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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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Isw2 associates with centromeres.(A) Aggregate plot of Isw1, Isw2, and Chd1 ChIP/input signal at all 16 yeast centromeres. (B) V-plot of Isw2 ChIP data for all 16 yeast centromeres showing enrichment of Isw2 to the CDEIII side of centromeres. (C) Sequence logo of all 16 yeast centromeres spanning 400 bp centered on the centromere midpoint. A+T are represented as red and G+C are represented as blue, demonstrating the high A+T content of centromeres. The binding of Isw2 to centromeres is thus consistent with its preference for association with regions of high A+T content. The sequence logo was generated with WebLogo (http://weblogo.berkeley.edu).
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pgen-1003317-g003: Isw2 associates with centromeres.(A) Aggregate plot of Isw1, Isw2, and Chd1 ChIP/input signal at all 16 yeast centromeres. (B) V-plot of Isw2 ChIP data for all 16 yeast centromeres showing enrichment of Isw2 to the CDEIII side of centromeres. (C) Sequence logo of all 16 yeast centromeres spanning 400 bp centered on the centromere midpoint. A+T are represented as red and G+C are represented as blue, demonstrating the high A+T content of centromeres. The binding of Isw2 to centromeres is thus consistent with its preference for association with regions of high A+T content. The sequence logo was generated with WebLogo (http://weblogo.berkeley.edu).

Mentions: The enrichment of Isw2 at the chromosome III centromere led us to investigate Isw2 centromeric association in more detail. Aggregate analysis of remodeler signal at all 16 yeast centromeres revealed robust enrichment of Isw2, but not Isw1 or Chd1 (Figure 3A). To precisely delineate the regions of the centromere bound by Isw2, we employed V-plotting [30]. In a V-plot, the midpoint of each paired-end fragment is assigned a dot in two-dimensional space, wherein the X-axis value is the distance of the fragment midpoint from a defined genomic feature and the Y-axis value is the length of the fragment. V-plotting of Isw2 ChIP and input data revealed striking enrichment of Isw2 to the right of centromere midpoints, over the CDEII and CDEIII regions (Figure 3B). Analysis of centromeric sequence composition confirmed the A+T rich nature of yeast centromeres, further supporting the preference of Isw2 for A+T rich DNA (Figure 3C). The association of Isw2 with centromeres is consistent with previous X-ChIP results showing association of Isw2 with two yeast centromeres [33] as well as studies demonstrating a role for Isw2 in pericentromeric nucleosome dynamics [34] and centromeric association of the human ISWI-containing RSF complex [35].


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

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

Isw2 associates with centromeres.(A) Aggregate plot of Isw1, Isw2, and Chd1 ChIP/input signal at all 16 yeast centromeres. (B) V-plot of Isw2 ChIP data for all 16 yeast centromeres showing enrichment of Isw2 to the CDEIII side of centromeres. (C) Sequence logo of all 16 yeast centromeres spanning 400 bp centered on the centromere midpoint. A+T are represented as red and G+C are represented as blue, demonstrating the high A+T content of centromeres. The binding of Isw2 to centromeres is thus consistent with its preference for association with regions of high A+T content. The sequence logo was generated with WebLogo (http://weblogo.berkeley.edu).
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003317-g003: Isw2 associates with centromeres.(A) Aggregate plot of Isw1, Isw2, and Chd1 ChIP/input signal at all 16 yeast centromeres. (B) V-plot of Isw2 ChIP data for all 16 yeast centromeres showing enrichment of Isw2 to the CDEIII side of centromeres. (C) Sequence logo of all 16 yeast centromeres spanning 400 bp centered on the centromere midpoint. A+T are represented as red and G+C are represented as blue, demonstrating the high A+T content of centromeres. The binding of Isw2 to centromeres is thus consistent with its preference for association with regions of high A+T content. The sequence logo was generated with WebLogo (http://weblogo.berkeley.edu).
Mentions: The enrichment of Isw2 at the chromosome III centromere led us to investigate Isw2 centromeric association in more detail. Aggregate analysis of remodeler signal at all 16 yeast centromeres revealed robust enrichment of Isw2, but not Isw1 or Chd1 (Figure 3A). To precisely delineate the regions of the centromere bound by Isw2, we employed V-plotting [30]. In a V-plot, the midpoint of each paired-end fragment is assigned a dot in two-dimensional space, wherein the X-axis value is the distance of the fragment midpoint from a defined genomic feature and the Y-axis value is the length of the fragment. V-plotting of Isw2 ChIP and input data revealed striking enrichment of Isw2 to the right of centromere midpoints, over the CDEII and CDEIII regions (Figure 3B). Analysis of centromeric sequence composition confirmed the A+T rich nature of yeast centromeres, further supporting the preference of Isw2 for A+T rich DNA (Figure 3C). The association of Isw2 with centromeres is consistent with previous X-ChIP results showing association of Isw2 with two yeast centromeres [33] as well as studies demonstrating a role for Isw2 in pericentromeric nucleosome dynamics [34] and centromeric association of the human ISWI-containing RSF complex [35].

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