Investigation of 3D Chromatin Architecture Rewiring During Muscle Satellite Cells activation and aging [HiC SC]

3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging. The in situ Hi-C libraries were prepared as previously reported. Briefly, isolated SCs were digested using 100U DpnII overnight at 37 °C and then filled in with biotin for 1.5 hours at 37 °C; ligated for 4.5 hours at room temperature. DNA was purified by ethanol precipitation, and then sheared into 300-400bp fragments using Covaris S220. DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification as described. The libraries were then sequenced via the Illumina HiSeq X Ten system at Genewiz company.