Multiscale footprints reveal the organization of cis-regulatory elements.

ABSTRACT: Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time¹. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size. Using these multiscale footprints, we created the seq2PRINT framework, which uses deep learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Ap

SUBMITTER: Hu Y 

PROVIDER: S-EPMC11839466 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature