Genomic nucleosome organization reconstituted with pure proteins

By Nils Krietenstein, Megha Wal, Shinya Watanabe, Bongsoo Park, C. Peterson, B. Franklin Pugh, Philipp Korber. 2016

246 citations recorded by the source corpus.

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 RSC, ISW2, INO80, and ISW1a. We identify direct, specific and sufficient contributions that in vivo observations validate. First, RSC clears promoters by translating poly(dA:dT) into directional nucleosome removal. Second, partial redundancy is recapitulated where INO80 alone, or ISW2 at Abf1/Reb1sites, positions +1 nucleosomes. Third, INO80 and ISW2 each align downstream nucleosomal arrays. Fourth, ISW1a tightens the spacing to canonical repeat lengths. Such a minimal set of rules and proteins establishes core mechanisms by which promoter chromatin architecture arises through a blend of redundancy and specialization.

Subfields: Molecular Biology

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In Molecular Biology

1. Patrick Cramer
2. Shinya Watanabe
3. C. Peterson
4. K. Hopfner
5. Philipp Korber
6. Manuela Moldt
7. Björn Wallner

Citations in the corpus

• Precise genome-wide mapping of single nucleosomes and linkers in vivo (2018, unknown): “Our model also can account for previous observations that DNA sequence is unable to generate the stereotypical nucleosome organization near TSSs, without help from ATP-dependent chromatin remodelers [57, 96].”
• Ruler elements in chromatin remodelers set nucleosome array spacing and phasing (2020, methodology): “Merged data of replicates are shown, individual replicates in Figure S1B,C. (D) Composite plots for MNase-seq data averaged over the indicated number of replicates (n) as in panel B but only for genes highlighted in red in panel B. INO80, ISW2, ISW1a and Chd1, but not Fun30 align regular arrays at t”