Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.

ABSTRACT: Topologically associating domains (TADs) are essential components of three-dimensional (3D) genome organization and significantly influence gene transcription regulation. However, accurately identifying TADs from sparse chromatin contact maps and exploring the structural and functional elements within TADs remain challenging. To this end, we develop TADGATE, a graph attention auto-encoder that can generate imputed maps from sparse Hi-C contact maps while adaptively preserving or enhancing the underlying topological structures, thereby facilitating TAD identification. TADGATE captures specific attention patterns with two types of units within TADs and demonstrates TAD organization relates to chromatin compartmentalization with diverse biological properties. We identify many structural and f

SUBMITTER: Dang D 

PROVIDER: S-EPMC11879124 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature