Protocol: Chromatin immunoprecipitation (ChIP) methodology to investigate histone modifications in two model diatom species View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12

AUTHORS

Xin Lin, Leïla Tirichine, Chris Bowler

ABSTRACT

In this report we describe a chromatin immunoprecipitation (ChIP) protocol for two fully sequenced model diatom species Phaeodactylum tricornutum and Thalassiosira pseudonana. This protocol allows the extraction of satisfactory amounts of chromatin and gives reproducible results. We coupled the ChIP assay with real time quantitative PCR. Our results reveal that the two major histone marks H3K4me2 and H3K9me2 exist in P. tricornutum and T. pseudonana. As in other eukaryotes, H3K4me2 marks active genes whereas H3K9me2 marks transcriptionally inactive transposable elements. Unexpectedly however, T. pseudonana housekeeping genes also show a relative enrichment of H3K9me2. We also discuss optimization of the procedure, including growth conditions, cross linking and sonication. Validation of the protocol provides a set of genes and transposable elements that can be used as controls for studies using ChIP in each diatom species. This protocol can be easily adapted to other diatoms and eukaryotic phytoplankton species for genetic and biochemical studies. More... »

PAGES

48

Journal

TITLE

Plant Methods

ISSUE

1

VOLUME

8

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1746-4811-8-48

DOI

http://dx.doi.org/10.1186/1746-4811-8-48

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1026666913

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23217141


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