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ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.

Zentner GE, Tsukiyama T, Henikoff S - PLoS Genet. (2013)

Bottom Line: Although these remodelers act in gene bodies, we find that they are also highly enriched at nucleosome-depleted regions (NDRs), where they bind to extended regions of DNA adjacent to particular transcription factors.Surprisingly, catalytically inactive remodelers show similar binding patterns.We find that remodeler occupancy at NDRs and gene bodies is associated with nucleosome turnover and transcriptional elongation rate, suggesting that remodelers act on regions of transient nucleosome unwrapping or depletion within gene bodies subsequent to transcriptional elongation.

View Article: PubMed Central - PubMed

Affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

ABSTRACT
ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30-85 bp of extranucleosomal DNA to reposition nucleosomes, but linker DNA in S. cerevisiae averages <20 bp. To address this discrepancy between in vitro and in vivo observations, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution on native chromatin. Although these remodelers act in gene bodies, we find that they are also highly enriched at nucleosome-depleted regions (NDRs), where they bind to extended regions of DNA adjacent to particular transcription factors. Surprisingly, catalytically inactive remodelers show similar binding patterns. We find that remodeler occupancy at NDRs and gene bodies is associated with nucleosome turnover and transcriptional elongation rate, suggesting that remodelers act on regions of transient nucleosome unwrapping or depletion within gene bodies subsequent to transcriptional elongation.

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N-ChIP-seq localizes ISWI and CHD remodelers throughout the genome.(A) Size distributions of mapped paired-end 2.5′ and 10′ MNase-digested wild-type Isw1, Isw2, and Chd1 ChIP and input fragments. Slight variations in the amount of supernucleosomal (>251 bp) fragments are attributable to minor variation in the degree of MNase digestion for each sample, as evidenced by slight differences in the nucleosomal maxima for each sample. (B) Binding profiles for 10′ MNase-digested Isw1, Isw2, and Chd1 samples across a representative region of the genome. The number of paired-end reads overlapping each genomic position (counts/bp) is indicated on the Y-axis. See Figure S1 for additional remodeler binding profiles.
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pgen-1003317-g001: N-ChIP-seq localizes ISWI and CHD remodelers throughout the genome.(A) Size distributions of mapped paired-end 2.5′ and 10′ MNase-digested wild-type Isw1, Isw2, and Chd1 ChIP and input fragments. Slight variations in the amount of supernucleosomal (>251 bp) fragments are attributable to minor variation in the degree of MNase digestion for each sample, as evidenced by slight differences in the nucleosomal maxima for each sample. (B) Binding profiles for 10′ MNase-digested Isw1, Isw2, and Chd1 samples across a representative region of the genome. The number of paired-end reads overlapping each genomic position (counts/bp) is indicated on the Y-axis. See Figure S1 for additional remodeler binding profiles.

Mentions: ChIP and input samples were prepared for sequencing using a modified protocol that recovers fragments as small as ∼25 bp, enabling base-pair resolution mapping of remodeler occupancy [30]. Samples treated with MNase for 2.5′ displayed a nucleosomal peak centered at ∼170 bp, which was shifted to ∼160 bp in the 10′ samples (Figure 1A). Examination of these size distributions indicated that ChIP samples were enriched for supernucleosomal DNA fragments relative to nucleosomes. To assess this observation systematically, we determined the area under the curve for nucleosomal (141–250 bp) and supernucleosomal (251–428 bp) fragments from each sample. ChIP samples, regardless of factor, displayed supernucleosomal/nucleosomal ratios 1.74–3.87 (2.5′ MNase, P = 0.009) and 2.26–2.76 (10′ MNase, P = 0.002) times greater than that seen in input samples (Table S2), suggesting that Isw1, Isw2, and Chd1 participate in the protection of large stretches of DNA.


ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.

Zentner GE, Tsukiyama T, Henikoff S - PLoS Genet. (2013)

N-ChIP-seq localizes ISWI and CHD remodelers throughout the genome.(A) Size distributions of mapped paired-end 2.5′ and 10′ MNase-digested wild-type Isw1, Isw2, and Chd1 ChIP and input fragments. Slight variations in the amount of supernucleosomal (>251 bp) fragments are attributable to minor variation in the degree of MNase digestion for each sample, as evidenced by slight differences in the nucleosomal maxima for each sample. (B) Binding profiles for 10′ MNase-digested Isw1, Isw2, and Chd1 samples across a representative region of the genome. The number of paired-end reads overlapping each genomic position (counts/bp) is indicated on the Y-axis. See Figure S1 for additional remodeler binding profiles.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585014&req=5

pgen-1003317-g001: N-ChIP-seq localizes ISWI and CHD remodelers throughout the genome.(A) Size distributions of mapped paired-end 2.5′ and 10′ MNase-digested wild-type Isw1, Isw2, and Chd1 ChIP and input fragments. Slight variations in the amount of supernucleosomal (>251 bp) fragments are attributable to minor variation in the degree of MNase digestion for each sample, as evidenced by slight differences in the nucleosomal maxima for each sample. (B) Binding profiles for 10′ MNase-digested Isw1, Isw2, and Chd1 samples across a representative region of the genome. The number of paired-end reads overlapping each genomic position (counts/bp) is indicated on the Y-axis. See Figure S1 for additional remodeler binding profiles.
Mentions: ChIP and input samples were prepared for sequencing using a modified protocol that recovers fragments as small as ∼25 bp, enabling base-pair resolution mapping of remodeler occupancy [30]. Samples treated with MNase for 2.5′ displayed a nucleosomal peak centered at ∼170 bp, which was shifted to ∼160 bp in the 10′ samples (Figure 1A). Examination of these size distributions indicated that ChIP samples were enriched for supernucleosomal DNA fragments relative to nucleosomes. To assess this observation systematically, we determined the area under the curve for nucleosomal (141–250 bp) and supernucleosomal (251–428 bp) fragments from each sample. ChIP samples, regardless of factor, displayed supernucleosomal/nucleosomal ratios 1.74–3.87 (2.5′ MNase, P = 0.009) and 2.26–2.76 (10′ MNase, P = 0.002) times greater than that seen in input samples (Table S2), suggesting that Isw1, Isw2, and Chd1 participate in the protection of large stretches of DNA.

Bottom Line: Although these remodelers act in gene bodies, we find that they are also highly enriched at nucleosome-depleted regions (NDRs), where they bind to extended regions of DNA adjacent to particular transcription factors.Surprisingly, catalytically inactive remodelers show similar binding patterns.We find that remodeler occupancy at NDRs and gene bodies is associated with nucleosome turnover and transcriptional elongation rate, suggesting that remodelers act on regions of transient nucleosome unwrapping or depletion within gene bodies subsequent to transcriptional elongation.

View Article: PubMed Central - PubMed

Affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

ABSTRACT
ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30-85 bp of extranucleosomal DNA to reposition nucleosomes, but linker DNA in S. cerevisiae averages <20 bp. To address this discrepancy between in vitro and in vivo observations, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution on native chromatin. Although these remodelers act in gene bodies, we find that they are also highly enriched at nucleosome-depleted regions (NDRs), where they bind to extended regions of DNA adjacent to particular transcription factors. Surprisingly, catalytically inactive remodelers show similar binding patterns. We find that remodeler occupancy at NDRs and gene bodies is associated with nucleosome turnover and transcriptional elongation rate, suggesting that remodelers act on regions of transient nucleosome unwrapping or depletion within gene bodies subsequent to transcriptional elongation.

Show MeSH
Related in: MedlinePlus