Structural basis of nucleosome retention during transcription elongation

Abstract

In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow transcription and how DNA rewraps to retain nucleosomes has been unclear. Here, we report the 3.0-angstrom cryo–electron microscopy structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex stalled 54 base pairs within the nucleosome. The structure provides a mechanistic basis for nucleosome retention during transcription elongation where upstream DNA emerging from the Pol II cleft has rewrapped the proximal side of the nucleosome. The structure uncovers a direct role for Pol II and transcription elongation factors in nucleosome retention and explains how nucleosomes are retained to prevent the disruption of chromatin structure across actively transcribed genes.

Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT

“…It was previously proposed that RNAPII alone can pass through a nucleosome through a looped-template intermediate (“Ø loop”) without shifting the nucleosome position ( 45 , 50 , 51 ). A recently reported structure of an RNAPII-nucleosome complex contained an approximately 90-bp looped-template DNA, which was proposed to mediate the nucleosome retention ( 52 ). These Ø-loop and 90-bp-loop models are likely to differ from our current mechanism, which relies on elongation factors and histone chaperones.…”

Histone H2Bub dynamics in the 5′ region of active genes are tightly linked to the UV-induced transcriptional response

“…Indeed, H2Bub is required for FACT activity in genic regions [83] , which tethers the proximal H2A-H2B dimer removed during nucleosome traversal. Their concerted action facilitates nucleosome reassembly in the wake of RNAPII [84] , as transcribed DNA rewraps around a conserved nucleosome (same histones molecules) to guarantee that epigenetic marks are retained during transcription [85] . In this way, while the RNAPII complex moves forward, the ubiquitin moiety is removed from H2B, by SAGA DUB or other ATXN7L3-mediated DUBs, after nucleosome clearance.…”

Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate

“…The dissociation of the proximal H2AH2B dimer creates an O-loop with DNA unwrapped from the nucleosome three DNA turns at a time. [78,79] The loop was then rewrapped on upstream DNA, promoting unwrapping of the distal DNA and translocation of the nucleosome toward the promoter, with relocation by chromatin remodelers occurring at a later step. [79] The findings open the possibility of a conformational change of flipons in the O-ring DNA that alters outcomes.…”