Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq

Rekha M Dhillon-Richardson; Alexandra K Haugan; Megan L Martik

doi:10.1007/978-1-0716-2847-8_19

Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq

Methods Mol Biol. 2023:2599:271-282. doi: 10.1007/978-1-0716-2847-8_19.

Authors

Rekha M Dhillon-Richardson¹, Alexandra K Haugan¹, Megan L Martik²

Affiliations

¹ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
² Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. martik@berkeley.edu.

Abstract

Interactions between transcription factors and regulatory DNA can be described by gene regulatory networks. These networks provide a systems-level view of embryonic tissue development. Here, we describe a protocol for the isolation, identification, and experimental manipulation of tissue-specific cis-regulatory elements during zebrafish embryonic development using low-input ATAC-seq. With the methods described, genome-wide assessments of regulatory DNA in small populations of developing tissues can be identified, allowing for the construction of gene regulatory networks.

Keywords: Assay for transposase-accessible chromatin using sequencing (ATAC-seq); Embryonic Development; Enhancer screening; Fluorescence-activated cell sorting (FACS); Gene Regulatory Networks; Zebrafish.

MeSH terms

Animals
Chromatin Immunoprecipitation Sequencing*
Embryonic Development
Female
Gene Regulatory Networks
Zebrafish* / genetics

Grants and funding

R00 HD100587/HD/NICHD NIH HHS/United States