Activation and repression of transcription in eukaryotes involve changes in thechromatin fiber that can be accomplished by covalent modification of the histonetails or the replacement of the canonical histones with other variants. The histoneH2A variant of Drosophila melanogaster, H2Av,localizes to the centromeric heterochromatin and is recruited to an ectopicheterochromatin site formed by a transgene array. His2Av behavesgenetically as a PcG gene and mutations in His2Av suppressposition effect variegation (PEV), suggesting that this histone variant isrequired for euchromatic silencing and heterochromatin formation. His2Avmutants show reduced acetylation of histone H4 at Lys 12, decreased methylationof histone H3 at Lys 9, and a reduction in HP1 recruitment to the centromericregion. Neither H2Av accumulation nor histone H4 Lys 12 acetylation is affected bymutations in either Su(var)3-9 or Su(var)2-5. The results suggest anordered cascade of events leading to the establishment of heterochromatin,requiring the recruitment of the histone H2Av variant followed by H4 Lys 12acetylation as necessary steps before H3 Lys 9 methylation and HP1 recruitmentcan take place (Swaminathan, 2005).

The basic unit of chromatin is the nucleosome, which is made up of 146 bp of DNAwrapped around a histone octamer composed of two molecules each of the histonesH2A, H2B, H3, and H4. Activation of gene expression requires the transcriptionalmachinery to overcome the compaction of chromatin: work in recent years hasuncovered several strategies to accomplish this goal. ATP-dependent chromatinremodeling has been studied extensively as a mechanism to make the DNAaccessible to the transcription apparatus. Covalentmodification of the unstructured and solvent-exposed N-terminal tails ofhistones has also been shown to participate in processes such as activation orrepression of transcription and chromosome condensation and segregation (Swaminathan, 2005 and references therein).

Replacement of canonical histones with other variants might provide analternative mechanism for controlling transcription by inducing alterednucleosomal structures; in fact, recent work has implicated ATP-dependentchromatin remodeling complexes in the process of histone variant replacement(Krogan, 2003; Mizuguchi, 2004). The role of histonevariants, and specially those of H3 and H2A, in various nuclear processes hasbeen long appreciated.There are at least three different families of H2A variants present in a varietyof organisms from yeast to mammals, and the degree of conservation among membersof each family is greater than than to the canonical H2A.H2AX is thought to play a role in DNA double-strand break repair; the serine inthe SQEY motif of H2AX is phosphorylated at the site of the DNA damage andserves as a signal for the recruitment of repair proteins. Macro H2A1, another H2A variant, has been shown to have a role inX-chromosome inactivation and dosage compensation in mammals, where it is foundto localize to the inactive X after silencing has been established (Swaminathan, 2005).

H2A.Z, the Drosophila version of which is the subject of this overview, is a third histone H2A variant highly conserved across species and,therefore, likely to play an important role in chromatin function (van Daal, 1988; Stargell, 1993). H2A.Z is an essential protein in Drosophila and in mice (van Daal, 1992; Faast, 2001), and has been implicated in both activation and repression oftranscription (Dhillon, 2000; Santisteban, 2000;Larochelle, 2003). Gene expression analyses using whole-genomemicroarrays show that H2A.Z (named Htz1 in yeast) is involved in both activationand silencing of transcription in Saccharomyces cerevisiae (Meneghini, 2003). Recent studies have also shown that H2A.Z is enriched in thepericentric heterochromatin (Rangasamy,2003) during early mammalian development (Swaminathan, 2005).

Heterochromatin consists of highly compacted DNA that is present around thecentromeres and telomeres and is also dispersed at certain sites along thechromosomes. Heterochromatin has been found to be essential for proper chromosome segregationand genomic stability and for maintaining dosagecompensation by inactivating one of the X chromosomes in female mammals. Recent studies have helped elucidate several steps in thepathway leading to the formation of heterochromatin. The earliest step established so far requires the RNAi machinery for targeting of smallRNAs to heterochromatin by the RNA-induced initiation oftranscriptional gene silencing (RITS) complex.Subsequent steps require deacetylation of histone H3 Lys 9 followed bymethylation of the same residue by Su(var)3-9. This modified histone then recruitsHP1, which in turns recruits the Suv4-20 methyltransferase totrimethylate histone H4 at Lys 20 (Swaminathan, 2005 and references therein).

Given the large number of suppressors and enhancers of PEV identified inDrosophila, there must be additional stepsinvolved in the establishment and maintenance of heterochromatin. Althoughacetylation of histone tails is generally correlated with transcriptionactivation, and establishment of heterochromatin requires deacetylation of H3Lys 9, acetylation of other residues in H3 or H4 might also play a role insilencing processes.Histone acetyl transferases have been found to be physically associated withSu(var)3-9, and mutations in a MYST domainacetyltransferase behave as suppressors of PEV.These results support the idea that acetylation of specific histone residuesmight be involved in the formation of heterochromatin. This study demonstrates thatthe H2A.Z variant of Drosophila, H2Av, plays a role in Pc-mediatedsilencing and in the establishment of centromeric heterochromatin. In addition,acetylation of H4 Lys 12 is required subsequent to H2Av replacement but beforeH3 Lys 9 methylation. The results highlight the complexity of the multistepprocess leading to heterochromatin formation in higher eukaryotes (Swaminathan, 2005).

The establishment of heterochromatin has so far been defined as a four-stepprocess initiated by the RNAi machinery through the production of small RNAshomologous to centromeric DNA repeats that are recruited to prospectiveheterochromatic regions as part of the RNA-induced initiation oftranscriptional gene silencing (RITS) complex. The next step described in this process thus far is thedeacetylation and subsequent methylation of histone H3 Lys 9, which serves torecruit HP1. HP1 thenrecruits the Suv4-20 methyltransferase to trimethylate histone H4 at Lys 20. The work described heresuggests that heterochromatin formation is more complex than previously thought,and it involves at least two additional steps. One step requires recruitment ofH2Av or replacement of the canonical histone H2A for the H2Av variant. Thisrequirement is highlighted by the observation that mutations in theHis2Av gene act as suppressors of position effect variegation bymodulating the silencing effect of heterochromatin on the adjacent whitegene (Swaminathan, 2005).

The replacement of H2A for H2Av is not specific to heterochromatin, and it mayalso take place in silenced regions of the euchromatin, since it appears thatHis2Av behaves genetically as a PcG gene. PcG proteins areresponsible for the maintenance of epigenetic silencing of the homeotic genesduring Drosophila development. The His2Av genecan be classified as a PcG gene, since mutations in His2Av enhancethe phenotype of Pc mutants, suppress the phenotype of mutations intrxG genes, and cause ectopic expression of the Ant gene. Theinvolvement of H2Av in Pc-mediated silencing is not completely unexpected, sinceH2Av is critical for the establishment of pericentric heterochromatin and bothprocesses share similar strategies. Heterochromatin-induced silencing requiresmethylation of H3 at Lys 9 by the Su(var)3-9 histone methyltransferase, whereasPc-induced silencing involves the recruitment of the ESC-E(z) complex tomethylate H3 at Lys 27. Although the modified residues are different, in bothcases the modification serves as a tag to bind chromo domain-containingproteins, HP1 in the case of pericentric heterochromatin and Pc in euchromaticsilencing. Given the parallels between the two processes, it was surprising tofind that replacement of H2Av was required for subsequent H3 Lys 9 methylationin heterochromatin but not for H3 Lys 27 methylation in silenced regions ofeuchromatin. This later conclusion is supported by the observation that neitherH3 Lys 27 methylation nor E(z) recruitment is affected by mutations inHis2Av (Swaminathan, 2005).

The requirement of H2Av for Pc recruitment but not for H3 Lys 27 methylationpoints to a slightly different strategy in the establishment of silencing in theeuchromatin compared to heterochromatin. Heterochromatic silencing appears toinvolve a series of events that take place in a linear pathway; each event isdependent on the previous one for proper heterochromatin assembly. In thiscascade of events, replacement of H2A by H2Av appears to be an early step in theprocess, although the results cannot distinguish among the possibilities thatH2Av is recruited before, after, or in parallel to the recruitment of the RITScomplex by the RNAi machinery. Surprisingly, the observed effects of H2Av onPc-mediated silencing point to several possible mechanisms, all slightlydifferent from that involved in heterochromatin formation. One formalpossibility that would be consistent with the results but that is considered lesslikely is that H2Av acts downstream of Pc; recruitment of this protein would berequired for H2Av replacement, which would then in turn stabilize the binding ofthe Pc complex. A second possibility is that H2Av replacement is a relativelylate event in the process, acting downstream of H3 Lys 27 methylation instead ofbeing required for this modification. In this scenario, H2Av would not berequired for the recruitment of the ESC–E(z) complex, but it would berequired subsequently to alter chromatin structure and allow Pc recruitment.Alternatively, euchromatic Pc-mediated silencing might be accomplished by tworelatively independent parallel pathways that converge at the end to ensure Pcbinding to the chromatin. One pathway would alter chromatin structure byrecruiting ESC–E(z) and methylating H3 at Lys 27; a second parallel butindependent pathway would further alter chromatin structure by replacing H2A forH2Av. Both processes would then be required for the recruitment of thePc-containing PRC-1 complex (Swaminathan, 2005).

The apparent association of H2Av with silenced regions might appear puzzling inview of findings in other systems. In Tetrahymena, H2A.Z is present inthe transcriptionally active macronucleus, but it is not detected in thesilenced micronucleus. In S. cerevisiae, theH2A.Z histone variant Htz1 is required for the expression of SWI/SNF-dependentgenes such as PHO5 and GAL1; interestingly, although Htz1 isrequired for activation, it is present at higher levels in the promoters ofthese genes when they are repressed than when they are transcriptionally active(Santisteban, 2000). Nevertheless, Htz1 has also been shown to bepresent at silenced loci in yeast, and to be required for HMR andtelomere-induced silencing (Dhillon, 2000). A detailed analysisof the role of Htz1 in gene expression in yeast using whole-genome microarraysresulted in the identification of 214 genes that are activated and 107 genesthat are repressed by Htz1. Htz1-activated genes are located adjacent toheterochromatin; Htz1 is enriched in the promoters and coding regions ofactivated genes (Meneghini, 2003), where it appears to block the spreading of heterochromaticsilencing (Swaminathan, 2005).

One possible explanation for the functional differences between the yeast andDrosophila H2A.Z homologs is that Drosophila lacks H2A.X, and,therefore, H2Av plays the roles of both histone variants. Nevertheless, thelocalization of H2A.Z in heterochromatin is not limited to Drosophila.Studies in mice also show an association of this histone variant withpericentric heterochromatin (Rangasamy, 2003). The apparentcontradiction between the two conflicting roles for H2A.Z in various organismscould be explained if the role of this histone variant is to assemble achromatin that is more accessible to other chromatin-remodeling complexes, andthat the final result depends on the type of factors recruited toH2A.Z-containing chromatin. This possible role is consistent with the findingthat the functionally essential C-terminal domain of H2A.Z (Clarkson,1999) is exposed on the surface of H2A.Z-containing nucleosomes, andtherefore it could serve to recruit other factors (Suto, 2000).Analytical ultracentrifugation experiments suggest that nucleosomesreconstituted with H2A.Z have decreased stability compared to thosereconstituted with the canonical H2A histone, and therefore might allow greateraccessibility of various factors to H2A.Z-containing chromatin (Abbott,2001). The decrease in stability is also supported by the crystal structureof H2A.Z-containing nucleosomes, which suggests an altered interface between theH2A.Z-H2B dimer and the H3-H4 tetramer (Suto, 2000). Alternatively, the exposed domain of H2A.Z could mediate internucleosome interactions to give rise to higher-order compacted chromatin structures (Fan, 2002). The H2A.Z-containing chromatin fiber contains regularly spaced nucleosomes (Wallrath, 1995), an arrangement that is characteristic of pericentric heterochromatin (Swaminathan, 2005).

The results discussed here suggest a complex multistep model forheterochromatin assembly. The nature ofthe first step in the process might involve the RNAi machinery and therecruitment of the RITS complex, although it is also possible that H2Avrecruitment takes place prior to this step. The mechanism by which H2Avrecruitment is controlled is unclear. Recent studies in yeast have shown that acomplex containing swr1, an Snf-2-related ATP-dependent chromatin-remodelingfactor, is able to efficiently exchange H2A for H2A.Z (Krogan, 2003;Kobor, 2004; Mizuguchi, 2004). A Drosophila homologof SWR1 is domino, which has been characterized as a PcGgene and a dominant suppressor of PEV. It is plausiblethat RITS recruits a Domino-containing chromatin-remodeling complex, which inturn replaces histone H2A for H2Av. This alteration would then facilitate therecruitment of histone-modifying enzymes that would further change chromatinstructure. The current results suggest that the next step in the process requires theacetylation of histone H4 Lys 12, but the nature of the enzyme responsible foracetylation of H4 Lys 12 is not known. A candidate for this role could be theproduct of the chameau gene, which encodes a MYST domain histoneacetyltransferase. Mutations in chameau behave as PcG genes andsuppress PEV (Grienenberger, 2002), but they fail to affect H4 Lys 12acetylation, suggesting that the Chameauprotein affects a different step in the establishment of heterochromatin.Acetylation of H4 Lys 12 is then followed by methylation of H3 Lys 9 andrecruitment of HP1, which in turn tethers Svar4-20 to methylate H4 Lys 20.Additional steps are likely to be required in this complex process. Analysis ofthe large collection of Su(var) and E(var) mutations identified inDrosophila should make possible the elucidation of additional steps inthis pathway, resulting in a comprehensive understanding of the molecular eventsinvolved in heterochromatin formation (Swaminathan, 2005).

Nucleosome organization in the Drosophila genome

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. This study produced a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the Drosophila and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines (Mavrich, 2008).

Knowledge of the precise location of nucleosomes in a genome is essential to understand the context in which chromosomal processes such as transcription and DNA replication operate. A common theme to emerge from recent genome-wide maps of nucleosome locations is a general deficiency of nucleosomes in promoter regions and an enrichment of certain histone modifications towards the 5' end of genes. A high resolution genomic map of nucleosome locations in the budding yeast S. cerevisiae has further revealed the nucleosomal context of cis-regulatory elements and transcriptional start sites. However, such context has not been established in multicellular eukaryotes, and so fundamental questions remain: Is there a common theme by which genes of multicellular eukaryotes position their nucleosomes with respect to functional chromosomal elements? Are such themes and their underlying rules evolutionarily conserved across eukaryotes? What are the functional implications for those themes that differ across the major eukaryotic lines? To address these questions, a genome-wide high-resolution map of H2A.Z (also known as H2Av) and bulk nucleosome locations was produced in the Drosophila embryo. H2A.Z is widely distributed in Drosophila, but some evidence points to specialized roles. In Saccharomyces, H2A.Z replaces H2A at the 5' end of active genes, and thus provides a focused representation of promoter chromatin architecture (Mavrich, 2008).

Drosophila embryos are composed of a wide variety of cell types in which subsets of genes may elicit distinct gene expression programs. Global gene expression profiles during all stages of Drosophila development from 8-12 h post fertilization to a young adult fly are correlated, which possibly reflects the broad expression pattern of the large repertoire of housekeeping genes in most cell types during development. This general spatial and temporal independence of gene expression provides impetus to use whole embryos to develop a reference nucleosome map. Indeed, a map reveals that nucleosomes are generally well organized, despite cell type heterogeneity (Mavrich, 2008).

Embryos were treated with formaldehyde, and H2A.Z nucleosome core particles were immunopurified. H2A.Z-containing nucleosomes (652,738) were sequenced and mapped to 207,025 consensus locations in the Drosophila r5.2 reference genome, thereby providing >3-fold depth of coverage (see browser at http://drosophila.atlas.bx.psu.edu/). Correction for micrococcal nuclease (MNase) digestion bias was imposed. Those 112,750 nucleosomes detected three or more times were further analysed, although patterns were identical when all nucleosomes were analysed. The internal median error of the data was 4 bp (Mavrich, 2008).

H2A.Z nucleosomes were predominantly distributed at 175-bp intervals from the TSS (compared to 165-bp in Saccharomyces, demonstrating that a predominant organizational pattern exists for H2A.Z nucleosomes in Drosophila embryos that transcends a spatial and temporal context. The H2A.Z pattern was compared to the distribution of bulk nucleosomes (that is, those containing any combination of H2A.Z and H2A), determined using high-density tiling arrays (36-bp probe spacing). Within genic regions, the same organizational pattern was found. For both data sets, a nucleosome-depleted region was evident immediately upstream of the +1 nucleosome, which probably reflects a nucleosome-free core promoter region (NFR), as first detected in Saccharomcyces. Like Saccharomyces, a -1 nucleosome was detected ~180 bp upstream of the TSS. However, in contrast, it lacked H2A.Z (Mavrich, 2008).

Surprisingly, the genic array of Drosophila nucleosomes started ~75 bp further downstream from the equivalent position in Saccharomyces, placing the +1 nucleosome at +135. This shift has important implications in how the TSS is presented to RNA polymerase II (Pol II). In Saccharomyces, the TSS resides within the nucleosome border, potentially allowing the nucleosome to regulate start-site selection and efficiency. In Drosophila, the predominant arrangement of nucleosomes might allow unimpeded access to the TSS, with potential blockage occurring downstream after initiation (Mavrich, 2008).

Drosophila have well-defined core promoter elements, such as TATA, initiator (Inr), downstream promoter element (DPE) and motif ten element (MTE), which bind to the general transcription machinery, although these elements are not found in most genes. For genes lacking these core promoter elements or having a DPE, the canonical nucleosome organization was observed, which was more robust when only H2A.Z-containing nucleosomes were examined. In contrast, genes containing TATA, Inr or MTE had a diminished canonical nucleosome organization and a diminished NFR, indicating that these classes of genes may have a more compact and gene-specific chromatin architecture, including a positioned nucleosome over the TSS. Consequently, they might be more dependent on chromatin remodelling for expression. When genes become transcriptionally competent, resident nucleosomes could adopt a more open and canonical organization, which includes replacing H2A with H2A.Z. Three observations support this hypothesis. First, H2A.Z and bulk nucleosomes at highly expressed genes were more uniformly organized than those at genes with a lower expression. Second, bulk nucleosomes for genes that contained H2A.Z at their 5' end displayed the canonical pattern, whereas those lacking H2A.Z did not. Third, within any class of genes except those having an Inr, H2A.Z nucleosomes adopted a more canonical organization than the bulk set of nucleosomes. These results suggest that transcription and the presence of H2A.Z are linked to an open and uniform chromatin architecture at promoter regions (Mavrich, 2008).

Recent genome sequencing of 12 Drosophila species of differing evolutionary distance has provided an unprecedented opportunity to identify conserved DNA sequence. By comparing the distribution of motifs around the TSS, four recurring patterns were found: 27 motifs were classified as 'nucleosomal', 57 as 'anti-nucleosomal', 12 as 'fixed', and 98 as 'random'. Nucleosomal and anti-nucleosomal patterns matched the general distribution of where nucleosomes were relatively enriched or depleted, respectively, relative to the TSS. Fixed elements were at a defined distance from the TSS, and random elements lacked patterning. The nucleosomal and anti-nucleosomal patterns suggest that certain motifs are organized to be downstream of the TSS in the midst of nucleosomal arrays, whereas others are organized to be upstream of the TSS, where nucleosomes are relatively depleted (Mavrich, 2008).

The organizational relationship of these DNA motifs to individual H2A.Z nucleosomes was examined within the whole genome. Notably, nucleosomal motifs were consistently enriched on the H2A.Z nucleosome surface, whereas anti-nucleosomal motifs were consistently depleted. Individual fixed motifs were mostly depleted of H2A.Z nucleosomes. These findings along with several controls suggest that motifs and nucleosomes adopt a preferred organization around each other, regardless of their genomic location. This organization could be linked to co-evolution of base sequence composition bias in and around nucleosomes. The functional importance of such context remains to be determined (Mavrich, 2008).

Whether the positions of Drosophila H2A.Z nucleosomes are at least partly defined by the underlying DNA sequence pattern was examined, and whether such a pattern might be evolutionarily conserved was investigated. The frequency of dinucleotides across Drosophila H2A.Z nucleosomal DNA was examined because 10-bp periodic patterns of certain dinucleotides enhance the wrapping and positioning of DNA around the histone core. As seen in Saccharomyces, 10-bp periodic patterns of A and/or T (A/T) dinucleotides running counter-phase to G/C dinucleotides was observed. The modest amplitudes of the pattern suggest that such periodicities are infrequent, and are thus used selectively (that is, most nucleosomes lack underlying positioning signals) (Mavrich, 2008).

The rules of nucleosome positioning were further investigated by scanning promoter regions for correlations to nucleosome positioning sequences previously identified for a relatively small number of eukaryotic nucleosomes, in which AA/TT or CC/GG dinucleotides occur in a biased and/or periodic arrangement across nucleosomal DNA. Unlike in yeast, the AA/TT positioning pattern failed to identify nucleosome locations. However, the CC/GG pattern reproduced the exact position of the +1 nucleosomes, indicating that the Drosophila +1 nucleosome may be positioned in part by CC/GG-based positioning sequences that are used preferentially in metazoans. Consistent with this, +1 nucleosomes are highly positioned around the 5' end of genes (Mavrich, 2008).

Despite H2A.Z being enriched at the 5' end of genes, substantial levels were detected throughout the genome, which allowed examination of nucleosome organization at the 3' end of genes. Notably, H2A.Z nucleosome levels spiked near the open reading frame (ORF) end points and then dropped precipitously further downstream into the intergenic regions, where transcripts terminate. The spike occurred ~30 bp upstream from the stop codon and ~160 bp upstream of the transcript poly(A) site. A similar nucleosome drop-off was seen when bulk nucleosomes were examined, but was not evident at genes that lacked H2A.Z. Thus, like the 5' end, the presence of H2A.Z may be linked to a more open chromatin architecture at the 3' end of genes. The change in nucleosome density coincided with alterations in nucleosome positioning sequences. Thus, such '3' NFRs' might be defined in part by the underlying DNA sequence. Conceivably, 3' NFRs might function in transcription termination (Mavrich, 2008).

The location of the +1 nucleosome at the 5' end of genes is notable because its upstream border resides at approximately +62 (relative to the TSS), which is near where Pol II pauses during the transcription cycle. To examine the potential linkage between Pol II pausing and nucleosome positions, the genome-wide location of Pol II was determined in embryos at 1,956 putatively paused genes. Pol II was concentrated in a ~300 bp region that peaked around +90, which overlaps the region bound by the +1 nucleosome; this is consistent with other recent placements. Indeed, the distribution of paused Pol II, as directly measured by permanganate reactivity of thymines on a statistically robust subset of ~50 genes, indicates that pausing occurs between +20 and +50, with the centre at +35. This high-resolution permanganate footprinting data, which represents the most definitive means of assessing Pol II pausing, places the front edge of Pol II (~16 bp downstream of the bubble) within ~10 bp of the +1 nucleosome border (Mavrich, 2008).

The location of the +1 H2A.Z nucleosome was similar (but not identical) whether or not paused Pol II was present, indicating that Pol II was not likely to be the cause of the nucleosome shift compared to Saccharomyces. Instead, the positioned +1 nucleosome might be contributing to Pol II pausing, which is consistent with other studies. Other factors including negative elongation factor (NELF) are likely to make significant contributions to pausing as well (Mavrich, 2008).

Intriguingly, genes that contained a paused Pol II showed a ~10 bp downstream shift of H2A.Z nucleosomes. The same shift was observed if H2A.Z sequencing reads (rather than nucleosomes) or bulk nucleosomes are plotted. The shift suggests that, as part of the pausing process, Pol II collides with the +1 nucleosome, possibly displacing it downstream by one turn of the DNA helix. If the downstream nucleosomes are positioned mainly by the principles of statistical positioning, rather than the underlying DNA sequence, then a shift of the +1 nucleosome is expected to have a ripple effect on downstream nucleosomes (Mavrich, 2008).

To test the prediction that Pol II is engaging the +1 nucleosome, bulk mononucleosomes were prepared from formaldehyde-crosslinked embryos and immunoprecipitated with antibodies directed against Pol II. DNA corresponding to mononucleosomes (~150 bp) was gel-purified and mapped to the entire Drosophila genome with high-resolution tiling arrays. The distribution of nucleosome-Pol II crosslinking at Pol II-paused genes peaked at the +1 nucleosome. This was not seen at genes lacking a paused Pol II or H2A.Z. The selective enrichment at +1 demonstrates that Pol II is predominantly engaged with the +1 nucleosome, and therefore the +1 nucleosome may be instrumental in establishing the paused state (Mavrich, 2008).

The high resolution map of Drosophila nucleosomes reveals evolutionarily conserved and divergent principles of nucleosome organization. Genes that possess H2A.Z nucleosomes are likely to have experienced a transcription event. They tend to have nucleosome-free promoter and termination regions and intervening arrays of uniformly positioned nucleosomes that become less uniform towards the 3' end of the gene. H2A.Z nucleosomes in general might not block assembly of the transcription machinery at transcriptionally 'experienced' promoters. However, repressed promoters or those containing Inr elements do seem to have an H2A nucleosome over the TSS (Mavrich, 2008).

Conserved DNA sequence motifs (and thus any proteins that bind to them) tend to have an organizational relationship with nucleosomes. 'Anti-nucleosomal' motifs including those for proteins such as Engrailed, Even skipped, Fushi tarazu, Giant, Hunchback and Knirps tend to be located upstream of the TSS and might contribute to the exclusion of nucleosomes over the core promoter. Indeed some have anti-nucleosomal activity. 'Nucleosomal' motifs include sites for achaete, antennapedia, dorsal, tramtrack and others. Their preference for locations downstream of the TSS where nucleosomes are well organized raises the possibility that they contribute to nucleosome organization (Mavrich, 2008).

In Saccharomyces, the location of the TSS just inside the +1 nucleosome border allows the nucleosome potentially to exert control over initiation; however, in Drosophila, most genes might position the +1 nucleosome to interact with a transcriptionally engaged paused polymerase. It is not known whether the +1 nucleosome is causative or just participatory in the pausing. It is now becoming clear that metazoans also regulate transcription through Pol II pausing rather than solely through transcription complex assembly. The nucleosome map and its context to DNA regulatory elements, presented here, provides a framework for designing experiments and analysing existing data to understand how metazoans regulate transcription (Mavrich, 2008).

GENE STRUCTURE

cDNA clone length - 913

Bases in 5' UTR - 149

Exons - 4

Bases in 3' UTR - 338

PROTEIN STRUCTURE

Amino Acids - 141

Structural Domains

The Tetrahymena histone H2A variant designated hv1 is localized exclusively inthe transcriptionally active macronucleus and is absent from the quiescentmicronucleus. A cDNA clone of the hv1 gene was used to screen aDrosophila cDNA library. A cross-hybridizing clone was recovered and shown bysequence analysis to code for a protein homologous to hv1 as well as to thechicken H2A variant, H2A.F, the sea urchin H2A variant, H2A.F/Z and themammalian H2A variant H2A.Z. Southern analysis of Drosophila genomic DNAindicates that the H2AvD (H2A variant Drosophila) gene is present in one copy.In situ hybridization places the locus at 97CD on chromosome 3, while theS-phase regulated histone genes are on chromosome 2. Thus the Drosophila H2Avariant should be accessible to genetic analysis, which will enable its functionto be determined (van Daal, 1988).

The H2AvD sequence contains the nonapeptide, which is conserved in all H2A's, at position 23-31, indicating that this cDNA encodes an H2A-like protein. However, it is clear that the sequence differs markedly from that of the H2A encoded in theDrosophila histone gene cluster. There are 52 amino acid changes in the first124 amino acids, which indicates a similarity of only 59%. This is approximatelythe same degree of similarity shown by the H2A variants of chicken (60%), seaurchin (56%-57%), mammals (56%) and Tetrahymena (62%-65%) relative to theirrespective major S-phase regulated H2A's. The cDNA sequence predicts that H2AvDis a larger molecular weight protein than H2A.1. An antibody to the carboxyterminal portion of H2AvD detects a protein of lower mobility than the major histone H2A on electrophoresis in SDS polyacrylamide gels. An H2A variant (D2) has been previously reported in Drosophila. D2 has a molecular weight of 13,400 daltons and differs from H2A.1 in that it contains no methionine residues and has an increased histidine content. H2AvD shares these properties (van Daal, 1988).

The amino and carboxy terminal ends of the Drosophila and Tetrahymena H2Avariants have diverged. However, there is a remarkably high similiarity when comparing the body of the protein in both variants. There are only 16 amino acid changes in the region of amino acids18-120, which gives a similarity of 84%. The carboxy terminal end of hvl (fromamino acid 121) is completely different from that of H2AvD in both amino acidcomposition and length. The N-terminus shows some sequence similarity (less than50%), but again the length is different. It should be noted that the majorTetrahymena histone H2A differs significantly from the major H2A's of the otherspecies. The H2A.l's of human, cow, rat and chicken are 95%-99% similar to eachother. The Drosophila and sea urchin H2A.l's are 81%-87% similar to those ofmammals, chicken and each other. However, the Tetrahymena H2A.1 is only 63-69%similar to those of other species, and so it is perhaps not surprising thatH2AvD is quite different from hvl, whereas, it is very similar (97%) to the seaurchin variant (van Daal, 1988).

A comparison of the deduced protein sequences of the H2A variants of chicken(H2A.F), sea urchin (H2A.F/Z) and mammals (H2A.Z) with that of Drosophila (H2AvD) shows clearly that the amino acid sequence of H2AvD is more closely related to thechicken, sea urchin and mammalian H2A variants than it is to the majorDrosophila H2A, H2A.l. The conservation in the first 122 amino acids isextremely high. There is 99% similarity between the Drosophila and the seaurchin proteins, with only one amino acid change (ser to asn at position 38).There is 98% similarity between H2AvD and the chicken and mammalian proteins.Both have two amino acid changes (ala to gln at position 21 and ser to thr atposition 38 in chicken and ala to thr at position 14 and ala to glu at position21 in mammals). The carboxyl ends of these four variants all differ. However,the Drosophila variant is the most divergent. The C terminal tail is longer thanthe others and its sequence is also dissimilar. Southern blotanalysis of Drosophila genomic DNA indicates that the H2AvD geneis unique (van Daal, 1988).

date revised: 25 July 2005

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