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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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ISWI and CHD remodelers associate with TFBSs.(A) V-plots of wild-type Isw1 ChIP and soluble input chromatin at binding sites for the Abf1 TF after 2.5′ and 10′ MNase digestion. Flanking nucleosomes are visualized as well-defined dot clusters on either side of the TFBS. Example fragments contributing to the generation of various V-plot features are shown schematically below each plot. Cyan arrows point to the position of each fragment midpoint within the V-plot. Similar results were seen for wild-type Isw2 and Chd1 at Abf1 sites and for Isw1, Isw2, and Chd1 at Cbf1, Mbp1, and Reb1 binding sites (Figures S3 and S4). (B) Interpretive schematic of V-plot results. DBPs; DNA-binding proteins.
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pgen-1003317-g004: ISWI and CHD remodelers associate with TFBSs.(A) V-plots of wild-type Isw1 ChIP and soluble input chromatin at binding sites for the Abf1 TF after 2.5′ and 10′ MNase digestion. Flanking nucleosomes are visualized as well-defined dot clusters on either side of the TFBS. Example fragments contributing to the generation of various V-plot features are shown schematically below each plot. Cyan arrows point to the position of each fragment midpoint within the V-plot. Similar results were seen for wild-type Isw2 and Chd1 at Abf1 sites and for Isw1, Isw2, and Chd1 at Cbf1, Mbp1, and Reb1 binding sites (Figures S3 and S4). (B) Interpretive schematic of V-plot results. DBPs; DNA-binding proteins.

Mentions: Previous work has demonstrated that sequence-specific TFs induce nucleosome depletion upon binding [36]–[41], presumably by exposing stretches of linker DNA. We therefore hypothesized that the enrichment of supernucleosomal DNA fragments in ChIP samples might reflect remodeler association with the extended linker DNA flanking binding sites for nucleosome-phasing TFs. We assessed transcription factor binding site (TFBS) occupancy of Isw1, Isw2, and Chd1 using V-plotting. We first analyzed remodeler occupancy at binding sites for the Abf1 TF. Consistent with our previous data [30], well-phased flanking nucleosomes were observed at Abf1 sites as discrete dot clusters to either side of the TFBS (Figure 4A and Figure S2A).


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

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

ISWI and CHD remodelers associate with TFBSs.(A) V-plots of wild-type Isw1 ChIP and soluble input chromatin at binding sites for the Abf1 TF after 2.5′ and 10′ MNase digestion. Flanking nucleosomes are visualized as well-defined dot clusters on either side of the TFBS. Example fragments contributing to the generation of various V-plot features are shown schematically below each plot. Cyan arrows point to the position of each fragment midpoint within the V-plot. Similar results were seen for wild-type Isw2 and Chd1 at Abf1 sites and for Isw1, Isw2, and Chd1 at Cbf1, Mbp1, and Reb1 binding sites (Figures S3 and S4). (B) Interpretive schematic of V-plot results. DBPs; DNA-binding proteins.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003317-g004: ISWI and CHD remodelers associate with TFBSs.(A) V-plots of wild-type Isw1 ChIP and soluble input chromatin at binding sites for the Abf1 TF after 2.5′ and 10′ MNase digestion. Flanking nucleosomes are visualized as well-defined dot clusters on either side of the TFBS. Example fragments contributing to the generation of various V-plot features are shown schematically below each plot. Cyan arrows point to the position of each fragment midpoint within the V-plot. Similar results were seen for wild-type Isw2 and Chd1 at Abf1 sites and for Isw1, Isw2, and Chd1 at Cbf1, Mbp1, and Reb1 binding sites (Figures S3 and S4). (B) Interpretive schematic of V-plot results. DBPs; DNA-binding proteins.
Mentions: Previous work has demonstrated that sequence-specific TFs induce nucleosome depletion upon binding [36]–[41], presumably by exposing stretches of linker DNA. We therefore hypothesized that the enrichment of supernucleosomal DNA fragments in ChIP samples might reflect remodeler association with the extended linker DNA flanking binding sites for nucleosome-phasing TFs. We assessed transcription factor binding site (TFBS) occupancy of Isw1, Isw2, and Chd1 using V-plotting. We first analyzed remodeler occupancy at binding sites for the Abf1 TF. Consistent with our previous data [30], well-phased flanking nucleosomes were observed at Abf1 sites as discrete dot clusters to either side of the TFBS (Figure 4A and Figure S2A).

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