Profiling nucleosome occupancy by MNase-seq: Experimental protocol and computational analysis

Alice Pajoro; Jose M. Muiño; Gerco C. Angenent; Kerstin Kaufmann

doi:10.1007/978-1-4939-7318-7_11

Profiling nucleosome occupancy by MNase-seq: Experimental protocol and computational analysis

Alice Pajoro^*, Jose M. Muiño, Gerco C. Angenent, Kerstin Kaufmann

^*Corresponding author for this work

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

7 Citations (Scopus)

Abstract

Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion combined with high throughput Illumina sequencing (MNase-seq). Nucleosome-associated DNA is relatively insensitive to digestion by micrococcal nuclease (MNase). Upon mild MNase treatment, the undigested nucleosomal DNA can be purified and sequenced allowing a precise localization of in vivo nucleosomes at a genome-wide level.

Original language	English
Title of host publication	Plant Chromatin Dynamics
Subtitle of host publication	Methods and Protocols
Editors	M. Bemer, C. Baroux
Publisher	Humana Press Inc.
Pages	167-181
ISBN (Electronic)	9781493973187
ISBN (Print)	9781493973170
DOIs	https://doi.org/10.1007/978-1-4939-7318-7_11
Publication status	Published - 2018

Publication series

Name	Methods in Molecular Biology
Volume	1675
ISSN (Print)	1064-3745

Keywords

Chromatin
MNase digestion
MNase-seq
Next-generation sequencing
Nucleosome occupancy

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abstract = "Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion combined with high throughput Illumina sequencing (MNase-seq). Nucleosome-associated DNA is relatively insensitive to digestion by micrococcal nuclease (MNase). Upon mild MNase treatment, the undigested nucleosomal DNA can be purified and sequenced allowing a precise localization of in vivo nucleosomes at a genome-wide level.",

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Profiling nucleosome occupancy by MNase-seq : Experimental protocol and computational analysis. / Pajoro, Alice; Muiño, Jose M.; Angenent, Gerco C.; Kaufmann, Kerstin.

Plant Chromatin Dynamics: Methods and Protocols. ed. / M. Bemer; C. Baroux. Humana Press Inc., 2018. p. 167-181 (Methods in Molecular Biology; Vol. 1675).

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

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