Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts

Akihiko Sakashita, Chikara Takeuchi, So Maezawa, Satoshi H. Namekawa

研究成果: Chapter

抄録

Precise regulation of gene expression is integral in development. Emerging studies have highlighted that super-enhancers (SEs), which are clusters of multiple enhancers, play critical roles in regulating cell type-specific gene expression via 3D chromatin, thereby defining the cellular identities of given cells. Here we provide optimized bioinformatics pipelines to identify SEs and 3D chromatin contacts. Our pipelines encompass the processing of chromatin immunoprecipitation sequencing (ChIP-seq) data to identify SEs and the processing of genome-wide chromosome conformation capture (Hi-C) data. We can then infer long-range chromatin contacts between SEs and other genomic regions. This integrative computational approach, which can be applied to CUT&RUN and CUT&Tag, alternative technologies to ChIP-seq, allows us to identify genomic locations of SEs and their 3D genome configuration, whereby multiple SEs act in concert. We show an analysis of mouse spermatogenesis as an example of this application.

本文言語English
ホスト出版物のタイトルMethods in Molecular Biology
出版社Humana Press Inc.
ページ123-146
ページ数24
DOI
出版ステータスPublished - 2023

出版物シリーズ

名前Methods in Molecular Biology
2577
ISSN(印刷版)1064-3745
ISSN(電子版)1940-6029

ASJC Scopus subject areas

  • 分子生物学
  • 遺伝学

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