Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing.

ABSTRACT: DNA-transcription factor (TF) interactions are essential for gene regulation. Fully characterizing TF recognition specificities and identifying their genomic binding targets are important to understand TF function and regulatory networks. Recently, high-throughput sequencing technology HT-SELEX (high-throughput systematic evolution of ligands by exponential enrichment) has been used to measure hundreds of TFs, providing massive datasets that comprise TF binding preferences. However, there is a need to develop comprehensive computational modeling to fully extract and characterize critical TF binding preferences and fail to distinguish genome-wide binding targets. In this study, we developed a global pairwise model called DCA-Scapes trained with experimental HT-SELEX data. Our approach uncov

SUBMITTER: Zhou Q 

PROVIDER: S-EPMC12214022 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature