TY - CHAP
T1 - ATAC-Seq Analysis of Accessible Chromatin
T2 - From Experimental Steps to Data Analysis
AU - Tatara, Mayu
AU - Ikeda, Taiyo
AU - Namekawa, Satoshi H.
AU - Maezawa, So
N1 - Publisher Copyright:
© 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2023
Y1 - 2023
N2 - Accessible chromatin often represents gene regulatory elements, including promoters and enhancers, essential for gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is one of the most popular techniques to investigate chromatin accessibility across the genome. Here we describe, step by step, a series of optimized experimental methods and bioinformatics pipelines for ATAC-seq analysis. As an example, we present an analysis of murine spermatogenic cells: a method to isolate germ cells, a reaction step using Tn5 transposase to insert sequencing adapters into accessible DNA, a library preparation method for high-throughput sequencing, and bioinformatics analysis of sequencing data. Overall, we introduce a framework of ATAC-seq analysis that can be applied to any cell population to identify cell-type-specific gene regulatory elements and their cis-regulatory networks.
AB - Accessible chromatin often represents gene regulatory elements, including promoters and enhancers, essential for gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is one of the most popular techniques to investigate chromatin accessibility across the genome. Here we describe, step by step, a series of optimized experimental methods and bioinformatics pipelines for ATAC-seq analysis. As an example, we present an analysis of murine spermatogenic cells: a method to isolate germ cells, a reaction step using Tn5 transposase to insert sequencing adapters into accessible DNA, a library preparation method for high-throughput sequencing, and bioinformatics analysis of sequencing data. Overall, we introduce a framework of ATAC-seq analysis that can be applied to any cell population to identify cell-type-specific gene regulatory elements and their cis-regulatory networks.
KW - ATAC-seq
KW - Accessible chromatin
KW - Germ cells
KW - Meiosis
KW - Spermatogenesis
UR - http://www.scopus.com/inward/record.url?scp=85139377445&partnerID=8YFLogxK
U2 - 10.1007/978-1-0716-2724-2_5
DO - 10.1007/978-1-0716-2724-2_5
M3 - Chapter
C2 - 36173566
AN - SCOPUS:85139377445
T3 - Methods in Molecular Biology
SP - 65
EP - 81
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -