Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo

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Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo

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Title: Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo
Author: Wei, Gong-Hong; Badis, Gwenael; Berger, Michael F; Kivioja, Teemu; Palin, Kimmo; Enge, Martin; Bonke, Martin; Jolma, Arttu; Varjosalo, Markku; Gehrke, Andrew R; Yan, Jian; Talukder, Shaheynoor; Turunen, Mikko; Taipale, Mikko; Stunnenberg, Hendrik G; Ukkonen, Esko; Hughes, Timothy R; Taipale, Jussi; Bulyk, Martha Leonia

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Citation: Wei, Gong-Hong, Gwenael Badis, Michael F. Berger, Teemu Kivioja, Kimmo Palin, Martin Enge, Martin Bonke, et al. 2010. Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. The EMBO Journal 29, no. 13: 2147-2160.
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Abstract: Members of the large ETS family of transcription factors (TFs) have highly similar DNA-binding domains (DBDs)—yet they have diverse functions and activities in physiology and oncogenesis. Some differences in DNA-binding preferences within this family have been described, but they have not been analysed systematically, and their contributions to targeting remain largely uncharacterized. We report here the DNA-binding profiles for all human and mouse ETS factors, which we generated using two different methods: a high-throughput microwell-based TF DNA-binding specificity assay, and protein-binding microarrays (PBMs). Both approaches reveal that the ETS-binding profiles cluster into four distinct classes, and that all ETS factors linked to cancer, ERG, ETV1, ETV4 and FLI1, fall into just one of these classes. We identify amino-acid residues that are critical for the differences in specificity between all the classes, and confirm the specificities in vivo using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for a member of each class. The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo.
Published Version: doi://10.1038/emboj.2010.106
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