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

Comparison of H3K9me2 Profiles in Wild-type and Su(var)3–906 Embryos(A) The bar graph compares the H3K9me2 enrichment factors in the light gene of y; cn bw sp (black) and Su(var)3–906 (red) embryos based on three and two trials, respectively. Symbols are the same as in Figure 1.(B) Comparison of the average H3K9me2 profile of heterochromatic genes (n = 63), Chromosome 4 genes (n = 72), and euchromatic genes (n = 105) in the two genotypes, plotted as described for Figure 4B.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2211541&req=5

pgen-0040016-g005: Comparison of H3K9me2 Profiles in Wild-type and Su(var)3–906 Embryos(A) The bar graph compares the H3K9me2 enrichment factors in the light gene of y; cn bw sp (black) and Su(var)3–906 (red) embryos based on three and two trials, respectively. Symbols are the same as in Figure 1.(B) Comparison of the average H3K9me2 profile of heterochromatic genes (n = 63), Chromosome 4 genes (n = 72), and euchromatic genes (n = 105) in the two genotypes, plotted as described for Figure 4B.

Mentions: To determine if the SU(VAR)3–9 HMTase was responsible for the H3K9me2 enrichment in and around heterochromatic genes, we examined the effects of a mutation Su(var)3–906 [24]. The ChIP assay revealed small but reproducible differences between the wild type and homozygous Su(var)3–906 in the relative levels of H3K9me2 across the lt gene (Figure 5A). To further investigate this effect, we performed two separate ChIP-chip hybridization comparisons of wild type and Su(var)3–906 embryos. We found that the landscape of H3K9/K14acet and H3K9me2 across 2Lh (Figure 3) and other heterochromatic regions (data not shown) appeared overall similar in the two genotypes. However, in the mutant embryos, the average profile of heterochromatic genes showed a slightly elevated level of H3K9me2 just upstream of the start site relative to the level observed within the transcribed region (Figure 5B). The average profile across euchromatic genes was not detectably altered in the mutant. A striking difference between the two genotypes was evident from examining H3K9me2 distribution on Chromosome 4. Relative to wild type embryos, Su(var)3–906 embryos showed a higher average level of H3K9me2 within Chromosome 4 genes and more pronounced regional increases along the length of the chromosome (Figure S3). This unexpected observation of localized increases, rather than reductions of H3K9me2 associated with Su(var)3–906 indicates that in embryos, SU(VAR)3–9 is not responsible for the majority of H3K9me2 in the regions we assayed here, but it apparently influences one or more HMTases that play more prominent roles.


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

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

Comparison of H3K9me2 Profiles in Wild-type and Su(var)3–906 Embryos(A) The bar graph compares the H3K9me2 enrichment factors in the light gene of y; cn bw sp (black) and Su(var)3–906 (red) embryos based on three and two trials, respectively. Symbols are the same as in Figure 1.(B) Comparison of the average H3K9me2 profile of heterochromatic genes (n = 63), Chromosome 4 genes (n = 72), and euchromatic genes (n = 105) in the two genotypes, plotted as described for Figure 4B.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0040016-g005: Comparison of H3K9me2 Profiles in Wild-type and Su(var)3–906 Embryos(A) The bar graph compares the H3K9me2 enrichment factors in the light gene of y; cn bw sp (black) and Su(var)3–906 (red) embryos based on three and two trials, respectively. Symbols are the same as in Figure 1.(B) Comparison of the average H3K9me2 profile of heterochromatic genes (n = 63), Chromosome 4 genes (n = 72), and euchromatic genes (n = 105) in the two genotypes, plotted as described for Figure 4B.
Mentions: To determine if the SU(VAR)3–9 HMTase was responsible for the H3K9me2 enrichment in and around heterochromatic genes, we examined the effects of a mutation Su(var)3–906 [24]. The ChIP assay revealed small but reproducible differences between the wild type and homozygous Su(var)3–906 in the relative levels of H3K9me2 across the lt gene (Figure 5A). To further investigate this effect, we performed two separate ChIP-chip hybridization comparisons of wild type and Su(var)3–906 embryos. We found that the landscape of H3K9/K14acet and H3K9me2 across 2Lh (Figure 3) and other heterochromatic regions (data not shown) appeared overall similar in the two genotypes. However, in the mutant embryos, the average profile of heterochromatic genes showed a slightly elevated level of H3K9me2 just upstream of the start site relative to the level observed within the transcribed region (Figure 5B). The average profile across euchromatic genes was not detectably altered in the mutant. A striking difference between the two genotypes was evident from examining H3K9me2 distribution on Chromosome 4. Relative to wild type embryos, Su(var)3–906 embryos showed a higher average level of H3K9me2 within Chromosome 4 genes and more pronounced regional increases along the length of the chromosome (Figure S3). This unexpected observation of localized increases, rather than reductions of H3K9me2 associated with Su(var)3–906 indicates that in embryos, SU(VAR)3–9 is not responsible for the majority of H3K9me2 in the regions we assayed here, but it apparently influences one or more HMTases that play more prominent roles.

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