P-TEFb regulates nucleosome positioning at promoters

Nucleosomes are believed to be a barrier to RNA polymerase II (RNA Pol II) transcription, yet the phased positioning of promoter-proximal nucleosomes correlates with active transcription. The mechanism underlying this paradox is unclear. It is well established that positive transcription elongation factor b (P-TEFb), the kinase component of the super elongation complex (SEC), controls the release of paused RNA Pol II into productive elongation. Here, we show that acute depletion or inhibition of SEC in mouse embryonic stem cells (mESCs) disrupts nucleosome positioning and leads to cryptic transcription specifically within the early elongation zone. Mechanistically, SEC directly phosphorylates the chromatin remodeler CHD1, which enhances its binding to H3K4me2/3-marked nucleosomes and incorporation into elongation condensates, contributing to proper nucleosome spacing. Phosphorylation-deficient CHD1 mutations, including disease-associated variants, recapitulate the effects of SEC inhibition on nucleosome positioning, alongside impaired RNA Pol II pause release and attenuated elongation. Thus, our study demonstrates a critical role of SEC in establishing nucleosome positioning, which is essential for proper early elongation.