A04 - Reading DNA sequence for nucleosome positioning by remodelers and barriers
We showed that the combination of specific ATP-dependent nucleosome remodeling enzymes and barrier proteins suffices to generate basic nucleosome organization at yeast promoters. Now we use genome-wide reconstitution biochemistry to study the mechanisms how the yeast RSC and INO80 remodeling complexes translate DNA sequences into nucleosome organization, and how they co-operate with barrier proteins in nucleosome positioning.
Genome-wide in vitro reconstitution of in vivo-like nucleosome positions for S. cerevisiae. Shown are stacks of >4700 rows (= genes) with colour coded (yellow for high, blue for low) TSS-aligned and clustered nucleosome occupancy data. Salt gradient dialysis (SGD; just DNA, histones and buffer) reconstitutes only some nucleosome positions that are similar to chromatin prepared ex vivo. However, incubation of this salt dialysis chromatin with a wild type yeast whole cell extract (wt WCE) and ATP generates physiological nucleosome positions. ATP-dependent chromatin remodeling enzymes, like the INO80 complex just on its own, contribute crucially to this proper nucleosome positioning. We study the molecular mechanisms how remodeling enzymes turn DNA sequence information into nucleosome positioning. Figure generated with data from Zhang et al., 2011, Science, and Krietenstein et al., 2016, Cell.