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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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Schematic View of D. melanogaster Major Autosomes, Chromosomes 2 and 3(A) The chromosomes of a wild-type strain showing location of heterochromatin (filled rectangles), euchromatin (open rectangles) on left (L) and right (R) arms, centromeres (circle), and regions (underlined) that were included in the tiling microarray. The triangles indicate the positions of the breakpoints in the T(2;3)ltx13 translocation.(B) Structure of the T(2;3)ltx13 translocation. Heterochromatin of 2L is denoted 2Lh.
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pgen-0040016-g002: Schematic View of D. melanogaster Major Autosomes, Chromosomes 2 and 3(A) The chromosomes of a wild-type strain showing location of heterochromatin (filled rectangles), euchromatin (open rectangles) on left (L) and right (R) arms, centromeres (circle), and regions (underlined) that were included in the tiling microarray. The triangles indicate the positions of the breakpoints in the T(2;3)ltx13 translocation.(B) Structure of the T(2;3)ltx13 translocation. Heterochromatin of 2L is denoted 2Lh.

Mentions: To obtain global perspectives of H3K9me2 and H3K9/14acet profiles in heterochromatin, we used a ChIP-chip approach. The genome tiling array contained probes for heterochromatic regions of the genome, as assembled and annotated in the D. melanogaster genome project Release 5.1 (R5.1) [39,40]. Specifically, we focused on the proximal ends of the assembled genome sequence corresponding to the euchromatin-heterochromatin (eu-het) transition zones and extending into distal heterochromatin of the long 2L, 2R and 3L chromosome arms (Figure 2A). We also included a segment of 3R distal euchromatin and the entire sequenced region of the small Chromosome 4 for comparisons among chromosomal regions. To circumvent the cross-hybridization problem of repetitive sequences, genome sequence was masked for annotated TEs and remaining sequences were used to design overlapping 50-mer oligonucleotides probes with 40 bp resolution. This probe set was subject to stringent filtering to eliminate repetitive sequences, and remaining probes were used for the microarray (Materials and Methods). Probe density necessarily varied across heterochromatin due to repeat filtering.


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

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

Schematic View of D. melanogaster Major Autosomes, Chromosomes 2 and 3(A) The chromosomes of a wild-type strain showing location of heterochromatin (filled rectangles), euchromatin (open rectangles) on left (L) and right (R) arms, centromeres (circle), and regions (underlined) that were included in the tiling microarray. The triangles indicate the positions of the breakpoints in the T(2;3)ltx13 translocation.(B) Structure of the T(2;3)ltx13 translocation. Heterochromatin of 2L is denoted 2Lh.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0040016-g002: Schematic View of D. melanogaster Major Autosomes, Chromosomes 2 and 3(A) The chromosomes of a wild-type strain showing location of heterochromatin (filled rectangles), euchromatin (open rectangles) on left (L) and right (R) arms, centromeres (circle), and regions (underlined) that were included in the tiling microarray. The triangles indicate the positions of the breakpoints in the T(2;3)ltx13 translocation.(B) Structure of the T(2;3)ltx13 translocation. Heterochromatin of 2L is denoted 2Lh.
Mentions: To obtain global perspectives of H3K9me2 and H3K9/14acet profiles in heterochromatin, we used a ChIP-chip approach. The genome tiling array contained probes for heterochromatic regions of the genome, as assembled and annotated in the D. melanogaster genome project Release 5.1 (R5.1) [39,40]. Specifically, we focused on the proximal ends of the assembled genome sequence corresponding to the euchromatin-heterochromatin (eu-het) transition zones and extending into distal heterochromatin of the long 2L, 2R and 3L chromosome arms (Figure 2A). We also included a segment of 3R distal euchromatin and the entire sequenced region of the small Chromosome 4 for comparisons among chromosomal regions. To circumvent the cross-hybridization problem of repetitive sequences, genome sequence was masked for annotated TEs and remaining sequences were used to design overlapping 50-mer oligonucleotides probes with 40 bp resolution. This probe set was subject to stringent filtering to eliminate repetitive sequences, and remaining probes were used for the microarray (Materials and Methods). Probe density necessarily varied across heterochromatin due to repeat filtering.

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