A whole-body atlas of enhancer and super-enhancer regulatory networks reveals tissue-specific hub enhancers and hierarchical regulatory logic in pigs

Enhancer regulatory networks are central determinants of tissue identity and function, yet their hierarchical organization across pig tissues remains poorly understood, largely due to incomplete tissue coverage and genetic heterogeneity. Here, leveraging genetically matched full-sibling pig pair, we generated epigenomic profiles from 151 anatomical sites across 58 tissues and reconstructed 20,468 typical enhancer regulatory networks at whole-body scale. Tissue-specific enhancers were preferentially enriched in more complex networks, and 1,535 networks showed tissue-specific functional relevance. In parallel, we identified 477 super-enhancer-mediated core regulatory circuitries involving 368 transcription factors, revealing an additional layer of tissue-specific regulation. These two frameworks were highly complementary, identifying distinct sets of hub enhancers with limited overlap. Hub enhancers identified by both frameworks were strongly enriched for CTCF, implicating three-dimensional chromatin architecture in tissue-specific regulation. Integrating single-cell chromatin accessibility and transcriptomic data from the thymus further resolved hub enhancer activity to cellular resolution. Together, this whole-body atlas provides a valuable resource for decoding enhancer regulatory hierarchies and tissue-specific gene regulatory programs in pigs.