Remodeling of Individual Nucleosomes in Nucleosome Arrays

Research output: Contribution to book/Conference proceedings/Anthology/ReportChapter in book/Anthology/ReportContributedpeer-review

Contributors

Abstract

Adenosin triphosphate (ATP)-dependent nucleosome remodeling factors sculpt the nucleosomal landscape of eukaryotic chromatin. They deposit, evict, or reposition nucleosomes along DNA in a process termed nucleosome sliding. Remodeling has traditionally been analyzed using mononucleosomes as a model substrate. In vivo, however, nucleosomes form extended arrays with regular spacing. Here we describe how regularly spaced nucleosome arrays can be reconstituted in vitro and how these arrays can be used to dissect remodeling in the test tube. We outline two assays. Both assays exploit the changes in the accessibility of DNA to restriction enzymes during the remodeling reaction. The first assay uses the restriction enzyme to cleave the restriction site as soon as it becomes accessible during remodeling. As such, this assay mostly reports the kinetic parameter of the "forward" reaction of nucleosome remodeling. In contrast, the second assay measures how fast a particular nucleosome in the array reaches its steady-state position.

Details

Original languageEnglish
Title of host publicationMolecular Motors
EditorsChristophe Lavelle, Antoine Le Gall
Place of PublicationNew York
PublisherHumana New York
Pages271-291
Number of pages21
ISBN (electronic)978-1-0716-4280-1
ISBN (print)978-1-0716-4279-5
Publication statusPublished - 2025
Peer-reviewedYes

Publication series

SeriesMethods in Molecular Biology (MIMB)
Volume2881
ISSN1064-3745

External IDs

Scopus 85213538055

Keywords

ASJC Scopus subject areas

Keywords

  • Adenosin triphosphate (ATP)-dependent nucleosome remodeling, Chromatin reconstitution, Chromatin remodeling enzyme, Histone; Chromatin accessibility, ISWI, Nucleosome arrays, Nucleosome sliding/repositioning, Snf2-family ATPase