Partitioned usage of chromatin remodelers by nucleosome-displacing factors

Hengye Chen, Hungyo Kharerin, Archana Dhasarathy, Michael Kladde, Lu Bai

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

Nucleosome-displacing-factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we design a high-throughput method to systematically study the interplay between NDFs and CRs. By combining an integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measure the impact of CRs on NDRs generated by individual NDFs. We find that CRs are dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity toward certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and NDR length-dependent manner. Overall, our study provides a framework to investigate how NDFs and CRs cooperate to regulate chromatin opening.

Original languageEnglish (US)
Article number111250
JournalCell Reports
Volume40
Issue number8
DOIs
StatePublished - Aug 23 2022

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology

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