Profiling Chromatin Accessibility at Single-cell Resolution

How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Ge...

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Autores principales:	Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo A. Stratton, Arzina Jaffer, Nizar Bahlis, Sorana Morrissy, Jeff A. Biernaskie
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Single-cell ATAC-seq Gene regulation Epigenetics Single-cell multi-omics Cis-regulatory elements Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5aca11c01c014409a829dd0a2d1013a8
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spelling	oai:doaj.org-article:5aca11c01c014409a829dd0a2d1013a82021-11-16T04:09:21ZProfiling Chromatin Accessibility at Single-cell Resolution1672-022910.1016/j.gpb.2020.06.010https://doaj.org/article/5aca11c01c014409a829dd0a2d1013a82021-04-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1672022921000115https://doaj.org/toc/1672-0229How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Genome-wide chromatin accessibility measurements can impart insights into regulatory sequences (in)accessible to DNA-binding proteins at a single-cell resolution. This review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies to integrate multi-omic measurements, and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.Sarthak SinhaAnsuman T. SatpathyWeiqiang ZhouHongkai JiJo A. StrattonArzina JafferNizar BahlisSorana MorrissyJeff A. BiernaskieElsevierarticleSingle-cell ATAC-seqGene regulationEpigeneticsSingle-cell multi-omicsCis-regulatory elementsBiology (General)QH301-705.5ENGenomics, Proteomics & Bioinformatics, Vol 19, Iss 2, Pp 172-190 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Single-cell ATAC-seq Gene regulation Epigenetics Single-cell multi-omics Cis-regulatory elements Biology (General) QH301-705.5
spellingShingle	Single-cell ATAC-seq Gene regulation Epigenetics Single-cell multi-omics Cis-regulatory elements Biology (General) QH301-705.5 Sarthak Sinha Ansuman T. Satpathy Weiqiang Zhou Hongkai Ji Jo A. Stratton Arzina Jaffer Nizar Bahlis Sorana Morrissy Jeff A. Biernaskie Profiling Chromatin Accessibility at Single-cell Resolution
description	How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Genome-wide chromatin accessibility measurements can impart insights into regulatory sequences (in)accessible to DNA-binding proteins at a single-cell resolution. This review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies to integrate multi-omic measurements, and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.
format	article
author	Sarthak Sinha Ansuman T. Satpathy Weiqiang Zhou Hongkai Ji Jo A. Stratton Arzina Jaffer Nizar Bahlis Sorana Morrissy Jeff A. Biernaskie
author_facet	Sarthak Sinha Ansuman T. Satpathy Weiqiang Zhou Hongkai Ji Jo A. Stratton Arzina Jaffer Nizar Bahlis Sorana Morrissy Jeff A. Biernaskie
author_sort	Sarthak Sinha
title	Profiling Chromatin Accessibility at Single-cell Resolution
title_short	Profiling Chromatin Accessibility at Single-cell Resolution
title_full	Profiling Chromatin Accessibility at Single-cell Resolution
title_fullStr	Profiling Chromatin Accessibility at Single-cell Resolution
title_full_unstemmed	Profiling Chromatin Accessibility at Single-cell Resolution
title_sort	profiling chromatin accessibility at single-cell resolution
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/5aca11c01c014409a829dd0a2d1013a8
work_keys_str_mv	AT sarthaksinha profilingchromatinaccessibilityatsinglecellresolution AT ansumantsatpathy profilingchromatinaccessibilityatsinglecellresolution AT weiqiangzhou profilingchromatinaccessibilityatsinglecellresolution AT hongkaiji profilingchromatinaccessibilityatsinglecellresolution AT joastratton profilingchromatinaccessibilityatsinglecellresolution AT arzinajaffer profilingchromatinaccessibilityatsinglecellresolution AT nizarbahlis profilingchromatinaccessibilityatsinglecellresolution AT soranamorrissy profilingchromatinaccessibilityatsinglecellresolution AT jeffabiernaskie profilingchromatinaccessibilityatsinglecellresolution
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Profiling Chromatin Accessibility at Single-cell Resolution

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