Genome-wide analysis of chromatin accessibility using ATAC-seq

• Published in: Methods in cell biology Vol. 151; pp. 219 - 235
• Main Authors: Shashikant, Tanvi, Ettensohn, Charles A
• Format: Journal Article
• Language: English
• Published: United States 01.01.2019
• Subjects: Animals; Chromatin - genetics; Echinodermata - genetics; Echinodermata - growth & development; Enhancer Elements, Genetic - genetics; High-Throughput Nucleotide Sequencing - methods; Promoter Regions, Genetic - genetics; Regulatory Sequences, Nucleic Acid - genetics; Sequence Analysis, DNA - methods; Silencer Elements, Transcriptional - genetics; Transposases - chemistry; Transposases - genetics; Chromatin accessibility; cis-regulatory module; Sea urchins; Enhancer; cis-regulatory element; Gene regulatory network; Tn5; Method; Echinoderms; ATAC-seq
• ISSN: 0091-679X
• DOI: 10.1016/bs.mcb.2018.11.002

Programs of gene transcription are controlled by cis-acting DNA elements, including enhancers, silencers, and promoters. Local accessibility of chromatin has proven to be a highly informative structural feature for identifying such regulatory elements, which tend to be relatively open due to their interactions with proteins. Recently, ATAC-seq (assay for transposase-accessible chromatin using sequencing) has emerged as one of the most powerful approaches for genome-wide chromatin accessibility profiling. This method assesses DNA accessibility using hyperactive Tn5 transposase, which simultaneously cuts DNA and inserts sequencing adaptors, preferentially in regions of open chromatin. ATAC-seq is a relatively simple procedure which can be applied to only a few thousand cells. It is well-suited to developing embryos of sea urchins and other echinoderms, which are a prominent experimental model for understanding the genomic control of animal development. In this chapter, we present a protocol for applying ATAC-seq to embryonic cells of sea urchins.