Multimodal learning decodes the global binding landscape of chromatin-associated proteins.

ABSTRACT: Chromatin-associated proteins (CAPs), including over 1,600 transcription factors, bind directly or indirectly to the genomic DNA to regulate gene expression and determine a myriad of cell types. Mapping their genome-wide binding and co-binding landscape is essential towards a mechanistic understanding of their functions in gene regulation and resulting cellular phenotypes. However, due to the lack of techniques that effectively scale across proteins and biological samples, their genome-wide binding profiles remain challenging to obtain, particularly in primary cells. Here we present Chromnitron, a multimodal foundation model that accurately predicts CAP binding landscapes across hundreds of proteins in unseen cell types. Via in silico perturbation experiments, we show that the model

SUBMITTER: Tan J 

PROVIDER: S-EPMC12363962 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature