Measuring occupancies of the nucleosome and nucleosome-interacting factors in vivo in Saccharomyces cerevisiae genome-wide.
Journal
Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302
Informations de publication
Date de publication:
10 2023
10 2023
Historique:
received:
26
04
2023
revised:
26
07
2023
accepted:
11
08
2023
pmc-release:
01
10
2024
medline:
19
9
2023
pubmed:
21
8
2023
entrez:
20
8
2023
Statut:
ppublish
Résumé
Nucleosomes are the repeating units of chromatin. The presence of nucleosomes poses a major impediment to all DNA-dependent processes. As a result, access to DNA in chromatin is dynamically regulated by many factors, including ATP-dependent chromatin remodeling complexes. Digestion of chromatin by micrococcal nuclease (MNase) followed by chromatin immunoprecipitation (ChIP) and sequencing can be leveraged to determine nucleosome occupancy, positioning, and the ability of chromatin interacting factors to alter chromatin accessibility. Here we describe the procedure for performing MNase and MNase ChIP-seq in detail.
Identifiants
pubmed: 37598811
pii: S1046-2023(23)00136-6
doi: 10.1016/j.ymeth.2023.08.007
pmc: PMC10529416
mid: NIHMS1930445
pii:
doi:
Substances chimiques
Nucleosomes
0
Chromatin
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
167-175Subventions
Organisme : NIGMS NIH HHS
ID : R15 GM126449
Pays : United States
Organisme : NIGMS NIH HHS
ID : R15 GM148919
Pays : United States
Informations de copyright
Copyright © 2023 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Cell. 2007 Feb 23;128(4):707-19
pubmed: 17320508
Science. 2022 Sep 9;377(6611):eabp9466
pubmed: 35981082
Genes Dev. 2018 May 1;32(9-10):695-710
pubmed: 29785963
Nat Rev Mol Cell Biol. 2017 Jul;18(7):407-422
pubmed: 28512350
Commun Biol. 2022 Jan 10;5(1):2
pubmed: 35013515
Science. 2005 Jul 22;309(5734):626-30
pubmed: 15961632
Nat Rev Mol Cell Biol. 2015 Mar;16(3):178-89
pubmed: 25650798
Cell. 2012 Jun 22;149(7):1461-73
pubmed: 22726434
Nat Rev Genet. 2009 Mar;10(3):161-72
pubmed: 19204718
Nucleic Acids Res. 1981 Jun 25;9(12):2659-73
pubmed: 6269057
Science. 1974 May 24;184(4139):868-71
pubmed: 4825889
Biophys J. 2018 May 22;114(10):2279-2289
pubmed: 29628211
Genetics. 2021 Apr 15;217(4):
pubmed: 33857307
Trends Genet. 2010 Nov;26(11):476-83
pubmed: 20832136
Cell. 1988 Dec 23;55(6):1137-45
pubmed: 2849508