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TitleA spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.
Journal, issue, pagesEMBO J, Year 2026
Publish dateApr 2, 2026
AuthorsGuohui Xie / Xuan Du / Yifang Tan / Yuxing Zhou / Cheng Chi / Sixian Zhou / Colette L Picard / Songge Chai / Lei Wu / Danling Zhu / Jun Zhao / Yan Xue / Sisi Li / Steven E Jacobsen / Zhe Wu / Jiamu Du /
PubMed AbstractDNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding ...DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding RNA guides DNA methylation through the RNA-directed DNA methylation (RdDM) pathway; however, how these RNAs are selected is unknown. Here, we show that the 3'-ends of Pol V transcripts are enriched at A-rich template DNA (A-rich-DNA). Arabidopsis RdDM regions possess AT-rich boundaries genome-wide, suggesting that Pol V likely terminates at A-rich-DNA, which subsequently defines the DNA methylation landscape in plants. A-rich-DNA successfully stops Pol V transcription in vitro. Structural snapshots of Pol V transcribing A-rich-DNA show that accumulation of unstable rU:dA pairs in the RNA-DNA hybrid promotes transcription bubble collapse and spontaneous transcription termination. These findings identify an intrinsic Pol V termination signal that shapes genomic DNA methylation patterning in plants and reveals a common mechanism for spontaneous transcription termination.
External linksEMBO J / PubMed:41928006
MethodsEM (single particle)
Resolution2.96 - 4.06 Å
Structure data

61961

9k11

EMDB-61961, PDB-9k11:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 0U scaffold at 2.96 Angstrom
Method: EM (single particle) / Resolution: 2.96 Å

61962

9k12

EMDB-61962, PDB-9k12:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 1U sacffold at 3.5 Angstrom
Method: EM (single particle) / Resolution: 3.46 Å

61963

9k13

EMDB-61963, PDB-9k13:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 2U sacffold at 3.04 Angstrom
Method: EM (single particle) / Resolution: 3.04 Å

61964

9k14

EMDB-61964, PDB-9k14:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 3U sacffold at 3.8 Angstrom
Method: EM (single particle) / Resolution: 3.8 Å

61965

9k15

EMDB-61965, PDB-9k15:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 4U sacffold at 3.32 Angstrom
Method: EM (single particle) / Resolution: 3.32 Å

61966

9k16

EMDB-61966, PDB-9k16:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 5U sacffold at 3.19 Angstrom
Method: EM (single particle) / Resolution: 3.19 Å

61967

9k17

EMDB-61967, PDB-9k17:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 6U sacffold at 3.04 Angstrom
Method: EM (single particle) / Resolution: 3.04 Å

61968

9k18

EMDB-61968, PDB-9k18:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 7U sacffold at 3.42 Angstrom
Method: EM (single particle) / Resolution: 3.42 Å

61969

9k19

EMDB-61969, PDB-9k19:
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 8U sacffold at 4.06 Angstrom
Method: EM (single particle) / Resolution: 4.06 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

Source
  • brassica oleracea (wild cabbage)
KeywordsTRANSCRIPTION / DNA-dependent RNA polymerase V / plant

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