Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq

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Open or accessible chromatin typifies euchromatic regions and helps define cell type-specific transcription programs. DNA replication massively disorders chromatin composition and structure, and how accessible regions are affected by and recover from this disruption has been unclear. Here, we present repli-ATAC-seq, a protocol to profile accessible chromatin genome-wide on replicated DNA starting from 100,000 cells. In this method, replicated DNA is labeled with a short 5-ethynyl-2′-deoxyuridine (EdU) pulse in cultured cells and isolated from a population of tagmented fragments for amplification and next-generation sequencing. Repli-ATAC-seq provides high-resolution information on chromatin dynamics after DNA replication and reveals new insights into the interplay between DNA replication, transcription, and the chromatin landscape.

Original languageEnglish
Title of host publicationChromatin Accessibility : Methods and Protocols
EditorsGeorgi K. Marinov, William J. Greenleaf
Number of pages14
PublisherHumana Press
Publication date2023
ISBN (Print)978-1-0716-2898-0
ISBN (Electronic)978-1-0716-2899-7
Publication statusPublished - 2023
SeriesMethods in Molecular Biology

Bibliographical note

Publisher Copyright:
© 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

    Research areas

  • Accessible chromatin, Chromatin assembly, DNA replication, Nucleosome-free regions, repli-ATAC-seq, Transcription

ID: 339137052