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

Plant Methods

Chris Bowler¹  Leïla Tirichine¹  Xin Lin¹ 

[1] Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Génomique, Environnementale et Evolutive Section 3 CNRS UMR8197, 46 rue d’Ulm, Paris, 75005, France

关键词: Epigenomics;    Chromatin immunoprecipitation;    Histone modifications;    Thalassiosira pseudonana;    Phaeodactylum tricornutum;   

Others  :  821261
DOI  :  10.1186/1746-4811-8-48

 received in 2012-10-24, accepted in 2012-12-05,  发布年份 2012

【 摘 要 】

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.

【 授权许可】

   
2012 Lin et al.; licensee BioMed Central Ltd.

【 图 表 】

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