Dynamic interplay between ISW1, ISW2, RSC and CHD1 remodelers in chromatin organization in Saccharomyces cerevisiae

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

Bethesda

Seminario; Chromatin DECODE; 2015

Chromatin DECODE

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 with no change in nucleosome spacing, which is maintained at ~165 bp. Others have shown that the combined action of ISW1 and CHD1 is required to maintain nucleosome phasing. Here, we confirm this observation and show that nucleosome spacing in the isw1 mutant is reduced on average by 5 bp, to ~160 bp whereas the chd1 mutant shows little change. A more detailed analysis revealed that the absence of Isw1 or Chd1 has different effects on distinct groups of genes. In contrast, the isw2 mutant does not show any obvious changes in global chromatin structure but there are effects on a small group of genes. The chromatin organization in the multiple mutants agree with the effects observed in the single mutants, indicating that these remodeling complexes have specific 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.