The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo

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

Bethesda

Seminario; Yeast Club; 2015

NIH

ATP-dependent chromatin remodeling machines play a central role in gene regulation by manipulating chromatin structure. Most genes have a nucleosome-depleted region at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. In vitro, the three known yeast nucleosome spacing enzymes (CHD1, ISW1 and ISW2) form arrays with different spacing. We used genome-wide nucleosome sequencing to determine whether these enzymes space nucleosomes differently in vivo. We find that CHD1 and ISW1 compete to set the spacing on individual genes, such that CHD1 dominates genes with shorter spacing and ISW1 dominates genes with longer spacing. In contrast, ISW2 plays a minor role, limited to inactive genes. Genes with longer spacing have more linker histone, which directs chromatin folding. We propose that cells employ multiple spacing enzymes to regulate both nucleosome spacing and chromatin compaction.