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Molecular landscape of modified histones in Drosophila heterochromatic genes and euchromatin-heterochromatin transition zones.

Yasuhara JC, Wakimoto BT - PLoS Genet. (2007)

Bottom Line: We found that H3-di-methylated-at-lysine 9 (H3K9me2) was depleted at the 5' ends but enriched throughout transcribed regions of heterochromatic genes.Moreover, the profile was only subtly affected by a Su(var)3-9 mutation, implicating a histone methyltransferase other than SU(VAR)3-9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos.The results are also relevant for understanding the effects of chromosome aberrations and the megabase scale over which epigenetic position effects can operate in multicellular organisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Washington, Seattle, Washington, United States of America.

ABSTRACT
Constitutive heterochromatin is enriched in repetitive sequences and histone H3-methylated-at-lysine 9. Both components contribute to heterochromatin's ability to silence euchromatic genes. However, heterochromatin also harbors hundreds of expressed genes in organisms such as Drosophila. Recent studies have provided a detailed picture of sequence organization of D. melanogaster heterochromatin, but how histone modifications are associated with heterochromatic sequences at high resolution has not been described. Here, distributions of modified histones in the vicinity of heterochromatic genes of normal embryos and embryos homozygous for a chromosome rearrangement were characterized using chromatin immunoprecipitation and genome tiling arrays. We found that H3-di-methylated-at-lysine 9 (H3K9me2) was depleted at the 5' ends but enriched throughout transcribed regions of heterochromatic genes. The profile was distinct from that of euchromatic genes and suggests that heterochromatic genes are integrated into, rather than insulated from, the H3K9me2-enriched domain. Moreover, the profile was only subtly affected by a Su(var)3-9 mutation, implicating a histone methyltransferase other than SU(VAR)3-9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos. On a chromosomal scale, we observed a sharp transition to the H3K9me2 domain, which coincided with increased retrotransposon density in the euchromatin-heterochromatin (eu-het) transition zones on the long chromosome arms. Thus, a certain density of retrotransposons, rather than specific boundary elements, may demarcate Drosophila pericentric heterochromatin. We also demonstrate that a chromosome rearrangement that created a new eu-het junction altered H3K9me2 distribution and induced new euchromatic sites of enrichment as far as several megabases away from the breakpoint. Taken together, the findings argue against simple classification of H3K9me as the definitive signature of silenced genes, and clarify roles of histone modifications and repetitive DNAs in heterochromatin. The results are also relevant for understanding the effects of chromosome aberrations and the megabase scale over which epigenetic position effects can operate in multicellular organisms.

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Modified Histone Profiles of the 2Lh Genes Revealed by ChIP-chip AssaysComparison of H3K9/14acet (top) and H3K9me2 (below) profiles for the genotypes indicated at the top of each line shows the reproducibility of the profiles. ChIP-enrichment relative to total genomic DNA control is plotted. The raw data are shown as gray dots, and averages of five adjacent probes are shown as colored dots (blue for H3K9/14acet and brown for H3K9me2). The annotated heterochromatic genes are shown below with the depiction of exon/intron structures. Genes on the plus and minus strands are shown in the top and the bottom tiers, respectively. Black genes have cDNA evidence to support their existence and the positions of their annotated 5′ ends are marked by the gray vertical lines. Gray genes are based solely on computational predictions. x-Axis shows the R5.1 genome coordinates.
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pgen-0040016-g003: Modified Histone Profiles of the 2Lh Genes Revealed by ChIP-chip AssaysComparison of H3K9/14acet (top) and H3K9me2 (below) profiles for the genotypes indicated at the top of each line shows the reproducibility of the profiles. ChIP-enrichment relative to total genomic DNA control is plotted. The raw data are shown as gray dots, and averages of five adjacent probes are shown as colored dots (blue for H3K9/14acet and brown for H3K9me2). The annotated heterochromatic genes are shown below with the depiction of exon/intron structures. Genes on the plus and minus strands are shown in the top and the bottom tiers, respectively. Black genes have cDNA evidence to support their existence and the positions of their annotated 5′ ends are marked by the gray vertical lines. Gray genes are based solely on computational predictions. x-Axis shows the R5.1 genome coordinates.

Mentions: Reproducible H3K9/14acet and H3K9me2 profiles were obtained in the ChIP-chip studies (Figure 3), permitting a comparison with the standard ChIP results (Figure 1). Specifically, the ChIP-chip assay showed strong H3K9/14acet enrichment in the 5′ regions of heterochromatic genes, but did not indicate as high an enrichment of H3K9me2 as anticipated based on standard ChIP. Nonetheless, the observed pattern was consistent with earlier results. As shown for 2Lh in Figure 3, H3K9me2 was enriched in intergenic regions and throughout these heterochromatic genes but not near the transcription start-regions. This was also true for genes with little or no association with H3K9/14acet (e.g., Chitinase, CG17018, and CG40006 genes in Figures 3 and 4A).


Molecular landscape of modified histones in Drosophila heterochromatic genes and euchromatin-heterochromatin transition zones.

Yasuhara JC, Wakimoto BT - PLoS Genet. (2007)

Modified Histone Profiles of the 2Lh Genes Revealed by ChIP-chip AssaysComparison of H3K9/14acet (top) and H3K9me2 (below) profiles for the genotypes indicated at the top of each line shows the reproducibility of the profiles. ChIP-enrichment relative to total genomic DNA control is plotted. The raw data are shown as gray dots, and averages of five adjacent probes are shown as colored dots (blue for H3K9/14acet and brown for H3K9me2). The annotated heterochromatic genes are shown below with the depiction of exon/intron structures. Genes on the plus and minus strands are shown in the top and the bottom tiers, respectively. Black genes have cDNA evidence to support their existence and the positions of their annotated 5′ ends are marked by the gray vertical lines. Gray genes are based solely on computational predictions. x-Axis shows the R5.1 genome coordinates.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2211541&req=5

pgen-0040016-g003: Modified Histone Profiles of the 2Lh Genes Revealed by ChIP-chip AssaysComparison of H3K9/14acet (top) and H3K9me2 (below) profiles for the genotypes indicated at the top of each line shows the reproducibility of the profiles. ChIP-enrichment relative to total genomic DNA control is plotted. The raw data are shown as gray dots, and averages of five adjacent probes are shown as colored dots (blue for H3K9/14acet and brown for H3K9me2). The annotated heterochromatic genes are shown below with the depiction of exon/intron structures. Genes on the plus and minus strands are shown in the top and the bottom tiers, respectively. Black genes have cDNA evidence to support their existence and the positions of their annotated 5′ ends are marked by the gray vertical lines. Gray genes are based solely on computational predictions. x-Axis shows the R5.1 genome coordinates.
Mentions: Reproducible H3K9/14acet and H3K9me2 profiles were obtained in the ChIP-chip studies (Figure 3), permitting a comparison with the standard ChIP results (Figure 1). Specifically, the ChIP-chip assay showed strong H3K9/14acet enrichment in the 5′ regions of heterochromatic genes, but did not indicate as high an enrichment of H3K9me2 as anticipated based on standard ChIP. Nonetheless, the observed pattern was consistent with earlier results. As shown for 2Lh in Figure 3, H3K9me2 was enriched in intergenic regions and throughout these heterochromatic genes but not near the transcription start-regions. This was also true for genes with little or no association with H3K9/14acet (e.g., Chitinase, CG17018, and CG40006 genes in Figures 3 and 4A).

Bottom Line: We found that H3-di-methylated-at-lysine 9 (H3K9me2) was depleted at the 5' ends but enriched throughout transcribed regions of heterochromatic genes.Moreover, the profile was only subtly affected by a Su(var)3-9 mutation, implicating a histone methyltransferase other than SU(VAR)3-9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos.The results are also relevant for understanding the effects of chromosome aberrations and the megabase scale over which epigenetic position effects can operate in multicellular organisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Washington, Seattle, Washington, United States of America.

ABSTRACT
Constitutive heterochromatin is enriched in repetitive sequences and histone H3-methylated-at-lysine 9. Both components contribute to heterochromatin's ability to silence euchromatic genes. However, heterochromatin also harbors hundreds of expressed genes in organisms such as Drosophila. Recent studies have provided a detailed picture of sequence organization of D. melanogaster heterochromatin, but how histone modifications are associated with heterochromatic sequences at high resolution has not been described. Here, distributions of modified histones in the vicinity of heterochromatic genes of normal embryos and embryos homozygous for a chromosome rearrangement were characterized using chromatin immunoprecipitation and genome tiling arrays. We found that H3-di-methylated-at-lysine 9 (H3K9me2) was depleted at the 5' ends but enriched throughout transcribed regions of heterochromatic genes. The profile was distinct from that of euchromatic genes and suggests that heterochromatic genes are integrated into, rather than insulated from, the H3K9me2-enriched domain. Moreover, the profile was only subtly affected by a Su(var)3-9 mutation, implicating a histone methyltransferase other than SU(VAR)3-9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos. On a chromosomal scale, we observed a sharp transition to the H3K9me2 domain, which coincided with increased retrotransposon density in the euchromatin-heterochromatin (eu-het) transition zones on the long chromosome arms. Thus, a certain density of retrotransposons, rather than specific boundary elements, may demarcate Drosophila pericentric heterochromatin. We also demonstrate that a chromosome rearrangement that created a new eu-het junction altered H3K9me2 distribution and induced new euchromatic sites of enrichment as far as several megabases away from the breakpoint. Taken together, the findings argue against simple classification of H3K9me as the definitive signature of silenced genes, and clarify roles of histone modifications and repetitive DNAs in heterochromatin. The results are also relevant for understanding the effects of chromosome aberrations and the megabase scale over which epigenetic position effects can operate in multicellular organisms.

Show MeSH
Related in: MedlinePlus