2011
DOI: 10.1016/j.cell.2011.10.053
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Abstract: Summary Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this met… Show more

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Cited by 461 publications
(679 citation statements)
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References 68 publications
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“…These results suggest that cooperative interactions of T-box genes with different cofactors, as opposed to differences in DNA-binding sequence recognition, are the key means through which members of this family have diverged in function. Similar findings have been reported, for example, for Hox family transcription factors (38). Moreover, it is likely that regulation of temporal expression could contribute to differences in function.…”
Section: Resultssupporting
confidence: 86%
“…These results suggest that cooperative interactions of T-box genes with different cofactors, as opposed to differences in DNA-binding sequence recognition, are the key means through which members of this family have diverged in function. Similar findings have been reported, for example, for Hox family transcription factors (38). Moreover, it is likely that regulation of temporal expression could contribute to differences in function.…”
Section: Resultssupporting
confidence: 86%
“…A SELEX-seq experiment for the human TF dimer Max−Max was carried out as described previously (30). After two rounds of SELEX, the relative affinities of all 12-mers were calculated, and the data were preprocessed similarly to the uPBM data (see SI Methods).…”
Section: Methodsmentioning
confidence: 99%
“…Samples were sequenced on an Illumina HiSeq 2000 at the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center. The occurrence of every k-mer (lengths of 8-12 bp), summed over all reads, was counted using a sliding window of size k. To correct for biases in the initial DNA library, a standardized enrichment score (Z-score) was calculated by normalizing the counts of every kmer to the expected number of counts in the unenriched library, with a fifthorder Markov model derived from the sequenced starting library (59,60).…”
Section: Methodsmentioning
confidence: 99%