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

@article{citeulike:3196816, 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 protein2013DNA complexes (ChIP2013chip), 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 ChIP2013chip 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.}, address = {Institut de Biotechnologie des Plantes, UMR 8618, Centre National de la Recherche Scientifique, Universit de Paris Sud 11, 91405 Orsay, France; Unit de Recherche en Gnomique Vgtale, UMR INRA 1165-CNRS 8114-UEVE, 91057 Evry Cedex, France; Unit de Mathmatiques et Informatique Appliques, UMR AgroParisTech-INRA, 75231 Paris Cedex, France; Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium; Department of Molecular Genetics, Ghent University, 9052 Gent, Belgium; Warwick Horticultural Research International, University of Warwick, Warwick CV35 9EF, UK; Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Ume, Sweden; Abteilung Entwicklungsbiologie der Pflanzen, Max-Planck-Institut fr Zchtungsforschung, 50829 Kln, Germany; Institute of Plant Sciences, Eidgenssische Technische Hochschule Zurich, 8092 Zurich, Switzerland; Molecular Genetics Group, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands; Department of Biology, Genome Research, Bielefeld University, 33594 Bielefeld, Germany}, author = {Benhamed, Moussa and Martin-Magniette, Marie-Laure and Taconnat, Ludivine and Bitton, Fr\'{e}d\'{e}rique and Servet, Caroline and De Clercq, Rebecca and De Meyer, Bj\"{o}rn and Buysschaert, Caroline and Rombauts, St\'{e}phane and Villarroel, Raimundo and Aubourg, S\'{e}bastien and Beynon, Jim and Bhalerao, Rishikesh P. and Coupland, George and Gruissem, Wilhelm and Menke, Frank L. H. and Weisshaar, Bernd and Renou, Jean-Pierre and Zhou, Dao-Xiu and Hilson, Pierre}, citeulike-article-id = {3196816}, citeulike-linkout-0 = {http://dx.doi.org/10.1111/j.1365-313X.2008.03606.x}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18644002}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18644002}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/120696757/ABSTRACT}, doi = {10.1111/j.1365-313X.2008.03606.x}, journal = {The Plant Journal}, keywords = {promoter}, number = {9999}, posted-at = {2009-06-17 13:45:12}, priority = {2}, title = {Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5}, url = {http://dx.doi.org/10.1111/j.1365-313X.2008.03606.x}, volume = {9999}, year = {2008} }

TY - JOUR ID - citeulike:3196816 L3 - citeulike-article-id:3196816 N2 - 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 protein2013DNA complexes (ChIP2013chip), 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 ChIP2013chip 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. IS - 9999 JF - The Plant Journal AD - Institut de Biotechnologie des Plantes, UMR 8618, Centre National de la Recherche Scientifique, Universit de Paris Sud 11, 91405 Orsay, France; Unit de Recherche en Gnomique Vgtale, UMR INRA 1165-CNRS 8114-UEVE, 91057 Evry Cedex, France; Unit de Mathmatiques et Informatique Appliques, UMR AgroParisTech-INRA, 75231 Paris Cedex, France; Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Gent, Belgium; Department of Molecular Genetics, Ghent University, 9052 Gent, Belgium; Warwick Horticultural Research International, University of Warwick, Warwick CV35 9EF, UK; Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Ume, Sweden; Abteilung Entwicklungsbiologie der Pflanzen, Max-Planck-Institut fr Zchtungsforschung, 50829 Kln, Germany; Institute of Plant Sciences, Eidgenssische Technische Hochschule Zurich, 8092 Zurich, Switzerland; Molecular Genetics Group, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands; Department of Biology, Genome Research, Bielefeld University, 33594 Bielefeld, Germany TI - Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5 VL - 9999 KW - promoter AU - Benhamed, Moussa AU - Martin-Magniette, Marie-Laure AU - Taconnat, Ludivine AU - Bitton, Frédérique AU - Servet, Caroline AU - De Clercq, Rebecca AU - De Meyer, Björn AU - Buysschaert, Caroline AU - Rombauts, Stéphane AU - Villarroel, Raimundo AU - Aubourg, Sébastien AU - Beynon, Jim AU - Bhalerao, Rishikesh AU - Coupland, George AU - Gruissem, Wilhelm AU - Menke, Frank AU - Weisshaar, Bernd AU - Renou, Jean-Pierre AU - Zhou, Dao-Xiu AU - Hilson, Pierre PY - 2008/// UR - http://dx.doi.org/10.1111/j.1365-313X.2008.03606.x ER -