Structural basis of nucleosome remodeling by archaeal RNA polymerase during transcription elongation
- 1EMBL
Abstract
Transcription occurs in the context of histone-based chromatin in eukaryotes and most archaea. The archaeal RNA polymerase and histones are ancestral to their eukaryotic counterparts, yet how RNA polymerase traverses histone-bound DNA in archaea remains poorly understood. Here, we reconstitute a nucleosome-associated transcription elongation complex (TEC) from Pyrococcus furiosus and capture its structure across multiple elongation states by cryo-electron microscopy (cryo-EM). High-resolution structures reveal that the RNA polymerase engages a three-dimer HPfB nucleosome positioned downstream. We identify direct physical interactions between HPfB and Rpo1N RNA polymerase subunit, establishing a defined polymerase-histone interface during transcription. Structural comparisons across defined elongation states demonstrate that RNA polymerase first translocates on DNA using the proximal histone dimer as an anchor, followed by destabilisation of the distal dimer. The DNA exiting the nucleosome is partially unwrapped and is redirected traversing the Rpo4/7 stalk. At extended transcript lengths nucleosome organisation is lost, indicating that transcription elongation ultimately disrupts histone-DNA interactions. This work provides the first structural insight into transcription through chromatin in archaea, revealing a mechanism in which the archaeal RNA polymerase actively remodels nucleosomes via DNA redirection and histone displacement, aided by direct polymerase-histone contacts.
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BibTeX
@misc{ubartaite2026structural,
title = {{Structural basis of nucleosome remodeling by archaeal RNA polymerase during transcription elongation}},
author = {G. Ubartaite and D. Tarau and A. L. Bula and W. Hausner and D. Grohmann and S. O. Dodonova},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.29.754952},
url = {https://www.biorxiv.org/content/10.64898/2026.09.29.754952v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Structural basis of nucleosome remodeling by archaeal RNA polymerase during transcription elongation
AU - G. Ubartaite
AU - D. Tarau
AU - A. L. Bula
AU - W. Hausner
AU - D. Grohmann
AU - S. O. Dodonova
PY - 2026
DA - 2026/09/29
PB - bioRxiv
DO - 10.64898/2026.09.29.754952
UR - https://www.biorxiv.org/content/10.64898/2026.09.29.754952v1
AB - Transcription occurs in the context of histone-based chromatin in eukaryotes and most archaea. The archaeal RNA polymerase and histones are ancestral to their eukaryotic counterparts, yet how RNA polymerase traverses histone-bound DNA in archaea remains poorly understood. Here, we reconstitute a nucleosome-associated transcription elongation complex (TEC) from Pyrococcus furiosus and capture its structure across multiple elongation states by cryo-electron microscopy (cryo-EM). High-resolution structures reveal that the RNA polymerase engages a three-dimer HPfB nucleosome positioned downstream. We identify direct physical interactions between HPfB and Rpo1N RNA polymerase subunit, establishing a defined polymerase-histone interface during transcription. Structural comparisons across defined elongation states demonstrate that RNA polymerase first translocates on DNA using the proximal histone dimer as an anchor, followed by destabilisation of the distal dimer. The DNA exiting the nucleosome is partially unwrapped and is redirected traversing the Rpo4/7 stalk. At extended transcript lengths nucleosome organisation is lost, indicating that transcription elongation ultimately disrupts histone-DNA interactions. This work provides the first structural insight into transcription through chromatin in archaea, revealing a mechanism in which the archaeal RNA polymerase actively remodels nucleosomes via DNA redirection and histone displacement, aided by direct polymerase-histone contacts.
ER -