The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo
By Josefina Ocampo, Răzvan V. Chereji, P. Eriksson, D. J. Clark. 2016
135 citations recorded by the source corpus.
Abstract Adenosine triphosphate-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 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. Heavily transcribed genes show weak phasing and extreme spacing, either very short or very long, and are depleted of linker histone (H1). Genes with longer spacing are enriched in H1, which directs chromatin folding. We propose that CHD1 directs short spacing, resulting in eviction of H1 and chromatin unfolding, whereas ISW1 directs longer spacing, allowing H1 to bind and condense the chromatin. Thus, competition between the two remodelers to set the spacing on each gene may result in a highly dynamic chromatin structure.
Subfields: Molecular Biology, Plant Science
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In Molecular Biology
- Steven Henikoff
- Philipp Korber
- C. Peterson
- Shinya Watanabe
- B. Franklin Pugh
- Patrick Cramer
- Terri D. Bryson
- Srinivas Ramachandran
In Plant Science
Citations in the corpus
- Precise genome-wide mapping of single nucleosomes and linkers in vivo (2018, methodology): “When the space between the neighboring NDRs is a multiple of the typical nucleosome repeat length (NRL) (~ 165 bp in yeast [60]), we observe constructive interference of the two phasing signals, and well-positioned nucleosomes form a long regular array from one NDR to another.”
- Genomic nucleosome organization reconstituted with pure proteins (2016, background): “Our finding that RSC and INO80 generate NFRs and that INO80 also positions +1 nucleosomes may explain why these two features remained mostly unaffected in the isw1Δ isw2Δ chd1Δ triple mutant, which retains these remodelers (Gkikopoulos et al., 2011; Ocampo et al., 2016).”
- Ruler elements in chromatin remodelers set nucleosome array spacing and phasing (2020, background): “Merged data of replicates are shown, individual replicates in Figure S1B,C. (D) Composite plots for MNase-seq data averaged over the indicated number of replicates (n) as in panel B but only for genes highlighted in red in panel B. INO80, ISW2, ISW1a and Chd1, but not Fun30 align regular arrays at t”