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 proceedingChapterAcademicpeer-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 languageEnglish
Title of host publicationPlant Chromatin Dynamics
Subtitle of host publicationMethods and Protocols
EditorsM. Bemer, C. Baroux
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

Keywords

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

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