Limits...
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.

Show MeSH

Related in: MedlinePlus

Modified-Histone Profiles of Heterochromatic Genes as Revealed by ChIP-chip Assays(A) Each panel shows a single gene with profiles of H3K9/14acet-enrichment (top, blue), H3K9me2-enrichment (middle, brown), and gene structure depicted in 5′ → 3′ orientation (bottom, black). Scale bar (line in upper right) is 1 kb.(B) Each graph shows the average H3K9/14acet (blue, right y-axis) and H3K9me2 (brown, left y-axis) profiles of genes located in either in heterochromatin, Chromosome 4, or euchromatin of 3R, with n indicating number of genes in each class. To facilitate the analysis of euchromatic genes, only genes on the plus strand in a 3 Mb region of Chromosome 3R (coordinate 22.5–25.5Mb) were included. Gene sequences were aligned at the annotated 5′-ends (0 on the x-axis), broken into 100 bp windows, and the enrichment factors for all probes included in each window were averaged and plotted.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2211541&req=5

pgen-0040016-g004: Modified-Histone Profiles of Heterochromatic Genes as Revealed by ChIP-chip Assays(A) Each panel shows a single gene with profiles of H3K9/14acet-enrichment (top, blue), H3K9me2-enrichment (middle, brown), and gene structure depicted in 5′ → 3′ orientation (bottom, black). Scale bar (line in upper right) is 1 kb.(B) Each graph shows the average H3K9/14acet (blue, right y-axis) and H3K9me2 (brown, left y-axis) profiles of genes located in either in heterochromatin, Chromosome 4, or euchromatin of 3R, with n indicating number of genes in each class. To facilitate the analysis of euchromatic genes, only genes on the plus strand in a 3 Mb region of Chromosome 3R (coordinate 22.5–25.5Mb) were included. Gene sequences were aligned at the annotated 5′-ends (0 on the x-axis), broken into 100 bp windows, and the enrichment factors for all probes included in each window were averaged and plotted.

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 Heterochromatic Genes as Revealed by ChIP-chip Assays(A) Each panel shows a single gene with profiles of H3K9/14acet-enrichment (top, blue), H3K9me2-enrichment (middle, brown), and gene structure depicted in 5′ → 3′ orientation (bottom, black). Scale bar (line in upper right) is 1 kb.(B) Each graph shows the average H3K9/14acet (blue, right y-axis) and H3K9me2 (brown, left y-axis) profiles of genes located in either in heterochromatin, Chromosome 4, or euchromatin of 3R, with n indicating number of genes in each class. To facilitate the analysis of euchromatic genes, only genes on the plus strand in a 3 Mb region of Chromosome 3R (coordinate 22.5–25.5Mb) were included. Gene sequences were aligned at the annotated 5′-ends (0 on the x-axis), broken into 100 bp windows, and the enrichment factors for all probes included in each window were averaged and plotted.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0040016-g004: Modified-Histone Profiles of Heterochromatic Genes as Revealed by ChIP-chip Assays(A) Each panel shows a single gene with profiles of H3K9/14acet-enrichment (top, blue), H3K9me2-enrichment (middle, brown), and gene structure depicted in 5′ → 3′ orientation (bottom, black). Scale bar (line in upper right) is 1 kb.(B) Each graph shows the average H3K9/14acet (blue, right y-axis) and H3K9me2 (brown, left y-axis) profiles of genes located in either in heterochromatin, Chromosome 4, or euchromatin of 3R, with n indicating number of genes in each class. To facilitate the analysis of euchromatic genes, only genes on the plus strand in a 3 Mb region of Chromosome 3R (coordinate 22.5–25.5Mb) were included. Gene sequences were aligned at the annotated 5′-ends (0 on the x-axis), broken into 100 bp windows, and the enrichment factors for all probes included in each window were averaged and plotted.
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