Profiling Chromatin Accessibility at Single-cell Resolution
| Autor: | Jo Anne Stratton, Sorana Morrissy, Nizar J. Bahlis, Weiqiang Zhou, Ansuman T. Satpathy, Sarthak Sinha, Hongkai Ji, Arzina Jaffer, Jeff Biernaskie |
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| Rok vydání: | 2021 |
| Předmět: |
QH301-705.5
Computer science Regulator Transposases Review Computational biology Single-cell ATAC-seq Biochemistry Transcriptome 03 medical and health sciences 0302 clinical medicine Genetics Cis-regulatory elements Epigenetics Biology (General) Molecular Biology Single-cell multi-omics 030304 developmental biology Regulation of gene expression Profiling (computer programming) 0303 health sciences Genome Computational Biology Epigenome Chromatin Gene regulation Computational Mathematics Proteome Single-Cell Analysis 030217 neurology & neurosurgery |
| Zdroj: | Genomics, Proteomics & Bioinformatics Genomics, Proteomics & Bioinformatics, Vol 19, Iss 2, Pp 172-190 (2021) |
| ISSN: | 1672-0229 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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