박상우 (Johns Hopkins University) | 한빛사논문 > 한빛사

한빛사논문

조회299

박상우Sangwoo Park

Johns Hopkins University

Nucleic Acids Res., Sep 20 2023, gkad738 | https://doi.org/10.1093/nar/gkad738 Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning.

Sangwoo Park ¹, Giovanni B Brandani², Taekjip Ha ^1,3,4, Gregory D Bowman ⁴

¹Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

²Department of Biophysics, Graduate School of Science, Kyoto University, Japan.

³Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.

⁴TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.

Correspondence: Taekjip Ha, Gregory D Bowman

Abstract

Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers exhibit a sequence-dependent bias in nucleosome positioning, which presumably reflects properties of the DNA duplex. Here, we show how nucleosome positioning by the Chd1 remodeler is influenced by local DNA perturbations throughout the nucleosome footprint. Using site-specific DNA cleavage coupled with next-generation sequencing, we show that nucleosomes shifted by Chd1 can preferentially localize DNA perturbations - poly(dA:dT) tracts, DNA mismatches, and single-nucleotide insertions - about a helical turn outside the Chd1 motor domain binding site, super helix location 2 (SHL2). This phenomenon occurs with both the Widom 601 positioning sequence and the natural +1 nucleosome sequence from the Saccharomyces cerevisiae SWH1 gene. Our modeling indicates that localization of DNA perturbations about a helical turn outward from SHL2 results from back-and-forth sliding due to remodeler action on both sides of the nucleosome. Our results also show that barrier effects from DNA perturbations can be extended by the strong phasing of nucleosome positioning sequences.

논문정보

형식Research article
게재일2023년 09월 (BRIC 등록일 2023-10-05)
연구진국외 연구진
분야

댓글 작성 로그인

CV 열람하기

연락처 보기