Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq

Kensaku Murano; Yuka W Iwasaki; Haruhiko Siomi

doi:10.1007/978-1-4939-7339-2_11

Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq

Methods Mol Biol. 2018:1680:165-177. doi: 10.1007/978-1-4939-7339-2_11.

Authors

Kensaku Murano¹, Yuka W Iwasaki¹, Haruhiko Siomi²

Affiliations

¹ Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan.
² Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan. awa403@keio.jp.

PMID: 29030848
DOI: 10.1007/978-1-4939-7339-2_11

Abstract

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of Piwi in heterochromatin formation around transposable element loci, we have used ATAC-seq to examine chromatin accessibility at target transposable elements in a Drosophila cultured cell line, ovarian somatic cells (OSCs). In this chapter, we describe our method to profile open chromatin structure in OSCs using ATAC-seq.

Keywords: ATAC-seq; Chromatin accessibility; Drosophila; Heterochromatin; OSC; Small RNA; Transposons.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromatin / genetics*
Chromatin Assembly and Disassembly*
Computational Biology / methods
DNA Transposable Elements
Drosophila
Female
Gene Library
High-Throughput Nucleotide Sequencing
Ovary / cytology*
RNA, Small Untranslated
Sequence Analysis, DNA* / methods

Substances

Chromatin
DNA Transposable Elements
RNA, Small Untranslated