Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements

Smith, Emily Louise, Mok, Gi Fay ORCID: https://orcid.org/0000-0002-5202-9062 and Münsterberg, Andrea ORCID: https://orcid.org/0000-0002-4577-4240 (2022) Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements. Biochemical Society Transactions, 50 (3). pp. 1167-1177. ISSN 0300-5127

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Abstract

Mapping accessible chromatin across time scales can give insights into its dynamic nature, for example during cellular differentiation and tissue or organism development. Analysis of such data can be utilised to identify functional cis-regulatory elements (CRE) and transcription factor binding sites and, when combined with transcriptomics, can reveal gene regulatory networks (GRNs) of expressed genes. Chromatin accessibility mapping is a powerful approach and can be performed using ATAC-sequencing (ATAC-seq), whereby Tn5 transposase inserts sequencing adaptors into genomic DNA to identify differentially accessible regions of chromatin in different cell populations. It requires low sample input and can be performed and analysed relatively quickly compared with other methods. The data generated from ATAC-seq, along with other genomic approaches, can help uncover chromatin packaging and potential cis-regulatory elements that may be responsible for gene expression. Here, we describe the ATAC-seq approach and give examples from mainly vertebrate embryonic development, where such datasets have identified the highly dynamic nature of chromatin, with differing landscapes between cellular precursors for different lineages.

Item Type: Article
Additional Information: Funding Information: E.L.S. is supported by a doctoral studentship from the UKRI Biotechnology and Biological Sciences Research Council (BBSRC) Norwich Research Park Biosciences Doctoral Training Partnership (NRP DTP), G.F.M was funded by BBSRC project grant (BB/N007034/1) to A.M., G.F.M. is currently funded by British Heart Foundation grant (PG/19/76/34696).
Uncontrolled Keywords: biochemistry ,/dk/atira/pure/subjectarea/asjc/1300/1303
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 24 Jan 2024 01:35
Last Modified: 24 Jan 2024 01:35
URI: https://ueaeprints.uea.ac.uk/id/eprint/94238
DOI: 10.1042/BST20210834

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