The yeast ISW1, CHD1 and RSC chromatin remodelers have additive effects on global chromatin structure

JOSEFINA OCAMPO; RAZVAN V CHEREJI; PETER R ERIKSSON; DAVID J CLARK

Bethesda

Simposio; NIH RESEARCH FESTIVAL; 2014

NIH

Genome-wide nucleosome maps for yeast have revealed that nucleosomes are regularly spaced and show a global phasing relative to the transcription start site (TSS). In addition, most genes have a nucleosome depleted region (NDR) at the promoter. We have addressed the roles of four different chromatin remodeling complexes in nucleosome organization in vivo: ISW1, ISW2, CHD1 and the essential RSC complex. We constructed strains with the essential RSC8 gene under the control of the GAL promoter and isw1, isw2 or chd1 null mutations in all possible combinations in the same genetic background. In the absence of RSC we confirmed that all the nucleosomes shift towards the TSS with consequent narrowing and filling in of the NDR (Parnell et. al. 2008, Hartley and Madhani 2009) with no change in nucleosome spacing, which is maintained at ~165 bp (Ganguli et. al. submitted). Others have shown that the combined action of ISW1 and CHD1 is required to maintain nucleosome phasing (Gkikopoulos et. al., 2011). Here, we confirm this observation and show that nucleosome spacing in the isw1 mutant is reduced by 6 bp, to ~159 bp, whereas the chd1 mutant shows little change. In contrast, the isw2 mutant does not show any obvious changes in global chromatin structure. We observe that the chromatin structures of the double, triple and quadruple mutants represent the sum of the effects observed in the individual mutants, indicating that these remodeling complexes have distinct functions in chromatin organization. We propose that RSC determines the position of the +1 nucleosome, which is then used as a reference nucleosome by CHD1 and ISW1 to build nucleosomal arrays on genes, such that CHD1 sets a 159 bp spacing, which is increased to 165 bp by ISW1. Although 6 bp is only a small change in linker DNA length, a profound effect on chromatin higher order structure is predicted, due to a major change in the relative orientation of neighboring nucleosomes.