Better understanding of heart development and aging could help reveal the mechanisms of heart-associated diseases. We used the Tibetan pig, a miniature swine breed, as a human heart model. We applied in situ Hi-C and single nuclei RNA-seq, and examined changes in higher-order chromatin structure and transcription regulation from the fetal period (late development) to sexual maturity (young adult) and early senescence to understand their roles in physiological development and aging. We observed structural changes of the three-dimensional genome at multiple scales from territories to loops/PEIs.

1. Von Neumann entropy and compartmentalization strength indexes indicated higher plasticity and disorganization of chromatin structure in fetal and senescent stages, respectively, compared with that of the young adults.
2. Changes in intensity of B-B interactions and correlation between sequence features and A/B compartment switches revealed that heterochromatin gradually stacked and relaxed during development and senescence, respectively.
3. A finer examination of TADs and loops/PEIs showed higher correlation of gene expression and TAD connectivity, more space between dynamic boundaries and their targeted genes, and stronger ‘loop skew’ towards A compartments indicating that young adults tend to have more accurate regulation of transcription through finer control of chromatin structure dynamics.
4. Monotonic increases in long-range interactions and decreases in short-range interactions throughout development and senescence also indicate the gradual loss of chromatin conformation plasticity.
5. We also observed dynamic changes of expression profiles for functional relevant genes, accompanying the structural changes of the three-dimensional genome at multiple scales.

This study investigated 3D chromatin conformation in the heart in vivo across periods of development and senescence, and we observed similar features in fetal and senescent individuals compared with young adults. Additionally, by focusing on the late stage of development and the early stage of aging, this study expands our understanding of development and senescence in a broader temporal dimension because previous studies have mainly examined early stages of development or late stages of aging independently. Interestingly, the late stage of development showed similar chromatin structure features compared with early development, and the early stage of aging showed similar characteristics compared with late senescence. In summary, our study delivers a comprehensive view of in vivo chromatin structure dynamics during both development and aging, and provides novel insights into 3D chromatin conformation characteristics of late development and early senescence.

Hi-C,heart development,RNA_-seq,heart aging