@inbook{927fa63e41524f29be516c2c8d0aa927,
title = "Bioinformatics Pipelines for Identification of Super-Enhancers and 3D Chromatin Contacts",
abstract = "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.",
keywords = "ChIP-seq, Chromatin contact, Enhancer, Gene regulation, Hi-C, Meiosis, Promoter–enhancer interaction, Spermatogenesis, Super-enhancer, Transcription factor-binding",
author = "Akihiko Sakashita and Chikara Takeuchi and So Maezawa and Namekawa, {Satoshi H.}",
note = "Funding Information: We thank Katie Gerhardt for editing the manuscript, Yuka Kita-mura for critical reading of the manuscript, all members of Siomi Lab at Keio University School of Medicine, and Namekawa Lab at UC Davis for discussions and comments on this manuscript. This work was supported by JSPS Grants-in-Aid for Early-Career Scientists and Kato Memorial Bioscience Foundation Research Grant to A.S. and NIH grants R01 GM122776 and R35 GM141085 to S. H.N. Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2023",
doi = "10.1007/978-1-0716-2724-2_9",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "123--146",
booktitle = "Methods in Molecular Biology",
}