Chromatin Accessibility Dynamics in the Reprogramming of Somatic Cells to Pluripotency

Pluripotent stem cells have the incredible ability to self-renew indefinitely and to differentiate into all the cell types of the body. Remarkably, somatic cells can transition back into a pluripotent state through ectopic expression of the transcription factors OCT4, SOX2, KLF4, and MYC. This shift towards a state of higher differentiation potential represents an extraordinary capability to alter cell fate. However, reprogramming studies are challenging due to the inefficient and heterogeneous nature of the process. Single-cell analysis of chromatin accessibility changes uncovered enhanced enrichment for 3D chromatin reorganization factor (KLF4, MAZ, and PATZ1) binding in high-efficient reprogramming. Cells experience more changes upon withdrawal of the ectopic reprogramming factors, including a Tcfap2c-mediated maintenance of the pluripotent state. Development of a new computational algorithm, scCISINT, allowed for prediction of long-range interactions among differentially accessible regions across reprogramming clusters. We used CRISPRi repression at candidate interacting loci to validate the essential role of the putative long-range interactions in transforming cell fate. Altogether, our work has uncovered key gene expression and chromatin-associated features that guide cells along a path towards successful pluripotency acquisition. Single-cell ATAC-sequencing of mouse embryonic fibroblasts (MEFs), MEFs undergoing reprogramming, mouse embryonic stem cells, and mouse induced pluripotent stem cells