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High-resolution mapping reveals links of HP1 with active and inactive chromatin components.

de Wit E, Greil F, van Steensel B - PLoS Genet. (2007)

Bottom Line: Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin.Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin.These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.

ABSTRACT
Heterochromatin protein 1 (HP1) is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID) technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5' regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2), which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5' ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

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HP1 Binding to Individual Transposon Copies(A) Frequencies of copies of the different TE types that are target of HP1 (dark gray) in nonpericentric (top) and repeat-rich pericentric (bottom) regions. A TE copy was counted as an HP1 target if, in the unique flanking 1 kb on each side of the TE, at least one GATC fragment was significantly bound by HP1.(B) HP1-Dam/Dam–binding ratios at unique sequences within 1 kb of a TE are plotted as a function of the FRI20kb (see main text). Running mean with window size 20 is shown for HP1 binding as a function of the FRI20kb (red line).
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pgen-0030038-g006: HP1 Binding to Individual Transposon Copies(A) Frequencies of copies of the different TE types that are target of HP1 (dark gray) in nonpericentric (top) and repeat-rich pericentric (bottom) regions. A TE copy was counted as an HP1 target if, in the unique flanking 1 kb on each side of the TE, at least one GATC fragment was significantly bound by HP1.(B) HP1-Dam/Dam–binding ratios at unique sequences within 1 kb of a TE are plotted as a function of the FRI20kb (see main text). Running mean with window size 20 is shown for HP1 binding as a function of the FRI20kb (red line).

Mentions: Intergenic sequences in pericentric regions show extensive binding of HP1. Because these regions are rich in TEs, and because many TEs bind HP1 [13,14], we reasoned that TEs may provide important nucleation sites for pericentric heterochromatin. Microarray studies of repetitive sequences such as TEs are complicated by the fact that probes with homology to repeats cannot discern between individual repeat copies and thus only provide population averages. To obtain an estimate of HP1 binding to individual TE copies, we took advantage of the fact that methylation by tethered Dam spreads in cis over about 1–2 kb [47,52] and analyzed the level of targeted methylation detected at unique sequences within 1 kb from each TE integration site. These data indicate that the majority of TE copies in pericentric regions are bound by HP1. Strikingly, nearly all TE copies that have an FRI20kb higher than 0.4 have elevated HP1 (log2-ratios >1, Figure 6B). While this is much less frequently the case for TE copies in nonpericentric regions (Figure 6A).


High-resolution mapping reveals links of HP1 with active and inactive chromatin components.

de Wit E, Greil F, van Steensel B - PLoS Genet. (2007)

HP1 Binding to Individual Transposon Copies(A) Frequencies of copies of the different TE types that are target of HP1 (dark gray) in nonpericentric (top) and repeat-rich pericentric (bottom) regions. A TE copy was counted as an HP1 target if, in the unique flanking 1 kb on each side of the TE, at least one GATC fragment was significantly bound by HP1.(B) HP1-Dam/Dam–binding ratios at unique sequences within 1 kb of a TE are plotted as a function of the FRI20kb (see main text). Running mean with window size 20 is shown for HP1 binding as a function of the FRI20kb (red line).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1808074&req=5

pgen-0030038-g006: HP1 Binding to Individual Transposon Copies(A) Frequencies of copies of the different TE types that are target of HP1 (dark gray) in nonpericentric (top) and repeat-rich pericentric (bottom) regions. A TE copy was counted as an HP1 target if, in the unique flanking 1 kb on each side of the TE, at least one GATC fragment was significantly bound by HP1.(B) HP1-Dam/Dam–binding ratios at unique sequences within 1 kb of a TE are plotted as a function of the FRI20kb (see main text). Running mean with window size 20 is shown for HP1 binding as a function of the FRI20kb (red line).
Mentions: Intergenic sequences in pericentric regions show extensive binding of HP1. Because these regions are rich in TEs, and because many TEs bind HP1 [13,14], we reasoned that TEs may provide important nucleation sites for pericentric heterochromatin. Microarray studies of repetitive sequences such as TEs are complicated by the fact that probes with homology to repeats cannot discern between individual repeat copies and thus only provide population averages. To obtain an estimate of HP1 binding to individual TE copies, we took advantage of the fact that methylation by tethered Dam spreads in cis over about 1–2 kb [47,52] and analyzed the level of targeted methylation detected at unique sequences within 1 kb from each TE integration site. These data indicate that the majority of TE copies in pericentric regions are bound by HP1. Strikingly, nearly all TE copies that have an FRI20kb higher than 0.4 have elevated HP1 (log2-ratios >1, Figure 6B). While this is much less frequently the case for TE copies in nonpericentric regions (Figure 6A).

Bottom Line: Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin.Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin.These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.

ABSTRACT
Heterochromatin protein 1 (HP1) is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID) technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5' regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2), which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5' ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

Show MeSH
Related in: MedlinePlus