Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.

ABSTRACT: Transcription factor (TF)-DNA binding specificity, shaped by both sequence and epigenetic modifications, is central to gene regulation. Universal protein-binding microarrays (uPBMs), based on compact de Bruijn sequence designs, have emerged as powerful tools to characterize the specificity of hundreds of TFs. However, conventional uPBMs binding measurements are limited to direct measurement of short ($\le$8 bp) motifs composed of four canonical bases, lacking the ability to resolve the effects of extended sequence context or modifications. To address these limitations, we developed two enhanced platforms: Ex-uPBM, based on extended higher-order de Bruijn sequences, and Mod-uPBM, based on de Bruijn sequences that incorporate modified bases. Applying Ex-uPBM to known TFs allowed direct measu

SUBMITTER: Bayer Y 

PROVIDER: S-EPMC12746110 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature