Abstract
Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 A. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription. Eukaryotic transcription requires passage of RNA polymerase II (Pol II) through chromatin, which is impaired by nucleosomes. Here the authors report the cryo-EM structure of transcribing Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 A, providing insights into the mechanism of chromatin transcription.
Highlights
Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved
After our work was completed, similar structures of nucleosome core particle (NCP) complexes with the yeast Komagataella pastoris Pol II were reported[17], which together with our results provide a basis for investigating factordependent chromatin transcription
To investigate how Pol II passes through chromatin, we determined the structure of Pol II transcribing into a NCP
Summary
Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Pol II requires transcription elongation factors, chromatin remodelling enzymes and histone chaperones to overcome the nucleosomal barrier and to reestablish chromatin[7–11]. The mechanisms underlying these processes, remain poorly understood because Pol II complex structures have only been determined on linear DNA, and not on chromatin templates[12]. Comparison with known Pol II complex structures[13–15] suggests that transcription elongation factors can be accommodated in the presence of the nucleosome. After our work was completed, similar structures of NCP complexes with the yeast Komagataella pastoris Pol II were reported[17], which together with our results provide a basis for investigating factordependent chromatin transcription
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