A compendium of chromatin interaction maps in the Giant Panda genome

Elucidating transcriptional regulatory mechanisms within tissues is essential for both physiological and pathological studies of giant panda. Here, we generate transcriptomic profiles and construct 3D genome maps for nine giant panda tissues. For the first time, we describe alterations in 3D genome organization among giant panda tissues, providing evidence for changes of A/B compartmentalization, variations in topologically associating domains, and rewiring of promoter-enhancer interactions. We demonstrate that many 3D genome reorganization events are tissue-specific and these structural changes are associated with tissue-specific expression of genes and tissue-relevant biological functions. Furthermore, we use these 3D genome maps to systematically interpret adaptive evolution in giant panda genome, emphasizing importance of considering the genome as a 3D configuration when dissecting potential functions of DNA sequence variation. Collectively, our study increases understanding of functional regulatory mechanisms of giant panda tissues and provides a foundational dataset for analysis of tissue-specific regulatory networks in giant panda.