SNAP output for PDB entry 6j51 [SNAP web server]

PDB-id

6j51; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-RNA-DNA

Method

cryo-EM (4.2 Å)

Summary

RNA polymerase ii elongation complex bound with spt4-5 and foreign DNA, stalled at shl(-1) of the nucleosome, weak elf1 (+1 position)

Reference

Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019): "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912.

Abstract

RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.