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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 bind NDRs.Aggregate plots of log2(IP/input) signal ±1 kb of verified ORF 5′ and 3′ ends for (A) Chd1, (B) Isw1, and (C) Isw2 ranked separated into quintiles by average remodeler signal.
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pgen-1003317-g006: ISWI and CHD remodelers bind NDRs.Aggregate plots of log2(IP/input) signal ±1 kb of verified ORF 5′ and 3′ ends for (A) Chd1, (B) Isw1, and (C) Isw2 ranked separated into quintiles by average remodeler signal.

Mentions: The sharp patterns of phased nucleosomes on either side of binding sites for Abf1, Reb1 and other TFs is consistent with their known role in creating NDRs that lead to transcriptional activation [46]. Isw1and Chd1 position nucleosomes within gene bodies in vivo, while Isw2 generally positions nucleosomes flanking NDRs, preventing directional nucleosome shifting within gene bodies [16]–[21]. We therefore asked whether there is a relationship between remodeler occupancy and dynamics around individual TFBSs and features of adjacent genes. Consistent with their known functions, we observed enrichment of Chd1 and Isw1 within gene bodies (Figure 6A–6B), while Isw2 showed robust enrichment at NDRs, where TFBSs are generally located in yeast, with little gene body binding (Figure 6C). Strikingly, equal or slightly greater enrichment than that seen in gene bodies for Chd1 and Isw1 was observed at NDRs at the 5′ and 3′ ends of verified ORFs (Figure 6A–6B). We also detected Isw1 association with 5′ NDRs after adding a formaldehyde crosslinking step to our N-ChIP-seq protocol (Figure S6), indicating that remodeler-NDR association is not due to opportunistic, nonspecific interactions of remodelers with free DNA during chromatin preparation and immunoprecipitation. We assessed the association of remodeler binding with NDR size, reasoning that if remodeler-NDR interactions were simply due to the presence of large regions of naked DNA in the chromatin preparation, larger NDRs would display greater remodeler association. No such correlations were observed (Isw1 R2 = 0.0339; Isw2 R2 = 0.0397; Chd1 R2 = 0.0519), further arguing against nonspecific association of remodelers with free DNA during our experiments.


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 bind NDRs.Aggregate plots of log2(IP/input) signal ±1 kb of verified ORF 5′ and 3′ ends for (A) Chd1, (B) Isw1, and (C) Isw2 ranked separated into quintiles by average remodeler signal.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003317-g006: ISWI and CHD remodelers bind NDRs.Aggregate plots of log2(IP/input) signal ±1 kb of verified ORF 5′ and 3′ ends for (A) Chd1, (B) Isw1, and (C) Isw2 ranked separated into quintiles by average remodeler signal.
Mentions: The sharp patterns of phased nucleosomes on either side of binding sites for Abf1, Reb1 and other TFs is consistent with their known role in creating NDRs that lead to transcriptional activation [46]. Isw1and Chd1 position nucleosomes within gene bodies in vivo, while Isw2 generally positions nucleosomes flanking NDRs, preventing directional nucleosome shifting within gene bodies [16]–[21]. We therefore asked whether there is a relationship between remodeler occupancy and dynamics around individual TFBSs and features of adjacent genes. Consistent with their known functions, we observed enrichment of Chd1 and Isw1 within gene bodies (Figure 6A–6B), while Isw2 showed robust enrichment at NDRs, where TFBSs are generally located in yeast, with little gene body binding (Figure 6C). Strikingly, equal or slightly greater enrichment than that seen in gene bodies for Chd1 and Isw1 was observed at NDRs at the 5′ and 3′ ends of verified ORFs (Figure 6A–6B). We also detected Isw1 association with 5′ NDRs after adding a formaldehyde crosslinking step to our N-ChIP-seq protocol (Figure S6), indicating that remodeler-NDR association is not due to opportunistic, nonspecific interactions of remodelers with free DNA during chromatin preparation and immunoprecipitation. We assessed the association of remodeler binding with NDR size, reasoning that if remodeler-NDR interactions were simply due to the presence of large regions of naked DNA in the chromatin preparation, larger NDRs would display greater remodeler association. No such correlations were observed (Isw1 R2 = 0.0339; Isw2 R2 = 0.0397; Chd1 R2 = 0.0519), further arguing against nonspecific association of remodelers with free DNA during our experiments.

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