Chrombus-XMBD: a graph convolution model predicting 3D-genome from chromatin features.

ABSTRACT: The 3D conformation of the chromatin is crucial for transcriptional regulation. However, current experimental techniques for detecting the 3D structure of the genome are costly and limited to the biological conditions. Here, we described "ChrombusXMBD," a graph convolution model capable of predicting chromatin interactions ab initio based on available chromatin features. Using dynamic edge convolution with multihead attention mechanism, Chrombus encodes the 2D-chromatin features into a learnable embedding space, thereby generating a genome-wide 3D-contactmap. In validation, Chrombus effectively recapitulated the topological associated domains, expression quantitative trait loci, and promoter/enhancer interactions. Especially, Chrombus outperforms existing algorithms in predicting chromatin

SUBMITTER: Zeng Y 

PROVIDER: S-EPMC12047703 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature