期刊
NUCLEIC ACIDS RESEARCH
卷 45, 期 2, 页码 832-845出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw1198
关键词
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资金
- National Institutes of Health (NIH) [HG000249, GM101602]
- MOST China-EU Science and Technology Cooperation Program [2013DFE33080]
- National Natural Science Foundation of China [31471238]
- 100 talent award of the Chinese Academy of Sciences
- Science and Technology Planning Projects of Guangdong Province, China [2014B030301058, 2016A050503038]
- Chinese Government Scholarship (CGS)
- University of the Chinese Academy of Sciences (UCAS)
- NIH [HG000249]
Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.
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