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bioRxiv · 10.1101/143677

Transcription Factors Recognize DNA Shape Without Nucleotide Recognition

Samee, M. A. H.·Bruneau, B.·Pollard, K.
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Abstract

We hypothesized that transcription factors (TFs) recognize DNA shape without nucleotide sequence recognition. Motivating an independent role for shape, many TF binding sites lack a sequence-motif, DNA shape adds specificity to sequence-motifs, and different sequences can encode similar shapes. We therefore asked if binding sites of a TF are enriched for specific patterns of DNA shape-features, e.g., helical twist. We developed ShapeMF, which discovers these shape-motifs de novo without taking sequence information into account. We find that most TFs assayed in ENCODE have shape-motifs and bind regulatory regions recognizing shape-motifs in the absence of sequence-motifs. When shape- and sequence-recognition co-occur, the two types of motifs can be overlapping, flanking, or separated by consistent spacing. Shape-motifs are prevalent in regions co-bound by multiple TFs. Finally, TFs with identical sequence motifs have different shape-motifs, explaining their binding at distinct locations. These results establish shape-motifs as drivers of TF-DNA recognition complementary to sequence-motifs.

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Samee, M. A. H., Bruneau, B., Pollard, K.. 2017-05-29. Transcription Factors Recognize DNA Shape Without Nucleotide Recognition. https://doi.org/10.1101/143677

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