9K15

A cryo-EM structure of B. oleracea RNA polymerase V in complex with 4U sacffold at 3.32 Angstrom

Summary for 9K15

• Entry DOI: 10.2210/pdb9k15/pdb
• EMDB information: 61965
• Descriptor: DNA-directed RNA polymerase V largest subunit, DNA-directed RNA polymerase IV and V subunit 2, DNA (34-MER), ... (15 entities in total)
• Functional Keywords: dna-dependent rna polymerase v, transcription, plant
• Biological source: Brassica oleracea (wild cabbage); More
• Total number of polymer chains: 13
• Total formula weight: 518817.93

Authors

Xie, G.,Du, X.,Du, J. (deposition date: 2024-10-16, release date: 2026-04-15)

Primary citation

Xie, G.,Du, X.,Tan, Y.,Zhou, Y.,Chi, C.,Zhou, S.,Picard, C.L.,Chai, S.,Wu, L.,Zhu, D.,Zhao, J.,Xue, Y.,Li, S.,Jacobsen, S.E.,Wu, Z.,Du, J.
A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.
Embo J., 2026

PubMed Abstract: 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.

PubMed: 41928006
DOI: 10.1038/s44318-026-00763-7

Experimental method

ELECTRON MICROSCOPY (3.32 Å)