Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages165-177
Number of pages13
Volume1680
DOIs
Publication statusPublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1680
ISSN (Print)1064-3745

Fingerprint

Transposases
Chromatin
DNA Transposable Elements
Deoxyribonucleases
Heterochromatin
Sample Size
Drosophila
Cultured Cells
Cell Line

Keywords

  • ATAC-seq
  • Chromatin accessibility
  • Drosophila
  • Heterochromatin
  • OSC
  • Small RNA
  • Transposons

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Murano, K., Iwasaki, Y., & Siomi, H. (2018). Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq. In Methods in Molecular Biology (Vol. 1680, pp. 165-177). (Methods in Molecular Biology; Vol. 1680). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7339-2_11

Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq. / Murano, Kensaku; Iwasaki, Yuka; Siomi, Haruhiko.

Methods in Molecular Biology. Vol. 1680 Humana Press Inc., 2018. p. 165-177 (Methods in Molecular Biology; Vol. 1680).

Research output: Chapter in Book/Report/Conference proceedingChapter

Murano, K, Iwasaki, Y & Siomi, H 2018, Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq. in Methods in Molecular Biology. vol. 1680, Methods in Molecular Biology, vol. 1680, Humana Press Inc., pp. 165-177. https://doi.org/10.1007/978-1-4939-7339-2_11
Murano K, Iwasaki Y, Siomi H. Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq. In Methods in Molecular Biology. Vol. 1680. Humana Press Inc. 2018. p. 165-177. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7339-2_11
Murano, Kensaku ; Iwasaki, Yuka ; Siomi, Haruhiko. / Profiling open chromatin structure in the ovarian somatic cells using ATAC-seq. Methods in Molecular Biology. Vol. 1680 Humana Press Inc., 2018. pp. 165-177 (Methods in Molecular Biology).
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