Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.
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.
Wei
Gong-Hong
GH
Public Health Genomics Unit, National Institute for Health and Welfare (THL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland.
Badis
Gwenael
G
Berger
Michael F
MF
Kivioja
Teemu
T
Palin
Kimmo
K
Enge
Martin
M
Bonke
Martin
M
Jolma
Arttu
A
Varjosalo
Markku
M
Gehrke
Andrew R
AR
Yan
Jian
J
Talukder
Shaheynoor
S
Turunen
Mikko
M
Taipale
Mikko
M
Stunnenberg
Hendrik G
HG
Ukkonen
Esko
E
Hughes
Timothy R
TR
Bulyk
Martha L
ML
Taipale
Jussi
J
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D055106:Genome-Wide Association Study; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D011485:Protein Binding; D050783:Proto-Oncogene Proteins c-ets / Q000737:chemistry / Q000378:metabolism*; D017422:Sequence Analysis, DNA
D050783:Proto-Oncogene Proteins c-ets; D004247:DNA