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

Authors

• J Ocampo
• RV Chereji
• PR Eriksson
• DJ Clark

Abstract

In yeast, most genes have a nucleosome-depleted region at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. The nucleosome constitutes a barrier that can be circumvented by Chromatin Remodeling Complexes. They use the free energy obtained from adenosine triphosphate hydrolysis to modify chromatin structure, by altering interactions between histones and DNA. ISW1, ISW2 and CHD1 belong to this family of remodelers and possess nucleosome spacing activity. In vitro, they form arrays with different spacing. To determine whether these enzymes space nucleosomes differently in vivo, we constructed null mutants for all three spacing enzymes and mapped nucleosomal DNA obtained by micrococcal nuclease digestion of nuclei genome-wide. We find that CHD1 and ISW1 compete to set the spacing on most 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 transcriptionally inactive genes. Furthermore, we have studied the connections between spacing and transcription by mapping RNA polymerase II using ChIP-seq, and between spacing and linker histone (H1) using previously published ChIP-exo data. We found that heavily transcribed genes show weak phasing and extreme spacing, and are depleted of H1. Genes with longer spacing are enriched in H1. We propose that CHD1 directs short spacing, resulting in eviction of H1, whereas ISW1 directs longer spacing, allowing H1 to bind. Thus, competition between the two remodelers to set the spacing on each gene may result in a highly dynamic chromatin structure.

Scientific Focus Area: Genetics and Genomics

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