Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro.

ABSTRACT: Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding. Specifically, Co-SELECT leverages the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allows Co-SELECT to detect an evidence for the role of DNA shape features in TF binding. Our approa

SUBMITTER: Pal S 

PROVIDER: S-EPMC6649817 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature