9K16
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 5U sacffold at 3.19 Angstrom
Summary for 9K16
| Entry DOI | 10.2210/pdb9k16/pdb |
| EMDB information | 61966 |
| Descriptor | DNA (34-MER), DNA-directed RNA polymerase II, IV and V subunit 8, DNA-directed RNA polymerase subunit, ... (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 | 518803.91 |
| Authors | |
| 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 Cited by 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: 41928006DOI: 10.1038/s44318-026-00763-7 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.19 Å) |
Structure validation
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