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Genome-wide analysis of chromatin accessibility using ATAC-seq.
- Source :
-
Methods in cell biology [Methods Cell Biol] 2019; Vol. 151, pp. 219-235. Date of Electronic Publication: 2018 Dec 21. - Publication Year :
- 2019
-
Abstract
- 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.<br /> (© 2019 Elsevier Inc. All rights reserved.)
- Subjects :
- Animals
Echinodermata growth & development
Enhancer Elements, Genetic genetics
Promoter Regions, Genetic genetics
Regulatory Sequences, Nucleic Acid genetics
Silencer Elements, Transcriptional genetics
Transposases chemistry
Transposases genetics
Chromatin genetics
Echinodermata genetics
High-Throughput Nucleotide Sequencing methods
Sequence Analysis, DNA methods
Subjects
Details
- Language :
- English
- ISSN :
- 0091-679X
- Volume :
- 151
- Database :
- MEDLINE
- Journal :
- Methods in cell biology
- Publication Type :
- Academic Journal
- Accession number :
- 30948010
- Full Text :
- https://doi.org/10.1016/bs.mcb.2018.11.002