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TitleStructural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome.
Journal, issue, pagesNat Struct Mol Biol, Vol. 33, Issue 7, Page 1097-1104, Year 2026
Publish dateJun 25, 2026
AuthorsZhihui Chen / Cheng-Han Ho / Hiroki Tanaka / Tomoya Kujirai / Mitsuo Ogasawara / Haruhiko Ehara / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed AbstractThe overlapping dinucleosome (OLDN), a composite chromatin particle consisting of a hexasome and a canonical octasome, forms immediately downstream of transcription start sites, probably through ...The overlapping dinucleosome (OLDN), a composite chromatin particle consisting of a hexasome and a canonical octasome, forms immediately downstream of transcription start sites, probably through chromatin remodeling activity, and has been proposed to act as a transient regulatory intermediate during transcription. Nevertheless, how RNA polymerase II (RNAPII) engages with and transcribes through this unusual structure has remained unclear. Here we reconstituted OLDNs in vitro and performed transcription assays with RNAPII. We found that transcription efficiency was markedly higher when RNAPII initiated from the hexasome side than from the octasome side. Cryo-electron microscopy further revealed that transcription from the hexasome side induced pronounced conformational rearrangements, in which RNAPII progression dramatically opened the hexasome-octasome interface. These results identify a mechanism by which RNAPII senses the intrinsic transcriptional polarity of OLDNs and suggest that OLDNs function as dynamic, directionally sensitive regulators of transcription elongation.
External linksNat Struct Mol Biol / PubMed:42350665
MethodsEM (single particle)
Resolution3.74 - 6.74 Å
Structure data

64603

9uxw

EMDB-64603, PDB-9uxw:
RNA polymerase II elongation complex stalled at SHL(-0.5) in the hexasome of the overlapping dinucleosome
Method: EM (single particle) / Resolution: 3.74 Å

64642

9uz9

EMDB-64642, PDB-9uz9:
RNA polymerase II elongation complex stalled at SHL(-6) in the hexasome of the overlapping dinucleosome
Method: EM (single particle) / Resolution: 6.74 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • komagataella phaffii gs115 (fungus)
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / Chromatin / RNA Polymerase II / Overlapping dinucleosome

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