Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

• Published in: The EMBO journal 2010-07, Vol.29 (13), p.2147-2160
• Main Authors: 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, Bulyk, Martha L, Taipale, Jussi
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Binding Sites; cancer; Cell Line; ChIP-seq; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - metabolism; DNA-binding specificity; EMBO09; EMBO43; ETS family of transcription factors; Genome-Wide Association Study; Genomics; Humans; Life Sciences; Medicin och hälsovetenskap; Mice; Models, Molecular; Molecular biology; Physiology; Protein Binding; Proto-Oncogene Proteins c-ets - chemistry; Proto-Oncogene Proteins c-ets - metabolism; Research methodology; Sequence Analysis, DNA; transcription factor-DNA binding assay
• ISSN: 0261-4189; 1460-2075; 1460-2075
• DOI: 10.1038/emboj.2010.106

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.