The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome

Nucleic Acids Research
Joshua M TokudaGregory D Bowman

Abstract

Chromatin remodelers are ATP-dependent motors that reorganize DNA packaging by disrupting canonical histone-DNA contacts within the nucleosome. Here, we show that the Chd1 chromatin remodeler stimulates DNA unwrapping from the edge of the nucleosome in a nucleotide-dependent and DNA sequence-sensitive fashion. Nucleosome binding, monitored by stopped flow, was complex and sensitive to nucleotide, with AMP-PNP promoting faster binding than ADP·BeF3-. Nucleosome unwrapping by Chd1, examined by bulk FRET, occurred in the presence and absence of nucleotide and did not require the Chd1 DNA-binding domain. In AMP-PNP conditions, Chd1 unwrapped one side of the Widom 601 DNA more easily than the other, consistent with previous observations of 601 asymmetry and indicating that Chd1 amplifies intrinsic sequence properties of nucleosomal DNA. Using small angle X-ray scattering (SAXS) with contrast variation, we found distinct DNA conformations depending on the nucleotide analog bound to Chd1: with AMP-PNP, DNA primarily unwrapped in-plane with the nucleosomal disk, whereas with ADP·BeF3-, a significant fraction showed distinctive out-of-plane unwrapping as well. Taken together, our findings show tight coupling between entry/exit DNA of th...Continue Reading

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Citations

Aug 7, 2018·ELife·Ramasubramanian SundaramoorthyTom Owen-Hughes
Jun 23, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Rajivgandhi Sundaram, Dileep Vasudevan
Apr 14, 2019·Nature Communications·Anton SabantsevSebastian Deindl
Dec 12, 2018·Nature Structural & Molecular Biology·Keda ZhouKarolin Luger
Feb 10, 2021·Proceedings of the National Academy of Sciences of the United States of America·Hisashi Ishida, Hidetoshi Kono
Feb 9, 2021·Journal of Molecular Biology·Nathan Gamarra, Geeta J Narlikar

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Methods Mentioned

BETA
X-ray
FRET
size exclusion chromatography
PCR
salt gradient dialysis
x-ray scattering
the
acetylation

Software Mentioned

Mathematica
GAJOE
EOM
CRYSOL
DART
GNOM
3D

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