect to PRE and TRE function. However,
when tested for effects on white gene expression, deletion
of individual elements does not completely abolish either eye color
variegation or the responsiveness to trx and PcG
mutations. These differences suggest that repression of
white expression in adults may not accurately reflect the
function of these elements in the context of the entire Ubx
gene. Thus, cooperative interactions among multiple PREs and TREs are
required for proper function of the Ubx gene, and these interactions may involve activities not reflected in assays with reporters unrelated to Ubx expression (Tillib, 1999).
Interestingly, trx function is found to be required for
Ubx expression not only in its normal domain of expression
in the posterior region of the embryo but also in the anterior region, when Ubx is overexpressed due to a deletion of PREs. There
are clear differences between the anterior and posterior regions of the
embryo with respect to both the effect of a trx mutation and the requirements of TREs for the expression patterns of these transgenes. (1) In trx mutants, the loss of expression in the
anterior is much more severe than it is in the posterior. (2)
Anterior expression is very strong when one of the three TREs is
deleted, and only a simultaneous deletion of two TREs leads to a
decrease of this expression that is comparable with the effect of a
trxB11 null mutation. In the posterior, however,
deletion of only one element mimics an almost complete loss of
trx-related activity, and deletion of two elements has no
further effect. This might be explained by a different mode of
functioning in the anterior versus posterior regions of the embryo.
Such a functional difference is also suggested by the
observation that different trx protein products, which
result from alternatively spliced mRNAs, may be required for the
maintenance of expression of the ANT-C genes (in the anterior region)
and not for maintenance of BX-C gene expression (in the posterior
regions). This is based on an analysis of the effects of different
trx alleles on the two homeotic complexes and on the finding
that the expression of one of the early trx RNAs is
spatially restricted to the posterior region where the BX-C genes are
expressed. Based on these observations, it has been concluded
that there are quite complex requirements for the activities of the
three maintenance modules in different cells. Functionally similar
maintenance units may regulate other genes in the BX-C as well, since
the other Trx binding regions detected are associated with either
PRE function, Pc protein binding sites, or both (Tillib, 1999).
The finding of discrete TRE and PRE sequences
argues against a direct competition between the proteins of these
opposing groups for binding sites on DNA, although the question of
whether they normally occupy their response elements simultaneously
within a given module remains open. In addition, some data suggest that the association of trxG and PcG proteins with a particular gene depends
on its transcriptional status: (1) the strength of Trx binding to
salivary gland polytene chromosomes at the site of a transcriptionally
active gene, such as fork head, is much higher than it is at
the location of the BX-C, which is silent in the salivary glands; (2) immunoprecipitation of Pc protein from
Drosophila cells has been found to be more abundant at silenced
genes than at activated genes of the BX-C; (3) when
transcription of a reporter gene is induced by GAL4, several PcG
proteins are displaced from the chromosomal site of insertion of a
Fab-7 transgene. Although this is not
directly related to trxG functioning, it indicates that PcG proteins
are not bound abundantly to actively transcribed genes, suggesting that
there might be quantitative or qualitative differences in bound trxG
and PcG protein complexes depending on the transcriptional activity of
a particular gene. This work suggests that the occupancy of TREs and
PREs may be independent rather than mutually exclusive. Since the
formation of functional activating or silencing complexes may depend on
and in turn lead to the maintenance of the on-off state of
Ubx expression in a particular tissue, it is suggested that the
occupancy of the TRE by a functional trxG complex alters, directly or
indirectly, the composition of nearby PRE complexes without necessarily
abolishing binding by PcG proteins (Tillib, 1999).
How do active trxG and PcG protein complexes function? There have as
yet been no specific biochemical activities associated with PcG
proteins. Most of the PcG proteins are associated with chromosomes, and
it is assumed that they act by forming repressive multiprotein
complexes that prevent active transcription. One of the functions of
trxG proteins may be simply to counteract the formation of these
repressive PcG complexes and thus to increase the accessibility of
enhancers to the neighboring regions of DNA. However, there is growing
evidence that the trxG represents a heterogeneous family of proteins
with diverse functions. Some of them, such as Trx, Ash1, Ash2, Gaga,
and Zeste, are associated with particular sites on polytene chromosomes, while others, such as Brm and Snr1,
are found in chromatin remodeling complexes that may not be associated
with specific chromosomal regions. There is some evidence that one of
the functions of trxG proteins may be to recruit chromatin remodeling
complexes to DNA. Gaga factor is required for the function of one
chromatin remodeling complex, the Drosophila NURF complex, and Trx has been shown to physically interact with Snr1, a component of the Drosophila SWI/SNF complex.
However, there is no evidence thus far that these interactions are
mediated through particular TREs. In addition, there is evidence that
Trx and its human homolog, ALL-1/HRX, may be involved directly in the
activation of promoters, since both of these proteins possess
transactivation activity in cells. Therefore, it
is likely that trxG proteins not only can counteract formation of
PcG-mediated repressive chromatin structure but may also play a more
direct role in maintaining transcription (Tillib, 1999 and references).
In conclusion, three discrete TRE/PRE modules have been identified in the Ubx regulatory
region. These modules are contained within a complex, 3-kb maintenance unit in which each detected element
is essential with respect to both PRE and TRE function. Furthermore, it has been found that Trx binds sequences in other regulatory regions of the BX-C
that are consistently associated with either PRE function, Pc protein
binding, or both; this suggests the possibility that similar maintenance
units are employed for regulation of other genes in the complex.
Functional dissection of one of these modules has shown that the TRE and
PRE activities can be ascribed to separable DNA elements, even though
they are located within tens of nucleotides of one another. This
proximity suggests that there may be some direct interaction between
protein complexes formed at these elements. In addition, the TREs and
PREs that have been identified do not contain extensive sequence
similarities, suggesting that they are bound by protein complexes of
different composition (Tillib, 1999).
Papp, B. and Muller, J. (2006). Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev. 20: 2041-2054. PubMed Citation: 16882982
Polycomb group (PcG) and trithorax group (trxG) proteins act in an epigenetic fashion to maintain active and repressive states of expression of the Hox and other target genes by altering their chromatin structure. Genetically, mutations in trxG and PcG genes can antagonize each other's function, whereas mutations of genes within each group have synergistic effects. This study showd in Drosophila that multiple trxG and PcG proteins act through the same or juxtaposed sequences in the maintenance element (ME) of the homeotic gene Ultrabithorax. Surprisingly, trxG or PcG proteins, but not both, associate in vivo in any one cell in a salivary gland with the ME of an activated or repressed Ultrabithorax transgene, respectively. Among several trxG and PcG proteins, only Ash1 and Asx require Trithorax in order to bind to their target genes. Together, these data argue that at the single-cell level, association of repressors and activators correlates with gene silencing and activation, respectively. There is, however, no overall synergism or antagonism between and within the trxG and PcG proteins and, instead, only subsets of trxG proteins act synergistically (Petruk, 2008).
Despite much interest, there is little understanding of how the epigenetic
TRE/PRE-containing MEs function. One key unresolved issue pertains to the organization of these complex transcription regulatory elements with regard to the response elements/binding sites of particular trxG and PcG proteins. Response elements for several PcG proteins were mapped in the bxd ME previously, and some PcG proteins were detected at this DNA element in ChIP assays. However, information about the association of trxG proteins in the bxd ME is very limited. Several Trx-dependent TREs have been mapped in the bxd ME. In addition, Trx and Ash1 proteins have been detected at the bxd ME in ChIP assays. Given the apparent functional heterogeneity of the trxG proteins, it is revealing that besides Trx, many other trxG genes are essential for functioning of the bxd ME. Two of the interacting genes, skd and kto, encode components of the Drosophila Mediator complex, so it is possible that their role in the functioning of the bxd ME relates to the transcription of some of the non-coding RNAs that are known to be transcribed through this element. Ash2 is a component of several purified MLL (a human homolog of Trx) protein complexes. The identification of an ash2 response element in the bxd ME suggests that a second putative Trx-containing MLL-like complex might reside at the bxd ME. The genes urd and sls have only been minimally characterized, mainly as suppressors of Pc phenotypes. Therefore, it is premature to speculate about their function at this element, although they clearly interact there in some capacity (Petruk, 2008).
Identification of multiple TREs and PREs within the same ME raises an important question with regard to potential interdependency or competition in the association of proteins from the same and different protein families. To address this, focus was placed on the fine mapping of response elements for several major trxG genes that are essential for functioning of the bxd ME: ash1, the brm component of the BRM chromatin remodeling complex, and the ETP gene Asx. These proteins or components of their protein complexes (i.e. Snr1, a component of BRM) can physically associate with Trx. Thus, finding their response elements either in DNA fragments that are juxtaposed to (brm and ash1) or the same as (Asx) the previously mapped trx response element is consistent with direct interactions of these proteins with Trx. It should be noted, however, that all these proteins are components of protein complexes other than the Trx complex TAC1. Nevertheless, this suggests that there might be interdependency in recruitment and/or association of these protein complexes at the bxd ME. However, the results indicate that this suggestion is only partially true. Binding of the components of the BRM complex and of another trxG protein, Kis, were not affected by elimination of Trx. However, the association of Ash1 and Asx at all their sites on the salivary gland polytene chromosomes is completely dependent on the presence of Trx. Previous results of the reciprocal experiments indicated that binding of Trx is strongly decreased in ash1 mutant animals. This suggests that Trx, Ash1 and Asx represent a special, and at least partially interdependent, set of trxG proteins. This also suggests, in contrast to the previously mentioned genetic studies, that not all trxG proteins are mutually dependent in their functioning (Petruk, 2008).
Close proximity or even overlap between some TREs and PREs in the bxd ME suggests the existence of potential competitive relationships with regard to the binding of these functionally opposing groups of proteins. Furthermore, some ChIP assays indicate that some trxG and PcG proteins can bind to the bxd ME of both the activated and silenced gene, suggesting a potential interaction of these proteins on DNA. This was tested by asking whether binding of the components of two major PcG complexes, PRC1 and PRC2, is affected by elimination of Trx. No significant change was detected in the number or intensity of immunostained bands for all tested PcG proteins on the polytene chromosomes of trx mutant larvae. This suggests that not only is the association of PcG proteins independent of Trx, but also that Trx is not essential for preventing binding of the PcG proteins to their response elements. This is an important conclusion because some genetic studies have proposed that the main function of Trx and Ash1 is to prevent silencing by the PcG proteins (Petruk, 2008).
An important issue in understanding the molecular mechanism of trxG/PcG
functioning is to correlate their association at MEs with the state of expression of their target genes. Although most of the existing data were obtained in cultured cells, two studies addressed this issue in Drosophila larval tissues. ChIP analysis in larval imaginal discs suggests that some trxG and PcG proteins are associated with the bxd ME irrespective of the status of gene expression. However, the results of another study suggest alternative association of Trx and Pc at the site of the endogenous BX-C on polytene chromosomes from both fat body and salivary glands, where BX-C is correspondingly activated or repressed. Ideally, to resolve this issue it is essential to investigate the association of PcG and trxG proteins with the ME in the same tissue at the single-cell level and at a gene of defined expression status. Such a test system was established. In this system the bxd-ME-containing transgene is either activated or repressed in cells within the same salivary gland. Direct visualization of the association of different proteins to the site of insertion of this transgene clearly indicates that major trxG and PcG proteins bind to the bxd ME in an alternative fashion. Importantly, using markers for activated and repressed transcription, it was possible to correlate binding of trxG and PcG proteins in a single cell with either the activated or repressed bxd transgene, respectively. The differences between these results and those of Papp (2006) might be explained by technical differences and by the fact that trxG and PcG proteins may behave differently in different tissues and/or in polyploid versus diploid cells. It is important to note that although the current analysis is limited to studies of a transgene, the detected alternative association of Trx and Pc on the bxd ME transgene correlates well with the results obtained at the endogenous BX-C on polytene chromosomes. It is concluded, therefore, that on a cell-by-cell basis, binding of trxG and PcG proteins is strictly dependent on the status of gene expression, in that they bind alternatively to the epigenetic regulatory elements of either activated or repressed target genes, respectively (Petruk, 2008).
In summary, this is the first work on the fine mapping of multiple TREs at any target gene. This is also the first assessment of mutual dependencies within the trxG group of activators and between the trxG and PcG of antagonistic proteins. It provides a glance of the enormously complex regulatory element that binds proteins with opposite transcriptional regulatory activities. The main conclusions of this study are that two major trxG proteins, Trx and Ash1, and the ETP protein Asx, constitute a specific subgroup of interacting proteins that depend on each other in their functioning at the bxd ME and throughout the genome. Although multiple trxG proteins are essential for epigenetic functioning of the bxd ME, their association with this element and other binding sites in the genome might not necessarily require Trx and associated proteins, as exemplified by the components of the BRM complex and Kis. The components of the major PcG complexes, PRC1 and PRC2, also associate with target genes independently of Trx, Ash1 and Asx. Another important conclusion of this work is that trxG and PcG proteins are associated with the bxd ME only at activated and repressed genes, respectively. It will be important to determine whether the choice between the establishment of trxG-mediated activation or PcG-mediated repression occurs only at very specific early stages of development, or whether it can also occur at later developmental stages (Petruk, 2008).
Additional genes regulated by trithorax
Maintenance but not initiation of engrailed (en) gene expression in the Drosophila embryo requires trithorax, required to maintain stable long-term expression of the homeotic genes throughout the development. en expression is dependent on trx in only a subset of embryonic cells normally expressing en, including specific cells
in the nervous system and the dorsal fat body cells surrounding the gonad. Loss of en expression in
the dorsal fat body is correlated with the sterility of en females that also carry trx mutations. In
addition, trx is required for normal en expression in the posterior compartment of the developing
wing, reflected in enhancement of en phenotypes in en adults that also carry trx mutations. trx
appears to be dispensable for maintenance of en expression in other embryonic cells (Breen, 1995).
The proximal promoter of engrailed does not direct expression in a tissue or stage-specific manner, but contains promoter activity which can be activated by nearby genomic enhancers. Three so-called pairing sensitive sites (PS) have demonstrated sensitivity to the actions of Polycomb and trithorax group genes (Kassis, 1994).
Trithorax also regulates the homeotic gene forkhead. A strong Trithorax binding site is found at the cytological location of the forkhead gene in salivary gland chromosomes. When a genetic element containing the forkhead upstream regulatory region is inserted into ectopic chromosomal regions, the Trithorax protein can be found localized to these ectopic sites associated with forkhead regulatory DNA (Kuzin, 1994).
The wing imaginal disc is subdivided into a dorsal and a ventral compartments. A new dominant
homeotic mutation, Dorsal wing1 (Dlw1), transforms ventral into dorsal compartment in heterozygotes. This phenotype is similar to one of the dominant phenotypes of Polycomb mutants. Dlw+ is required for the specification of dorsal compartment. Some genes of the Polycomb group act as negative regulators of Dlw+, while some genes of the trithorax group act as positive
regulators (Tiong, 1995).
The in vivo distribution of the E(Z) protein shows it to be ubiquitously present in embryonic and larval nuclei. In salivary gland polytenized nuclei, the identifiable E(Z) chromosome binding sites are a subset of those described for other Polycomb-group proteins, suggesting that E(Z) may also participate in Polycomb-group complexes. E(Z) binds to chromosomes in a DNA sequence-dependent manner, as illustrated by the creation of a new E(Z)-binding site at the location of a P element reporter construct that contains a Polycomb response element (PRE). This P element contains a 14.5 kb segment from the bxd/pbx Ubx regulatory region. The sequences of one null and three temperature-sensitive E(z) alleles are presented. These mutations diminish all chromosome binding of E(Z) protein. It is suggested that a Cys-rich region altered in these mutations functions as a DNA binding
domain. E(Z) binding is noticibly weaker in trx mutants. A reduced level of E(Z) chromosome binding may be due to alteration in the expression of one or more other proteins that are involved in E(Z) binding and does not necessarily imply a direct interaction between E(Z) and TRX (Carrington, 1997).
Both in vitro and in vivo transcription assays have been used to delineate the promoter for the 6-kb E74 mRNA. In vitro transcription of a series of 3' deletions defined the 3' in vitro promoter boundary at position +43. Additional 5'-flanking sequences, between -181
and -83, are necessary for efficient transcription in transfected Kc tissue
culture cells. Two transcription factors that interact with the E74 promoter, Zeste and
GAGA, were studied in DNA-binding assays. Zeste binds to two sites within the E74 promoter. These sites overlap with three of the six GAGA-binding sites. The Zeste- and GAGA-binding sites lie within domains identified by deletion mapping as cis-acting transcriptional control elements (Thummel, 1989).
Rapid induction of the Drosophila melanogaster heat shock gene hsp70 is achieved through the binding of heat shock factor (HSF) to heat shock elements (HSEs) located upstream of the transcription start site. The subsequent recruitment of several other factors, including Spt5, Spt6 and FACT, is believed to facilitate Pol II elongation through nucleosomes downstream of the start site. This study reports a novel mechanism of heat shock gene regulation that involves modifications of nucleosomes by the TAC1 histone modification complex. After heat stress, TAC1 is recruited to several heat shock gene loci, where its components are required for high levels of gene expression. Recruitment of TAC1 to the 5'-coding region of hsp70 seems to involve the elongating Pol II complex. TAC1 has both histone H3 Lys 4-specific (H3-K4) methyltransferase (HMTase) activity and histone acetyltransferase activity through Trithorax (Trx) and CREB-binding protein (CBP), respectively. Consistently, TAC1 is required for methylation and acetylation of nucleosomal histones in the 5'-coding region of hsp70 after induction, suggesting an unexpected role for TAC1 during transcriptional elongation (Smith, 2004).
Much of the genome is transcribed into long non-coding RNAs (ncRNAs). Previous data have suggested that bithoraxoid (bxd) ncRNAs of the Drosophila bithorax complex prevent silencing of Ultrabithorax (Ubx), and recruit activating proteins of the trithorax group to their maintenance elements. This study found that, surprisingly, Ubx and several bxd ncRNAs are expressed in non-overlapping patterns in both embryos and imaginal discs, suggesting that transcription of these ncRNAs is associated with repression, not activation, of Ubx. The data rule out siRNA or miRNA-based mechanisms for repression by bxd ncRNAs. Rather, ncRNA transcription itself, acting in cis, represses Ubx. The Trithorax complex TAC1 (containing Trx, Sbf1 and dCBP) binds the Ubx coding region in nuclei expressing Ubx, and the bxd region in nuclei not expressing Ubx. It is proposed that TAC1 promotes the mosaic pattern of Ubx expression by facilitating transcriptional elongation of bxd ncRNAs, which represses Ubx transcription (Petruk, 2006).
The Hox genes of the bithorax complex (BX-C) have spatially restricted expression patterns that vary within and between segments and tissues. Transcription factors encoded by segmentation genes establish the patterns of the Hox genes Ubx, abd-A, and Abd-B of the BX-C in embryos. After the segmentation proteins decay, Hox expression patterns are maintained epigenetically by proteins of the trithorax group (trxG) and the Polycomb group (PcG). PcG genes maintain the silent state, whereas trxG genes maintain the active state of Hox genes. PcG and trxG proteins act through partially overlapping sets of response elements known as maintenance elements (Petruk, 2006).
One of the most startling discoveries of the genomic era has been that much of the genome is transcribed into non-coding RNAs (ncRNAs). Recent attention has focused on small interfering RNAs (siRNAs) and micro-RNAs (miRNAs) that modulate gene activity by an antisense mechanism termed RNA interference (RNAi), which interferes with mRNA stability or translation. However, the most abundant and least characterized class of ncRNAs are long and have mostly unknown functions (Petruk, 2006 and references therein).
The intergenic regions of the Hox genes in D. melanogaster produce many long ncRNAs that may regulate Hox gene coding sequences. Increasing attention has been directed to the role of transcription of MEs in the regulation of BX-C genes. Several ncRNAs are transcribed through a well-studied ME in the bxd regulatory region that lies between the Ubx and abd-A transcription units. The bxd ME regulates Ubx. Transcription through bxd precedes activation of Ubx coding RNAs (hereafter referred to as 'Ubx RNA', or simply as 'Ubx'), suggesting that ncRNAs might regulate Ubx. Transcription patterns of ncRNAs appear similar to those of the neighboring Hox genes and are collinear with regulatory domains along the chromosome. A synthesis of genetic and transgenic studies led to the idea that transcription of ncRNAs through MEs interferes with PcG-mediated silencing, perhaps by preventing recruitment of PcG proteins. A recent study suggests that transcription of MEs may recruit trxG proteins to maintenance elements. If indeed transcription of MEs simultaneously prevents PcG binding and establishes trxG binding, this could be a key element of Hox regulation. Clearly, this model requires that intergenic bxd RNAs are expressed in the same cells as Ubx. However double-labeling of intergenic and coding RNAs at high resolution has not been performed, so this attractive model has not been rigorously tested (Petruk, 2006 and references therein).
The trxG protein complex TAC1 plays important roles in maintaining expression of homeotic genes throughout embryogenesis. Recent attention has focused on the role of trxG proteins in histone modifications and in altering nucleosome positioning. TAC1 contains three proteins, Trx, Sbf1 and dCBP, and thus acetylates histones and methylates histone H3 at Lys-4 (H3-K4), due to the enzymatic activities of dCBP and the SET domain of Trx, respectively. How binding of Trx to MEs regulates expression of Hox genes is unclear. Because embryos have a mixture of cells expressing and not expressing each Hox gene, it has not been possible to determine precisely how trxG protein binding correlates with transcription of Ubx and bxd ncRNAs (Petruk, 2006).
This study shows that Ubx is repressed by bxd transcription. The bxd ncRNAs do not act by siRNA or miRNA-based mechanisms, but repress Ubx in cis through a transcription-dependent mechanism. Alternative association of TAC1 with either Ubx or bxd correlates with their transcription. TAC1 appears to be part of an interdependent network of general elongation factors that associate with active genes. It is suggested that a key role of TAC1 in establishing the mosaic pattern of Ubx expression is to promote elongation of bxd ncRNAs, which in turn represses expression of Ubx (Petruk, 2006).
An attractive notion has been that transcription of bxd ncRNAs, which precedes that of Ubx in embryos, facilitates correct spatial expression of Ubx. Previous studies showed that transcription through the ME could interfere with silencing, so it was proposed that bxd ncRNA transcription normally prevents recruitment of PcG proteins to the ME. However, the current experiments unambiguously demonstrate that Ubx and bxd ncRNAs are transcribed in different cells in embryos. The results also suggest that bxd ncRNAs do not facilitate Ubx expression in larval imaginal discs, as was recently proposed. Instead, transcription of ncRNAs correlates with repression of Ubx. It is possible that the abnormal transcription induced in previous studies interfered with transcription of ncRNAs in the BX-C, rather than with ME function, a possibility that can be tested experimentally. It will be interesting to use the system of sorting Ubx+ and Ubx− nuclei to examine binding of PcG proteins in nuclei where bxd ncRNAs either are, or are not, transcribed (Petruk, 2006).
The experiments rule out trans-repression by bxd ncRNAs, and instead support repression of Ubx in cis by transcription of these RNAs per se. A likely mechanism of this repression is transcriptional interference, since it was shown that ncRNA transcription extends into the region just upstream of the Ubx initiation site, which may well disrupt protein-DNA interactions required for Ubx initiation. However, this does not rule out promoter competition, and both of these mechanisms may contribute to the observed effects. Previous genetic studies and the results presented in this study show that bxd ncRNAs do not work by RNAi. An RNAi-based repression mechanism has been described for the miRNA produced by the iab-4 transcript, which directly interacts with the 3'-untranslated region of Ubx and prevents translation. This work showed that ectopic expression of iab-4 leads to homeotic phenotypes in the haltere, but do not show that loss of RNAi prevents this effect, nor has the effect of loss of function mutations of the iab-4 transcript been tested, so it remains to be seen if the iab-4 transcript is a bona fide miRNA (Petruk, 2006).
Since significant levels of bxd ncRNAs were not detected in imaginal discs, nor do they persist to late embryonic stages, they are unlikely be responsible for repression of Ubx throughout development. In fact, it has been reported that Trx is bound to the bxd ME in both wing and haltere discs, which have low and high levels of Ubx expression, respectively. The difference between binding of Trx to the bxd ME in embryos and in discs may be a consequence of the absence of transcription of bxd ncRNAs in discs and its presence in embryos, or to other uncharacterized differences between Ubx regulation in embryos and discs. Also, since Trx binds constitutively in some areas of the ME, Papp may have detected such binding in imaginal discs (Petruk, 2006).
Intergenic transcription also cannot explain repression of Ubx in the anterior of the embryo, where it is thought that hunchback and PcG genes set up and maintain the anterior boundary of Ubx expression. However, the pattern of bxd ncRNA transcription, which prefigures, in a complementary fashion, the mosaic pattern of Ubx expression within the parasegments of the embryonic trunk, appears to be essential for proper Ubx initiation. The Ubx pattern may then be maintained or modified at later embryonic stages through repression by other Hox proteins (i.e., abdA and AbdB) and by PcG genes. Thus, maintenance of Ubx expression likely requires multiple mechanisms that are employed at different developmental stages (Petruk, 2006).
The data support a role for Trx in transcriptional elongation as a mechanism for maintenance of a developmentally regulated gene. It has been argued that Trx does not have a direct role in activation of homeotic genes in Drosophila, but instead prevents repression of transcription by PcG proteins. However, the current data suggest that trx is required for recruitment of elongation factors and for efficient completion of transcripts. Therefore, maintenance of transcriptional activity by Trx may be a consequence of its role in elongation, and a block in elongation might lead to the establishment of PcG-mediated repression. Alternatively, Trx may be required only for normal levels of Hox gene expression, and not for maintenance of low levels of expression, a possibility consistent with at least some aspects of the trx mutant phenotype (Petruk, 2006).
This work strongly supports a general role for Trx and TAC1 in transcription, and agrees with previous findings that TAC1 relocates from other genes to the transcribed region of hsp70 following induction of the cellular stress response. The histone methyltransferase activity of Set1, the SET domain protein homologous to Trx, has a role in transcription, and MLL was suggested to play a similar role in mammals. It is suggested that this role is in transcriptional elongation, because Trx and elongation factors are co-ordinately recruited, because Trx binds downstream of the promoter more strongly to the 5’ than the 3’ end, and because transcripts extending to the 3’ end are more strongly affected by trx mutations, for both Ubx and bxd ncRNAs (Petruk, 2006).
TAC1 is also present at the promoter, and this is unaffected by mutations in elongation factors. Therefore, association of TAC1 with the promoter likely precedes the recruitment of elongation factors. Thus, TAC1 may play several distinct roles, one in initiation, another during the recruitment of the elongation complex and perhaps a third during subsequent elongation, where its ability to modify histones may be required for effective completion of long transcripts (Petruk, 2006).
This work provides the first direct evidence of the involvement of long ncRNAs in regulation of homeotic genes of Drosophila. Repression of Ubx is apparently mediated by expression of several intergenic ncRNAs in different germ layers of Ubx-expressing parasegments. TAC1 may be required for efficient read-through by Pol II into the region upstream of the Ubx initiation site, and as a result, for efficient repression of Ubx. Therefore, a direct link is proposed between elongation facilitated by the TAC1 epigenetic complex and repression of Ubx by intergenic transcription. A goal for the future will be to determine if other homeotic genes of Drosophila, and of other organisms, are also regulated by long ncRNAs whose expression is regulated by TAC1 proteins (Petruk, 2006).
Drosophila Polycomb group (PcG) and Trithorax group (TrxG) proteins are responsible for the maintenance of stable transcription patterns of many developmental regulators, such as the homeotic genes. ChIP-on-chip assay was used to compare the distribution of several PcG/TrxG proteins, as well as histone modifications in active and repressed genes across the two homeotic complexes ANT-C and BX-C. The data indicate the colocalization of the Polycomb repressive complex 1 [PRC1; containing the four PcG proteins Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and dRing/Sex combs extra (Sce)] with Trx and the DNA binding protein Pleiohomeotic (Pho) at discrete sequence elements as well as significant chromatin assembly differences in active and inactive regions. Trx binds to the promoters of active genes and noncoding transcripts. Most strikingly, in the active state, Pho covers extended chromatin domains over many kilobases. This feature of Pho, observed on many polytene chromosome puffs, reflects a previously undescribed function. At the hsp70 gene, it was demonstrated in mutants that Pho is required for transcriptional recovery after heat shock. Besides its presumptive function in recruiting PcG complexes to their site of action, these results now uncover that Pho plays an additional role in the repression of already induced genes (Beisel, 2007).
This work used two Drosophila tissue culture lines to map the distribution of chromatin proteins required for the transcriptional maintenance of the HOX genes. Although compromising on the precise developmental identity, the tissue culture cells provided a biochemically tractable homogeneous material, which currently would be difficult to obtain from whole animals. This choice was important to obtain the sharply delineated ChIP profiles, which show a highly significant correlation to mapped genetic elements in the two homeotic complexes. As such, the protein patterns obtained seem to reflect a valid situation as found in material from whole animals. In addition, the ChIP profiles uncovered a new function of Pho, which could be confirmed in whole animals (Beisel, 2007).
The results for SF4 cells are consistent with data that used a Schneider cell derivative for ChIP studies. PRC1 binds to discrete sequence elements, whereas H3K27me3 covers large genomic domains, including genic and intergenic regions. These observations indicate that H3K27me3 cannot be solely responsible for PRC1 targeting. How these H3K27 methylated domains influence HOX gene expression and whether the broad methylation pattern is the cause or consequence of gene silencing remains unclear. H3K27me3 may prevent the binding of activating protein factors as e.g., chromatin remodeling complexes and/or prevent the establishment of activating histone modifications. To this regard, a complementary pattern of H3K27me3 and H4ac, which is present in active gene regions, was detected (Beisel, 2007).
Several lines of evidence suggest that PcG proteins propagate their silencing effect by the direct interaction with the promoter region, which results in the inhibition of transcription initiation. In agreement with that, all promoter regions of the silent ANT-C HOX genes are occupied by PRC1. However, the Ubx promoter, which is silent in both cell lines, as well as the silent AbdB transcription units in Kc cells, are devoid of PRC1. Here, probably the numerous PREs, which are occupied by PRC1 in the Ubx and AbdB domains, build up a special chromatin structure that maintains the silent transcription state (Beisel, 2007).
In agreement with the observed H3K27me3 pattern in Drosophila cells, in mammalian Hox clusters inactive domains are covered by H3K27 and active domains are found entirely covered by H3K4 methylation. In contrast, the distribution of the enzymes setting the histone marks are completely different. In Drosophila E(Z), Trx, and Ash1 are bound at discrete sequence elements, whereas the mammalian homologues EZH2 and MLL1 localize to extended regions coincident with the methylation signals. MLL1 acts as a functional human equivalent of yeast Set1. Both proteins colocalize with RNA Pol II at the transcription start site of highly expressed genes and catalyze the trimethylation of H3K4 at this location. Only at active Hox genes MLL1 reveals a different binding behavior covering entire active chromatin domains. In contrast, the current data shows that Trx also localizes to promoter regions of silent HOX genes and does not show the spreading behavior of MLL1 but appears at additional discrete sites. A complete colocalization of Trx with PRC1 sites was observed at silent genes, i.e., in this expression state no obvious competition is taking place with regard to binding sites (Beisel, 2007).
The comparison of the AbdB gene with the Dfd gene shows that the maintenance of the active state can be performed in alternative ways. The absence of PcG complexes does not seem to be a prerequisite of the active state as observed at the promoter of Dfd in this study and at regulatory regions of Ubx in imaginal discs (Beisel, 2007).
In the active AbdB domain Ph stays bound in a minor but significant amount, and Psc is present in the active Dfd intron. In this regard, Ph and Psc could serve as recruiting platforms for other PRC1 subunits in case of the gene switching to the off state. However, both proteins have been reported to be associated with active genes. Consistent with this, Ph was also observed in the proximal part of both homeotic complexes binding actively transcribed non-HOX genes. The function of this binding behavior remains elusive (Beisel, 2007).
The transcription of noncoding RNAs (ncRNAs) seem to play an important, although diverse, role in the regulation of the BX-C. Noncoding transcription found through the bxd PRE is crucial for Ubx repression and transcription through Mcp overlaps with AbdB transcription in the embryo. NcRNA transcription in the AbdB domain coincides with an active AbdB gene indicates a nonuniversal, gene specific function for ncRNAs in the BX-C (Beisel, 2007).
In the silent state PRC1 is bound to all PREs in the AbdB domain and might be recruited by the action of sequence-specific factors like Pho and the E(Z) histone methyltransferase activity, which may also mark the entire domain as being inactive. In the active AbdB domain, ncRNA transcription may directly influence the binding of of PRC1 and E(Z) or may trigger the enzymatic activity of Trx. Consistent with this scenario, Trx has been shown to bind single-stranded DNA and RNA in vitro. The switch of Trx into an activating mode could lead to the methylation of histones and/or other proteins setting positive transcriptional marks and modulate their activity, respectively. In this case, the displacement of PcG proteins could be directly caused by the Trx action. The binding of Trx to the promoter regions of the active AbdB transcription units could either be caused by (transient) chromatin looping events bridging Trx-bound PREs with the promoters, or Trx could be recruited independently to the active HOX promoters by interaction with RNA Pol II, similar to MLL1, which is recruited to actively transcribed genes in mammalian cells. Trx- and TAC1-interacting histone acetyltransferases may then be responsible for setting epigenetic marks that maintain the active transcription state. Trx has been shown to be required for transcription elongation and it is localized in the gene body of active Ubx, caused by the interaction with elongation factors. In contrast, other studies that investigated the distribution of PcG and TrxG proteins at the active and repressed Ubx gene in imaginal discs found the same restricted Trx profile did the current study, namely Trx binding at discrete sites. These differences may be explained by the different Trx antibodies used. Trx is most probably proteolytically processed like human MLL which results in two fragments that form a heterodimeric complex. This raises the intriguing question whether the complete heterodimeric Trx complex might get recruited to the promoter and upon gene induction the N-terminal fragment tracked along the gene body together with elongation factors, whereas the C-terminal fragment stayed at the promoter (Beisel, 2007).
Pho maps were generated to investigate its role in the recruitment of PRC1. However, the distribution of Pho suggests that the protein also functions in the gene body of actively transcribed genes. The immunostaining of polytene chromosomes revealed that Pho seems not only to be limited to HOX gene control but plays a general role in gene regulation. The colocalization of Pho with strong signals of active Pol II on polytenes together with the effect of a pho-null mutation on the recovery of induced hsp70 indicates that Pho may be directly involved in the rerepression of highly active genes (Beisel, 2007).
It is difficult to imagine that the spreading of Pho is the result of the ability of this protein to bind sequence specifically to DNA. Instead, a model is proposed in which Pho either acts directly at the Pol II elongation complex or it interacts with a remodeling complex, carrying it along the chromatin fiber. In this line, Pho has been shown to interact with BRM and dINO80, two nucleosome remodeling complexes. Interestingly, heat-shock gene transcription is independent of BRM but involves the recruitment of the TAC1 complex, possibly through multiple interactions with the elongating Pol II complex. The simultaneous action of Trx and Pho at heat-shock genes is striking and might resemble their antagonistic functions at HOX genes. Further studies are necessary to unravel the exact molecular mechanism of Pho in this process (Beisel, 2007).
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