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

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Standard

Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq. / Stewart-Morgan, Kathleen R.; Groth, Anja.

Chromatin Accessibility: Methods and Protocols. ed. / Georgi K. Marinov; William J. Greenleaf. Humana Press, 2023. p. 71-84 (Methods in Molecular Biology, Vol. 2611).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Harvard

Stewart-Morgan, KR & Groth, A 2023, Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq. in GK Marinov & WJ Greenleaf (eds), Chromatin Accessibility: Methods and Protocols. Humana Press, Methods in Molecular Biology, vol. 2611, pp. 71-84. https://doi.org/10.1007/978-1-0716-2899-7_6

APA

Stewart-Morgan, K. R., & Groth, A. (2023). Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq. In G. K. Marinov, & W. J. Greenleaf (Eds.), Chromatin Accessibility: Methods and Protocols (pp. 71-84). Humana Press. Methods in Molecular Biology Vol. 2611 https://doi.org/10.1007/978-1-0716-2899-7_6

Vancouver

Stewart-Morgan KR, Groth A. Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq. In Marinov GK, Greenleaf WJ, editors, Chromatin Accessibility: Methods and Protocols. Humana Press. 2023. p. 71-84. (Methods in Molecular Biology, Vol. 2611). https://doi.org/10.1007/978-1-0716-2899-7_6

Author

Stewart-Morgan, Kathleen R. ; Groth, Anja. / Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq. Chromatin Accessibility: Methods and Protocols. editor / Georgi K. Marinov ; William J. Greenleaf. Humana Press, 2023. pp. 71-84 (Methods in Molecular Biology, Vol. 2611).

Bibtex

@inbook{6389a657b1114d4c9c6134d564e98b83,
title = "Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq",
abstract = "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.",
keywords = "Accessible chromatin, Chromatin assembly, DNA replication, Nucleosome-free regions, repli-ATAC-seq, Transcription",
author = "Stewart-Morgan, {Kathleen R.} and Anja Groth",
note = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2023",
doi = "10.1007/978-1-0716-2899-7_6",
language = "English",
isbn = "978-1-0716-2898-0",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "71--84",
editor = "Marinov, {Georgi K.} and Greenleaf, {William J.}",
booktitle = "Chromatin Accessibility",
address = "United States",

}

RIS

TY - CHAP

T1 - Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq

AU - Stewart-Morgan, Kathleen R.

AU - Groth, Anja

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 - 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.

AB - 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.

KW - Accessible chromatin

KW - Chromatin assembly

KW - DNA replication

KW - Nucleosome-free regions

KW - repli-ATAC-seq

KW - Transcription

U2 - 10.1007/978-1-0716-2899-7_6

DO - 10.1007/978-1-0716-2899-7_6

M3 - Book chapter

C2 - 36807065

AN - SCOPUS:85148679145

SN - 978-1-0716-2898-0

T3 - Methods in Molecular Biology

SP - 71

EP - 84

BT - Chromatin Accessibility

A2 - Marinov, Georgi K.

A2 - Greenleaf, William J.

PB - Humana Press

ER -

ID: 339137052