Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5

Moussa Benhamed, Marie Laure Martin-Magniette, Ludivine Taconnat, Frédérique Bitton, Caroline Servet, Rebecca De Clercq, Björn De Meyer, Caroline Buysschaert, Stéphane Rombauts, Raimundo Villarroel, Sébastien Aubourg, Jim Beynon, Rishikesh P. Bhalerao, George Coupland, Wilhelm Gruissem, Frank L.H. Menke, Bernd Weisshaar, Jean Pierre Renou, Dao Xiu Zhou*, Pierre Hilson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

88 Scopus citations

Abstract

We have assembled approximately 20 000 Arabidopsis thaliana promoter regions, compatible with functional studies that require cloning and with microarray applications. The promoter fragments can be captured as modular entry clones (MultiSite Gateway format) via site-specific recombinational cloning, and transferred into vectors of choice to investigate transcriptional networks. The fragments can also be amplified by PCR and printed on glass arrays. In combination with immunoprecipitation of protein-DNA complexes (ChIP-chip), these arrays enable characterization of binding sites for chromatin-associated proteins or the extent of chromatin modifications at genome scale. The Arabidopsis histone acetyltransferase GCN5 associated with 40% of the tested promoters. At most sites, binding did not depend on the integrity of the GCN5 bromodomain. However, the presence of the bromodomain was necessary for binding to 11% of the promoter regions, and correlated with acetylation of lysine 14 of histone H3 in these promoters. Combined analysis of ChIP-chip and transcriptomic data indicated that binding of GCN5 does not strictly correlate with gene activation. GCN5 has previously been shown to be required for light-regulated gene expression and growth, and we found that GCN5 targets were enriched in early light-responsive genes. Thus, in addition to its transcriptional activation function, GCN5 may play an important role in priming activation of inducible genes under non-induced conditions.

Original languageEnglish (US)
Pages (from-to)493-504
Number of pages12
JournalPlant Journal
Volume56
Issue number3
DOIs
StatePublished - Nov 2008

Keywords

  • Arabidopsis
  • ChIP-chip
  • Chromatin immunoprecipitation
  • Gateway site-specific recombination
  • Histone acetylation
  • Promoter

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology

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