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Structural basis of the nucleosome transition during RNA polymerase II passage

Nucleosomal DNA transcription In eukaryotes, the basic chromatin unit nucleosome stalls RNA polymerase II (RNAPII) when it transcribes genetic information on DNA. Using cryo–electron microscopy, Kujirai et al. explored seven structures of the RNAPII-nucleosome complex, in which RNAPII pauses at four locations on the nucleosome. These serial snapshots of the RNAPII progression reveal the molecular mechanism of how RNAPII peels the nucleosomal DNA off the histone stepwise. Science, this issue p. 595 Cryo–electron microscopy structures of RNA polymerase II (RNAPII)–nucleosome complexes reveal how RNAPII transcribes nucleosomal DNA. Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo–electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(−6), SHL(−5), SHL(−2), and SHL(−1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(−1) complexes are bound to a “foreign” DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.