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

H3K9me2 Landscapes in the Euchromatin-Heterochromatin Transition Zones(A–C) H3K9me2-enrichment relative to the genomic DNA reference control in the chromosome arms 2L (A), 3L (B), and 2R (C). Each panel corresponds to approximately one-sixth of the assembled genome sequence located at the proximal base of the chromosome arm (Figure 2A). Raw data are shown in gray and moving average values of 50 adjacent probes are shown in black. The R5.1 genomic coordinates are shown on the x-axes. Open triangles note locations of the R5.1 heterochromatin sequence reference points which are reported in FlyBase and were designated as heterochromatic by Smith et al. [39] based on chromosomal fluorescent in situ hybridization localizations. The asterisks indicate euchromatic regions with high TE-density. The bracket in (A) marks the interval containing lt, cta, and Chitinase genes.(D–F) Expanded views of the transition zones whose locations are marked by the dashed lines in (A–C). In each panel, the H3K9me2-enrichment values (moving average of ten adjacent probes) are shown in upper diagram and distributions of TEs, and genes are shown below. Genes are depicted in two tiers to distinguish 5′ to 3′ orientations. Apparent overlap among TEs and between TEs and genes are due to nesting events. Locations of the CG3635, nrm, and CG11665 genes, which are located at the abrupt transitions to the enriched H3K9me2 domains at the base of 2L, 3L, or 2R respectively, are noted.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2211541&req=5

pgen-0040016-g006: H3K9me2 Landscapes in the Euchromatin-Heterochromatin Transition Zones(A–C) H3K9me2-enrichment relative to the genomic DNA reference control in the chromosome arms 2L (A), 3L (B), and 2R (C). Each panel corresponds to approximately one-sixth of the assembled genome sequence located at the proximal base of the chromosome arm (Figure 2A). Raw data are shown in gray and moving average values of 50 adjacent probes are shown in black. The R5.1 genomic coordinates are shown on the x-axes. Open triangles note locations of the R5.1 heterochromatin sequence reference points which are reported in FlyBase and were designated as heterochromatic by Smith et al. [39] based on chromosomal fluorescent in situ hybridization localizations. The asterisks indicate euchromatic regions with high TE-density. The bracket in (A) marks the interval containing lt, cta, and Chitinase genes.(D–F) Expanded views of the transition zones whose locations are marked by the dashed lines in (A–C). In each panel, the H3K9me2-enrichment values (moving average of ten adjacent probes) are shown in upper diagram and distributions of TEs, and genes are shown below. Genes are depicted in two tiers to distinguish 5′ to 3′ orientations. Apparent overlap among TEs and between TEs and genes are due to nesting events. Locations of the CG3635, nrm, and CG11665 genes, which are located at the abrupt transitions to the enriched H3K9me2 domains at the base of 2L, 3L, or 2R respectively, are noted.

Mentions: The H3K9me2 profile characteristic of the long autosomal arms differed markedly from that observed for Chromosome 4. In euchromatic regions, the profile was typically flat (Figures S3 and 6). However, within the eu-het transition zones on 2L, 2R, and 3L, a sharp transition was observed between low levels of H3K9me2 in distal regions to enriched domains more proximally (Figure 6). Sequence inspection did not reveal common underlying sequences at the transition point, or conspicuous features such as large inverted repeats or tRNA genes that characterize the boundary elements of yeast silent chromatin domains [12,42]. However, the transitions coincided with increased density of retrotransposons including LTR-type and LINE-like TEs (Figure 6D–6F).


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

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

H3K9me2 Landscapes in the Euchromatin-Heterochromatin Transition Zones(A–C) H3K9me2-enrichment relative to the genomic DNA reference control in the chromosome arms 2L (A), 3L (B), and 2R (C). Each panel corresponds to approximately one-sixth of the assembled genome sequence located at the proximal base of the chromosome arm (Figure 2A). Raw data are shown in gray and moving average values of 50 adjacent probes are shown in black. The R5.1 genomic coordinates are shown on the x-axes. Open triangles note locations of the R5.1 heterochromatin sequence reference points which are reported in FlyBase and were designated as heterochromatic by Smith et al. [39] based on chromosomal fluorescent in situ hybridization localizations. The asterisks indicate euchromatic regions with high TE-density. The bracket in (A) marks the interval containing lt, cta, and Chitinase genes.(D–F) Expanded views of the transition zones whose locations are marked by the dashed lines in (A–C). In each panel, the H3K9me2-enrichment values (moving average of ten adjacent probes) are shown in upper diagram and distributions of TEs, and genes are shown below. Genes are depicted in two tiers to distinguish 5′ to 3′ orientations. Apparent overlap among TEs and between TEs and genes are due to nesting events. Locations of the CG3635, nrm, and CG11665 genes, which are located at the abrupt transitions to the enriched H3K9me2 domains at the base of 2L, 3L, or 2R respectively, are noted.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0040016-g006: H3K9me2 Landscapes in the Euchromatin-Heterochromatin Transition Zones(A–C) H3K9me2-enrichment relative to the genomic DNA reference control in the chromosome arms 2L (A), 3L (B), and 2R (C). Each panel corresponds to approximately one-sixth of the assembled genome sequence located at the proximal base of the chromosome arm (Figure 2A). Raw data are shown in gray and moving average values of 50 adjacent probes are shown in black. The R5.1 genomic coordinates are shown on the x-axes. Open triangles note locations of the R5.1 heterochromatin sequence reference points which are reported in FlyBase and were designated as heterochromatic by Smith et al. [39] based on chromosomal fluorescent in situ hybridization localizations. The asterisks indicate euchromatic regions with high TE-density. The bracket in (A) marks the interval containing lt, cta, and Chitinase genes.(D–F) Expanded views of the transition zones whose locations are marked by the dashed lines in (A–C). In each panel, the H3K9me2-enrichment values (moving average of ten adjacent probes) are shown in upper diagram and distributions of TEs, and genes are shown below. Genes are depicted in two tiers to distinguish 5′ to 3′ orientations. Apparent overlap among TEs and between TEs and genes are due to nesting events. Locations of the CG3635, nrm, and CG11665 genes, which are located at the abrupt transitions to the enriched H3K9me2 domains at the base of 2L, 3L, or 2R respectively, are noted.
Mentions: The H3K9me2 profile characteristic of the long autosomal arms differed markedly from that observed for Chromosome 4. In euchromatic regions, the profile was typically flat (Figures S3 and 6). However, within the eu-het transition zones on 2L, 2R, and 3L, a sharp transition was observed between low levels of H3K9me2 in distal regions to enriched domains more proximally (Figure 6). Sequence inspection did not reveal common underlying sequences at the transition point, or conspicuous features such as large inverted repeats or tRNA genes that characterize the boundary elements of yeast silent chromatin domains [12,42]. However, the transitions coincided with increased density of retrotransposons including LTR-type and LINE-like TEs (Figure 6D–6F).

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