Integrator complex bridges TFIID and RNA polymerase II to maintain pluripotency during development (PRO-Seq)

The mechanisms by which the expression of pluripotency and Polycomb networks are harmonized to allow the transition from the pluripotency to a differentiated state has not been fully elucidated. Integrator complex regulates transcription pause release and RNA processing in metazoans. Here, we show that acute depletion of INTS11 in mouse embryonic stem cells or its conditional deletion in mouse results in loss of stemness and block of early embryonic development, respectively. We show that Integrator plays a role in stemness and cellular differentiation by bridging the association of RNA polymerase II (RNAPII) and basal transcription factor (TFIID). While the catalytic endonuclease activity is required to enhance cellular reprogramming, depletion of INTS11 diminish RNAPII recruitment to promoters and super-enhancers of pluripotency and Polycomb genes leading to their repression. We place Integrator at pre-initiation complex formation linking the pluripotency and Polycomb pathways to ensure orderly cellular differentiation during development. Overall design: To determine how acute INTS11 loss affects RNAPII activity in mouse ESCs, we generated INTS11 degron ESCs. Upon removal of drug to induce INTS11 degradation for 0h, 1h, 3h and 6h, samples were isolated at indicated timepoints. Nuclear run-on assays (PRO-seq) were performed with ten million purified nuclei per sample.