| Structural highlights
Function
NRPE1_ARATH DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase V involved in RNA-directed DNA methylation-dependent (RdDM) silencing of endogenous repeated sequences, including transposable elements. Also required for full erasure of methylation when the RNA trigger is withdrawn. Seems also involved in the synthesis of short-interfering RNAs (siRNA). Essential component of a self-reinforcing loop coupling de novo DNA methylation to siRNA production. Involved in the maintenance of post-transcriptional RNA silencing.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
Publication Abstract from PubMed
De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.
A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex.,Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y Nat Commun. 2023 May 30;14(1):3118. doi: 10.1038/s41467-023-38619-x. PMID:37253723[13]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Onodera Y, Haag JR, Ream T, Costa Nunes P, Pontes O, Pikaard CS. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell. 2005 Mar 11;120(5):613-22. PMID:15766525 doi:10.1016/j.cell.2005.02.007
- ↑ Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJ. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet. 2005 Jul;37(7):761-5. PMID:15924141 doi:10.1038/ng1580
- ↑ Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 2005 Sep 1;19(17):2030-40. PMID:16140984 doi:10.1101/gad.348405
- ↑ Pontes O, Li CF, Costa Nunes P, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell. 2006 Jul 14;126(1):79-92. PMID:16839878 doi:10.1016/j.cell.2006.05.031
- ↑ Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4536-41. PMID:17360559 doi:10.1073/pnas.0611456104
- ↑ Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3145-50. PMID:18287047 doi:10.1073/pnas.0709632105
- ↑ Kanno T, Bucher E, Daxinger L, Huettel B, Bohmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ. A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet. 2008 May;40(5):670-5. doi: 10.1038/ng.119. Epub 2008 Apr 20. PMID:18425128 doi:https://dx.doi.org/10.1038/ng.119
- ↑ Eamens A, Vaistij FE, Jones L. NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis. Plant J. 2008 Aug;55(4):596-606. PMID:18433438 doi:10.1111/j.1365-313X.2008.03525.x
- ↑ Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu JK, Hagen G, Guilfoyle TJ, Pasa-Tolić L, Pikaard CS. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol Cell. 2009 Jan 30;33(2):192-203. PMID:19110459 doi:10.1016/j.molcel.2008.12.015
- ↑ Lahmy S, Pontier D, Cavel E, Vega D, El-Shami M, Kanno T, Lagrange T. PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):941-6. PMID:19141635 doi:10.1073/pnas.0810310106
- ↑ Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics. 2011 Mar;6(3):344-54. doi: 10.4161/epi.6.3.14242. Epub 2011 Mar 1. PMID:21150311 doi:https://dx.doi.org/10.4161/epi.6.3.14242
- ↑ Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014 Mar 6;507(7490):124-8. doi: 10.1038/nature12931. Epub 2014 Jan 22. PMID:24463519 doi:https://dx.doi.org/10.1038/nature12931
- ↑ Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y. A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex. Nat Commun. 2023 May 30;14(1):3118. PMID:37253723 doi:10.1038/s41467-023-38619-x
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