Multiple overlapping binding sites determine transcription factor occupancy.

ABSTRACT: Transcription factors (TFs) regulate gene expression by interacting with DNA in a sequence-specific manner. High-throughput in vitro technologies, such as protein-binding microarrays^1-6 and HT-SELEX (high-throughput systematic evolution of ligands by exponential enrichment)^7,8, have revealed the DNA-binding specificities of hundreds of TFs. However, they have limited ability to reliably identify lower-affinity DNA binding sites, which are increasingly recognized as important for precise spatiotemporal control of gene expression^9-19. Here, to address this limitation, we developed protein affinity to DNA by in vitro transcription and RNA sequencing (PADIT-seq), with which we comprehensively assayed the binding preferences of six TFs to all possible ten-base-p

SUBMITTER: Khetan S 

PROVIDER: S-EPMC12447533 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature