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 proceedingChapter

5 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 languageEnglish
Title of host publicationPlant Chromatin Dynamics
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages167-181
ISBN (Electronic)9781493973187
ISBN (Print)9781493973170
DOIs
Publication statusPublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1675
ISSN (Print)1064-3745

Fingerprint

Micrococcal Nuclease
Nucleosomes
Genome
Chromatin
Digestion
DNA
Genes

Keywords

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

Cite this

Pajoro, A., Muiño, J. M., Angenent, G. C., & Kaufmann, K. (2018). Profiling nucleosome occupancy by MNase-seq: Experimental protocol and computational analysis. In Plant Chromatin Dynamics: Methods and Protocols (pp. 167-181). (Methods in Molecular Biology; Vol. 1675). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7318-7_11
Pajoro, Alice ; Muiño, Jose M. ; Angenent, Gerco C. ; Kaufmann, Kerstin. / Profiling nucleosome occupancy by MNase-seq : Experimental protocol and computational analysis. Plant Chromatin Dynamics: Methods and Protocols. Humana Press Inc., 2018. pp. 167-181 (Methods in Molecular Biology).
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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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Pajoro, A, Muiño, JM, Angenent, GC & Kaufmann, K 2018, Profiling nucleosome occupancy by MNase-seq: Experimental protocol and computational analysis. in Plant Chromatin Dynamics: Methods and Protocols. Methods in Molecular Biology, vol. 1675, Humana Press Inc., pp. 167-181. https://doi.org/10.1007/978-1-4939-7318-7_11

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. Humana Press Inc., 2018. p. 167-181 (Methods in Molecular Biology; Vol. 1675).

Research output: Chapter in Book/Report/Conference proceedingChapter

TY - CHAP

T1 - Profiling nucleosome occupancy by MNase-seq

T2 - Experimental protocol and computational analysis

AU - Pajoro, Alice

AU - Muiño, Jose M.

AU - Angenent, Gerco C.

AU - Kaufmann, Kerstin

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - Chromatin

KW - MNase digestion

KW - MNase-seq

KW - Next-generation sequencing

KW - Nucleosome occupancy

U2 - 10.1007/978-1-4939-7318-7_11

DO - 10.1007/978-1-4939-7318-7_11

M3 - Chapter

SN - 9781493973170

T3 - Methods in Molecular Biology

SP - 167

EP - 181

BT - Plant Chromatin Dynamics

PB - Humana Press Inc.

ER -

Pajoro A, Muiño JM, Angenent GC, Kaufmann K. Profiling nucleosome occupancy by MNase-seq: Experimental protocol and computational analysis. In Plant Chromatin Dynamics: Methods and Protocols. Humana Press Inc. 2018. p. 167-181. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7318-7_11