Single-cell 3D genome structure reveals distinct human pluripotent states (RNA-Seq)

Pluripotent states of embryonic stem cells (ESCs) with distinct transcription profile affect their differentiation capacity and therapeutic potential. By single cell analysis of high-resolution three-dimensional (3D) genome structure, we show that remodeling genome structure is highly associated with pluripotent states of human ESCs (hESCs). Naive pluripotent state is featured with specialized 3D genome structures and clear chromatin compartmentation distinct from primed state. Naive pluripotent state may be achieved by remodeled active euchromatin compartment and less chromatin interaction in the nuclear center. This unique genome organization is linked to elevated chromatin accessibility on enhancers and thus high expression levels of naive pluripotent genes localized in this region. On the contrary, primed state exhibits intermingled genome organization. Moreover, active euchromatin and primed pluripotent genes are distributed in the nuclear periphery and yet repressive heterochromatin densely concentrated in the nuclear center, reducing chromatin accessibility and transcription of naive genes. Thus, inversion or relocation of heterochromatin to euchromatin compartmentation is related to regulating chromatin accessibility and thus define pluripotent states and cell identity. Naïve hPSCs are converted from Primed hPSCs based on the expression of HERVH after the treatment with several chemicals, and we illustrate the difference by RNA-seq, ATAC-seq, and CUT&Tag-seq between Naïve and Primed hPSCs.