Determination and inference of eukaryotic transcription factor sequence specificity
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Authors
Weirauch, Matthew T.Yang, Ally
Albu, Mihai
Cote, Atina G.
Montenegro-Montero, Alejandro
Drewe, Philipp
Najafabadi, Hamed S.
Lambert, Samuel A.
Mann, Ishminder
Cook, Kate
Zheng, Hong
Goity, Alejandra
van Bakel, Harm
Lozano, Jean-Claude
Galli, Mary
Lewsey, Mathew G.
Huang, Eryong
Mukherjee, Tuhin
Chen, Xiaoting
Reece-Hoyes, John S.
Govindarajan, Sridhar
Shaulsky, Gad
Walhout, Albertha J. M.
Bouget, Francois-Yves
Ratsch, Gunnar
Larrondo, Luis F.
Ecker, Joseph R.
Hughes, Timothy R.
Document Type
Journal ArticlePublication Date
2014-09-11
Metadata
Show full item recordAbstract
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only approximately 1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for approximately 34% of the approximately 170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.Source
Cell. 2014 Sep 11;158(6):1431-43. doi: 10.1016/j.cell.2014.08.009. Link to article on publisher's siteDOI
10.1016/j.cell.2014.08.009Permanent Link to this Item
http://hdl.handle.net/20.500.14038/49930PubMed ID
25215497Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1016/j.cell.2014.08.009