2016
DOI: 10.1016/j.cell.2016.09.045
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Genomic Nucleosome Organization Reconstituted with Pure Proteins

Abstract: Summary Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here we reconstitute four stages of nucleosome architecture using purified components: Yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RS… Show more

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Cited by 261 publications
(464 citation statements)
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“…In humans, the NRL ranges from ~178–205 bp, depending on histone modification state (Valouev et al, 2011), with activation marks having the shortest NRL. Thus, the underlying DNA sequence (Segal and Widom, 2009) and/or the proteins that interact with histones, such as Isw1a (Krietenstein et al, 2016), are more likely to specify this property.…”
Section: Discussionmentioning
confidence: 99%
“…In humans, the NRL ranges from ~178–205 bp, depending on histone modification state (Valouev et al, 2011), with activation marks having the shortest NRL. Thus, the underlying DNA sequence (Segal and Widom, 2009) and/or the proteins that interact with histones, such as Isw1a (Krietenstein et al, 2016), are more likely to specify this property.…”
Section: Discussionmentioning
confidence: 99%
“…(9). Similarly, INO80 has been shown to help position the +1 nucleosome [54], suggesting that INO80 may act as an additional energy barrier at TSS. Thus, incorporation of INO80 ChIP-seq information into the sequence model may help improve the prediction of nucleosome landscape.…”
Section: Discussionmentioning
confidence: 99%
“…Thus, incorporation of INO80 ChIP-seq information into the sequence model may help improve the prediction of nucleosome landscape. Lastly, it is known that ISW1 can tighten the spacing in nucleosome arrays downstream of TSS [54]. A plausible hypothesis is that ISW1 increases the effective chemical potential so that the nucleosomes in the region are more tightly packed.…”
Section: Discussionmentioning
confidence: 99%
“…One example where sequence context appears paramount is for the INO80 remodeler. In a genome-wide study of nucleosome positioning in Saccharomyces cerevisiae , INO80 was discovered to be responsible for the precise positioning of +1 nucleosomes, and could recapitulate in vivo nucleosome positions through DNA sequence alone 6 . Although further work will be needed to tease out the relationship between DNA sequence and INO80 action, nucleosome positioning by INO80 correlated with a predicted greater twist of DNA over the dyad of the +1 nucleosome, suggesting a mechanism of responding to DNA shape on the nucleosome.…”
Section: Introductionmentioning
confidence: 99%