EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation.
ATAC
CTCF
ChIP
Chromatin accessibility
DNA methylation
KLF4
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
21 11 2019
21 11 2019
Historique:
received:
28
06
2019
accepted:
04
10
2019
entrez:
23
11
2019
pubmed:
23
11
2019
medline:
6
2
2020
Statut:
epublish
Résumé
Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low-input, low sequencing depth method, EpiMethylTag, that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.
Identifiants
pubmed: 31752933
doi: 10.1186/s13059-019-1853-6
pii: 10.1186/s13059-019-1853-6
pmc: PMC6868874
doi:
Substances chimiques
Chromatin
0
KLF4 protein, human
0
Kruppel-Like Factor 4
0
Transcription Factors
0
Types de publication
Evaluation Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
248Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM122515
Pays : United States
Organisme : NIH HHS
ID : R35GM122515
Pays : United States
Références
Elife. 2013 Sep 03;2:e00726
pubmed: 24015356
Genome Res. 2012 Dec;22(12):2497-506
pubmed: 22960375
Mol Cell. 2017 Jun 1;66(5):711-720.e3
pubmed: 28529057
Genome Res. 2012 Jun;22(6):1139-43
pubmed: 22466172
Genome Res. 2012 Sep;22(9):1711-22
pubmed: 22955983
Nucleic Acids Res. 2005 Oct 13;33(18):5868-77
pubmed: 16224102
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Cell Biol. 2019 Oct;21(10):1179-1190
pubmed: 31548608
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Genesis. 2006 Jan;44(1):23-8
pubmed: 16400644
Science. 2017 May 5;356(6337):
pubmed: 28473536
Genome Res. 2012 Jun;22(6):1128-38
pubmed: 22466170
Nat Rev Genet. 2016 Aug 1;17(9):551-65
pubmed: 27479905
Cell Rep. 2015 Aug 18;12(7):1184-95
pubmed: 26257180
Genome Res. 2019 Jun;29(6):969-977
pubmed: 31160376
Lancet. 2018 Sep 1;392(10149):777-786
pubmed: 30100054
Nat Methods. 2015 Oct;12(10):963-965
pubmed: 26280331
Genome Res. 2012 Jun;22(6):1120-7
pubmed: 22466171
Stem Cell Reports. 2014 Oct 14;3(4):574-84
pubmed: 25358786
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Nat Protoc. 2013 Oct;8(10):2022-32
pubmed: 24071908
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Bioinformatics. 2015 Jul 15;31(14):2382-3
pubmed: 25765347
Bioinformatics. 2011 Jun 1;27(11):1571-2
pubmed: 21493656
Nature. 2011 Dec 14;480(7378):490-5
pubmed: 22170606
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Methods. 2017 Oct;14(10):959-962
pubmed: 28846090
Cell Stem Cell. 2008 Feb 7;2(2):160-9
pubmed: 18371437
Genome Biol. 2019 Nov 21;20(1):248
pubmed: 31752933
Genome Res. 2012 Sep;22(9):1680-8
pubmed: 22955980
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
PLoS Genet. 2013;9(12):e1003994
pubmed: 24367273