Slow RNAPII elongation enhances naive pluripotency rewiring while maintaining high replication fork speed.

Abstract

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 show that altering their elongation rates-specifically, slowed transcriptional elongation alongside rapid replication fork progression-does not elicit replicative stress. Instead, this independent kinetic variation accelerates the acquisition of naive pluripotency during in vitro dedifferentiation, 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 RNA polymerase II (RNAPII) elongation. 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.