Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

Transcription by RNA polymerase II (RNA Pol II) relies on the elongation factors PAF1 complex (PAF), RTF1, and SPT6. Here, we use rapid factor depletion and multi-omics analysis to investigate how these elongation factors influence RNA Pol II elongation activity in human cells. Whereas depletion of PAF subunits PAF1 and CTR9 has little effect on cellular RNA synthesis, depletion of RTF1 or SPT6 strongly compromises RNA Pol II activity, albeit in fundamentally different ways. RTF1 depletion decreases RNA Pol II velocity, whereas SPT6 depletion impairs RNA Pol II progression through nucleosomes. These results show that distinct elongation factors stimulate either RNA Pol II velocity or RNA Pol II progression through chromatin in vivo. Further analysis provides evidence for two distinct barriers to early elongation: the promoter-proximal pause site and the +1 nucleosome. It emerges that the first barrier enables loading of elongation factors that are required to overcome the second and subsequent barriers to transcription. [Display omitted] •The PAF1 complex and SPT6 have positive roles in transcription elongation•RTF1 and SPT6 stimulate RNA polymerase II elongation in distinct ways•Depletion of RTF1 decreases RNA polymerase II velocity•Loss of SPT6 hinders RNA polymerase II progression through nucleosomes Metazoan gene transcription requires RNA polymerase II and a large number of factors that help the polymerase to pass through genes. Žumer et al. utilize rapid depletion of endogenous proteins from human cells and sequencing approaches to show two distinct mechanisms of two such elongation factors: one controls polymerase speed, and the other controls polymerase passage through chromatin.