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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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High-Resolution HP1-Binding Profiles(A and B) Maps of Chromosome 2, (C) Chromosome 4, (D) pericentric light gene, (E) pericentric concertina gene, and (F) cytological region 31. Inset in (A) shows a more detailed view of the centromere-proximal 0.4 Mb of 2L. Each stick represents the mean HP1–Dam/Dam binding ratio of a single GATC fragment, for one representative experiment. Fragments significantly bound by HP1 are marked in red, fragments not significantly bound by HP1 are shown in black. Gaps originate from nonunique sequences for which binding cannot reliably be determined. Positions of genes (open rectangles) and TEs (gray rectangles) are shown in D–F. Arrows in (D) and (E) indicate orientation of the genes.
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pgen-0030038-g001: High-Resolution HP1-Binding Profiles(A and B) Maps of Chromosome 2, (C) Chromosome 4, (D) pericentric light gene, (E) pericentric concertina gene, and (F) cytological region 31. Inset in (A) shows a more detailed view of the centromere-proximal 0.4 Mb of 2L. Each stick represents the mean HP1–Dam/Dam binding ratio of a single GATC fragment, for one representative experiment. Fragments significantly bound by HP1 are marked in red, fragments not significantly bound by HP1 are shown in black. Gaps originate from nonunique sequences for which binding cannot reliably be determined. Positions of genes (open rectangles) and TEs (gray rectangles) are shown in D–F. Arrows in (D) and (E) indicate orientation of the genes.

Mentions: We defined HP1 target loci by using an error model specifically designed for DamID on high-density oligonucleotide arrays (see Materials and Methods). This error model takes into account that Dam only methylates adenines in the sequence GATC, and that, therefore, DNA fragments demarcated by two GATC motifs represent the smallest units in the DamID mapping technique. Using this error model, 9,565 out of 94,202 fragments (~10%) are significantly bound by HP1. We generated maps to visualize the HP1-binding profile on Chromosomes 2 and 4 (Figure 1A–1C). These maps show abundant presence of HP1 in the pericentric regions of Chromosome 2 (Figure 1A and 1B) and on Chromosome 4 (Figure 1C), which is consistent with our earlier low-resolution maps [13,14] and immunofluorescence microscopy data [10,11]. More detailed inspection shows that HP1 on Chromosome 4 covers large domains that are approximately 10–100 kb in size, interrupted by regions not bound by HP1 (Figure 1C). The pericentric region of Chromosome 2 also shows variable levels of HP1 signal, but no discrete domains are visible as observed on Chromosome 4. Instead, binding occurs mostly in one large uninterrupted patch (Figure 1A, insert). In contrast, target sites along the chromosome arms are more focal and span usually only single genes (see below).


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

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

High-Resolution HP1-Binding Profiles(A and B) Maps of Chromosome 2, (C) Chromosome 4, (D) pericentric light gene, (E) pericentric concertina gene, and (F) cytological region 31. Inset in (A) shows a more detailed view of the centromere-proximal 0.4 Mb of 2L. Each stick represents the mean HP1–Dam/Dam binding ratio of a single GATC fragment, for one representative experiment. Fragments significantly bound by HP1 are marked in red, fragments not significantly bound by HP1 are shown in black. Gaps originate from nonunique sequences for which binding cannot reliably be determined. Positions of genes (open rectangles) and TEs (gray rectangles) are shown in D–F. Arrows in (D) and (E) indicate orientation of the genes.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-0030038-g001: High-Resolution HP1-Binding Profiles(A and B) Maps of Chromosome 2, (C) Chromosome 4, (D) pericentric light gene, (E) pericentric concertina gene, and (F) cytological region 31. Inset in (A) shows a more detailed view of the centromere-proximal 0.4 Mb of 2L. Each stick represents the mean HP1–Dam/Dam binding ratio of a single GATC fragment, for one representative experiment. Fragments significantly bound by HP1 are marked in red, fragments not significantly bound by HP1 are shown in black. Gaps originate from nonunique sequences for which binding cannot reliably be determined. Positions of genes (open rectangles) and TEs (gray rectangles) are shown in D–F. Arrows in (D) and (E) indicate orientation of the genes.
Mentions: We defined HP1 target loci by using an error model specifically designed for DamID on high-density oligonucleotide arrays (see Materials and Methods). This error model takes into account that Dam only methylates adenines in the sequence GATC, and that, therefore, DNA fragments demarcated by two GATC motifs represent the smallest units in the DamID mapping technique. Using this error model, 9,565 out of 94,202 fragments (~10%) are significantly bound by HP1. We generated maps to visualize the HP1-binding profile on Chromosomes 2 and 4 (Figure 1A–1C). These maps show abundant presence of HP1 in the pericentric regions of Chromosome 2 (Figure 1A and 1B) and on Chromosome 4 (Figure 1C), which is consistent with our earlier low-resolution maps [13,14] and immunofluorescence microscopy data [10,11]. More detailed inspection shows that HP1 on Chromosome 4 covers large domains that are approximately 10–100 kb in size, interrupted by regions not bound by HP1 (Figure 1C). The pericentric region of Chromosome 2 also shows variable levels of HP1 signal, but no discrete domains are visible as observed on Chromosome 4. Instead, binding occurs mostly in one large uninterrupted patch (Figure 1A, insert). In contrast, target sites along the chromosome arms are more focal and span usually only single genes (see below).

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