Slow RNAPII elongation enhances naive-pluripotency rewiring while preserving replication fork speed

DNA replication and transcription must be intricately coordinated, as both machineries navigate the same chromatin landscape to ensure genome stability and proper cell function. Here, we uncover that a global imbalance between their elongation rates-- specifically, slowed transcriptional elongation alongside rapid replication fork progression--does not elicit replicative stress. Instead, this uncoupling accelerates the acquisition of naive pluripotency during in vitro de-differentiation, revealing an unexpected link between transcription kinetics and cell plasticity. Mechanistically, we show that the transition to naive pluripotency is accompanied by a distinctive alternative splicing program indicative of reduced RNAPII elongation, both in vitro and in vivo. These findings redefine the functional relationship between replication and transcription dynamics and uncover transcriptional velocity as a tunable layer of control over cellular identity transitions. HighlightsO_LIReplication and transcription elongation rates can be uncoupled genome-wide. C_LIO_LISlow transcription elongation accelerates the acquisition of naive pluripotency during in vitro de-differentiation. C_LIO_LIHigh replication fork speed is maintained in slow-transcribing cells during cell state transitions. C_LIO_LIAlternative splicing is distinctly regulated at the naive and primed pluripotency states, both in vitro and in vivo. C_LI