Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
04 11 2021
04 11 2021
Historique:
received:
17
05
2021
accepted:
04
10
2021
entrez:
5
11
2021
pubmed:
6
11
2021
medline:
28
12
2021
Statut:
epublish
Résumé
A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regularized non-negative matrix factorization for imputing and quantifying the open chromatin status of regulatory regions from sparse scATAC-seq experiments. We show that scOpen improves crucial downstream analysis steps of scATAC-seq data as clustering, visualization, cis-regulatory DNA interactions, and delineation of regulatory features. We demonstrate the power of scOpen to dissect regulatory changes in the development of fibrosis in the kidney. This identifies a role of Runx1 and target genes by promoting fibroblast to myofibroblast differentiation driving kidney fibrosis.
Identifiants
pubmed: 34737275
doi: 10.1038/s41467-021-26530-2
pii: 10.1038/s41467-021-26530-2
pmc: PMC8568974
doi:
Substances chimiques
Chromatin
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6386Informations de copyright
© 2021. The Author(s).
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