Structure of transcribing RNA polymerase II-nucleosome complex

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 Å. 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.

Fig. 1

Structure of Pol II–NCP complex. a–c Cartoon model viewed from the front (a), side (b), and top (c). Pol II subunits Rpb1–Rpb12, template DNA, non-template DNA, RNA, H2A, H2B, H3 and H4 are coloured in silver, sand, ruby, deep purple, slate, cyan, deepblue, forest green, orange, purple, yellow, green, blue, cyan, red, yellow, crimson, light blue and green, respectively. Colour code used throughout. Histone octamer dyad axis is indicated as a black line with white outline

Fig. 2

Pol II–NCP contacts. Rpb1 clamp head and Rpb2 lobe domains contact nucleosomal DNA around the NCP dyad. Clamp head and lobe domains are shown. Loops contacting nucleosomal DNA are indicated

Fig. 3

Accommodation of elongation factors. a Superposition of Pol II–NCP structure with the mammalian paused elongation complex PEC (PDB code 6GML) provides the location of DSIF and NELF. b Superposition of the mammalian activated elongation complex EC* (PDB code 6GMH) provides the location of PAF1 complex (PAF) and SPT6