Interplay among ATP-dependent remodelling machines determines nucleosome spacing in yeast

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

West Palm Beach

Conferencia; Transcription Chromatin and epigenetics; 2015

In yeast, most genes have a nucleosome-depleted region (NDR) at the promoter and an array of regularly spaced nucleosomes that is phased relative to the transcription start site. We addressed the roles of four remodeling machines (ISW1, ISW2, CHD1 and RSC) in specifying this chromatin organization. We sequenced nucleosomes from isogenic strains with the essential RSC8 gene linked to a GAL promoter and isw1, isw2 or chd1 null mutations in all combinations. Globally, RSC depletion results in a shift of the array into the NDR, isw1 null shows reduced spacing and both isw1 null and chd1 null show weakened phasing, whereas isw2 null has no effect. Generally, chromatin organization in the multiple mutants is the sum of the effects observed in the single mutants, indicating that these remodelers are not redundant but have distinct functions. Genes in wild type cells display a wide range in nucleosome spacing; transcriptionally active genes tend to exhibit extreme spacing. Our data suggest that, on active genes, RSC determines the location of the +1 nucleosome, which is used as a reference by the spacing enzymes, Isw1 and Chd1, to restore the nucleosomal array after transcription. Phasing on inactive genes also requires Isw2, which antagonizes RSC by shifting nucleosomal arrays in the opposite direction. Furthermore, inactive genes have longer spacing and are enriched in linker histone, suggesting that they may have more condensed chromatin than active genes.