Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming

Pluripotent genomes are folded in a topological hierarchy that reorganizes during differentiation. The extent to which chromatin architecture is reconfigured during somatic cell reprogramming is poorly understood. Here we integrate fine-resolution architecture maps with epigenetic marks and gene expression in embryonic stem cells (ESCs), neural progenitor cells (NPCs), and NPC-derived induced pluripotent stem cells (iPSCs). We find that most pluripotency genes reconnect to target enhancers during reprogramming. Unexpectedly, some NPC interactions around pluripotency genes persist in our iPSC clone. Pluripotency genes engaged in both “fully-reprogrammed” and “persistent-NPC” interactions exhibit over/undershooting of target expression levels in iPSCs. Additionally, we identify a subset of “poorly reprogrammed” interactions that do not reconnect in iPSCs and display only partially recovered, ESC-specific CTCF occupancy. 2i/LIF can abrogate persistent-NPC interactions, recover poorly reprogrammed interactions, reinstate CTCF occupancy, and restore expression levels. Our results demonstrate that iPSC genomes can exhibit imperfectly rewired 3D-folding linked to inaccurately reprogrammed gene expression. [Display omitted] •3D genome architecture is markedly reconfigured during reprogramming•Some pluripotency genes engage in persistent, NPC-like interactions in iPSCs that break apart in 2i•ESC-specific interactions that do not reconnect in iPSCs exhibit decreased CTCF binding•Imperfectly rewired iPSC genome topology is linked to inaccurately reprogrammed expression Phillips-Cremins and colleagues report high-resolution chromatin folding maps in primary NPCs and NPC-derived induced pluripotent stem cells. They find that iPSC genomes can exhibit an imperfectly rewired 3D-folding state linked to poorly reprogrammed, ESC-specific CTCF occupancy and inaccurately reprogrammed gene expression levels. 2i/LIF conditions can fully restore distinct topological hallmarks of pluripotency.