A dual role for H2A.Z.1 in modulating Initiating and Elongating RNAPII dynamics

RNA Polymerase II (RNAPII) pausing immediately downstream of the transcription start site (TSS) is a critical rate limiting step for the induction of most metazoan genes. During pause-release, RNAPII encounters a highly conserved +1 H2A.Z nucleosome, yet how this histone variant contributes to transcription is poorly understood. Here, using an inducible protein degron system combined with genomic approaches and live cell super-resolution microscopy, we show that H2A.Z.1 modulates RNAPII dynamics across most genes in murine embryonic stem cells (ESCs). Our quantitative analysis shows that H2A.Z.1 slows the rate of RNAPII pause release and consequently impacts Negative Elongation Factor (NELF) dynamics as well as nascent transcription. Consequently, H2A.Z.1 also impacts re-loading of the Pre-Initiation Complex (PIC) components TFIIB and TBP. Together, this work provides a critical mechanistic link between H2A.Z.1 and the proper induction of mammalian gene expression programs by regulating RNAPII dynamics and pause release. ChIP-seq, RNA-seq, NET-seq, and ChIP-nexus following H2A.Z.1 depletion