Genome-wide profiling of histone modifications and histone variants in Arabidopsis thaliana and Marchantia polymorpha

Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, Tomokazu Kawashima

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

4 Scopus citations

Abstract

Histone modifications and histone variants barcode the genome and play major roles in epigenetic regulations. Chromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is a well-established method to investigate the landscape of epigenetic marks at a genomic level. Here, we describe procedures for conducting ChIP, subsequent NGS library construction, and data analysis on histone modifications and histone variants in Arabidopsis thaliana. We also describe an optimized nuclear isolation procedure to prepare chromatin for ChIP in the liverwort, Marchantia polymorpha, which is the emerging model plant ideal for evolutionary studies.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
Pages93-106
Number of pages14
DOIs
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1610
ISSN (Print)1064-3745

Bibliographical note

Funding Information:
Thanks to S. Akimcheva and J. S. Russell for technical assistance and critical reading, respectively. AO was supported by a Grant-in-Aid for the Japan Society for the Promotion of Science (JSPS) Fellows. RY, TK, EA, and FB were funded by GMI and FWF (grants 2163-B16 linked to ERA-CAPS project EVOREPRO).

Publisher Copyright:
© Springer Science+Business Media LLC 2017.

Keywords

  • Arabidopsis thaliana
  • Chromatin immunoprecipitation
  • Histone modifications
  • Histone variants
  • Marchantia polymorpha

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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