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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 Is Linked to H3K4me2 and Histone H3.3 PatternsAlignment of HP1-bound genes to (A) their TSSs and (B) the 3′ end of their transcription units. TSS-aligned genes include upstream regions up until the next upstream gene; 3′ end aligned genes include downstream regions until the next downstream gene. Curves show running mean (window size 100) of HP1-binding ratios (log2) for nonpericentric (green) and pericentric target genes (blue). (C) H3K4me2 levels of TSS-aligned genes in nonpericentric regions with high (red) or low (black) levels of HP1 as defined in Figure 2. H3K4me2 levels were taken from Schubeler et al. [53]. (D) Frequency distribution of H3K4me2 levels around the TSS (−500 to +1000 bp) for genes with high (black line) and low (gray lines) HP1 levels, either all genes (dotted gray line) or expression matched (solid gray line). (E and F) TSS alignment of H3.3 levels for genes with high (red) and low (black) HP1 levels in nonpericentric (E) and pericentric (F) regions. H3.3 data were taken from Mito et al. [51]. In (C), (E), and (F) running mean window sizes correspond to 2% of the total number of datapoints.
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pgen-0030038-g004: HP1 Binding Is Linked to H3K4me2 and Histone H3.3 PatternsAlignment of HP1-bound genes to (A) their TSSs and (B) the 3′ end of their transcription units. TSS-aligned genes include upstream regions up until the next upstream gene; 3′ end aligned genes include downstream regions until the next downstream gene. Curves show running mean (window size 100) of HP1-binding ratios (log2) for nonpericentric (green) and pericentric target genes (blue). (C) H3K4me2 levels of TSS-aligned genes in nonpericentric regions with high (red) or low (black) levels of HP1 as defined in Figure 2. H3K4me2 levels were taken from Schubeler et al. [53]. (D) Frequency distribution of H3K4me2 levels around the TSS (−500 to +1000 bp) for genes with high (black line) and low (gray lines) HP1 levels, either all genes (dotted gray line) or expression matched (solid gray line). (E and F) TSS alignment of H3.3 levels for genes with high (red) and low (black) HP1 levels in nonpericentric (E) and pericentric (F) regions. H3.3 data were taken from Mito et al. [51]. In (C), (E), and (F) running mean window sizes correspond to 2% of the total number of datapoints.

Mentions: In order to elucidate the detailed distribution of HP1 in and around genes, we aligned all high-HP1 genes by their transcriptional start site (TSS) or by their 3′ ends and plotted a running mean of the HP1-binding log-ratios along the genes (Figure 4A and 4B). Again, we performed this analysis separately for pericentric and nonpericentric genes. This revealed that upstream of nonpericentric genes very little HP1 is bound. Within the genes, binding is low at the TSS and increases gradually until 1–2 kb into the gene, after which average HP1 levels reach a plateau that extends for the remainder of the gene (Figure 4A). Downstream of the 3′ ends the HP1 levels gradually decline (Figure 4B). Thus, in nonpericentric regions, HP1 is primarily associated with transcription units except for the first 1–2 kb. This pattern is qualitatively independent of the average binding level of HP1 along the entire gene (Figure S1A and S1B). Pericentric genes show a similar distribution pattern, but have much higher baseline levels of HP1 outside the transcription units. We also observed this pattern when we specifically analyzed genes on Chromosome 4 (data not shown). Taken together, HP1 shows characteristic binding patterns along genes that differ between pericentric and nonpericentric regions.


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 Is Linked to H3K4me2 and Histone H3.3 PatternsAlignment of HP1-bound genes to (A) their TSSs and (B) the 3′ end of their transcription units. TSS-aligned genes include upstream regions up until the next upstream gene; 3′ end aligned genes include downstream regions until the next downstream gene. Curves show running mean (window size 100) of HP1-binding ratios (log2) for nonpericentric (green) and pericentric target genes (blue). (C) H3K4me2 levels of TSS-aligned genes in nonpericentric regions with high (red) or low (black) levels of HP1 as defined in Figure 2. H3K4me2 levels were taken from Schubeler et al. [53]. (D) Frequency distribution of H3K4me2 levels around the TSS (−500 to +1000 bp) for genes with high (black line) and low (gray lines) HP1 levels, either all genes (dotted gray line) or expression matched (solid gray line). (E and F) TSS alignment of H3.3 levels for genes with high (red) and low (black) HP1 levels in nonpericentric (E) and pericentric (F) regions. H3.3 data were taken from Mito et al. [51]. In (C), (E), and (F) running mean window sizes correspond to 2% of the total number of datapoints.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0030038-g004: HP1 Binding Is Linked to H3K4me2 and Histone H3.3 PatternsAlignment of HP1-bound genes to (A) their TSSs and (B) the 3′ end of their transcription units. TSS-aligned genes include upstream regions up until the next upstream gene; 3′ end aligned genes include downstream regions until the next downstream gene. Curves show running mean (window size 100) of HP1-binding ratios (log2) for nonpericentric (green) and pericentric target genes (blue). (C) H3K4me2 levels of TSS-aligned genes in nonpericentric regions with high (red) or low (black) levels of HP1 as defined in Figure 2. H3K4me2 levels were taken from Schubeler et al. [53]. (D) Frequency distribution of H3K4me2 levels around the TSS (−500 to +1000 bp) for genes with high (black line) and low (gray lines) HP1 levels, either all genes (dotted gray line) or expression matched (solid gray line). (E and F) TSS alignment of H3.3 levels for genes with high (red) and low (black) HP1 levels in nonpericentric (E) and pericentric (F) regions. H3.3 data were taken from Mito et al. [51]. In (C), (E), and (F) running mean window sizes correspond to 2% of the total number of datapoints.
Mentions: In order to elucidate the detailed distribution of HP1 in and around genes, we aligned all high-HP1 genes by their transcriptional start site (TSS) or by their 3′ ends and plotted a running mean of the HP1-binding log-ratios along the genes (Figure 4A and 4B). Again, we performed this analysis separately for pericentric and nonpericentric genes. This revealed that upstream of nonpericentric genes very little HP1 is bound. Within the genes, binding is low at the TSS and increases gradually until 1–2 kb into the gene, after which average HP1 levels reach a plateau that extends for the remainder of the gene (Figure 4A). Downstream of the 3′ ends the HP1 levels gradually decline (Figure 4B). Thus, in nonpericentric regions, HP1 is primarily associated with transcription units except for the first 1–2 kb. This pattern is qualitatively independent of the average binding level of HP1 along the entire gene (Figure S1A and S1B). Pericentric genes show a similar distribution pattern, but have much higher baseline levels of HP1 outside the transcription units. We also observed this pattern when we specifically analyzed genes on Chromosome 4 (data not shown). Taken together, HP1 shows characteristic binding patterns along genes that differ between pericentric and nonpericentric regions.

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