An RNA polymerase II-and AGO4-associated protein acts in RNA-directed DNA methylation
Lorkovic, Zdravko J.
Matzke, Antonius J.
Pikaard, Craig S.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Desert Agriculture Initiative
Office of the VP
Plant Stress Genomics Research Lab
Online Publication Date2010-04-21
Print Publication Date2010-05
Permanent link to this recordhttp://hdl.handle.net/10754/325291
MetadataShow full item record
AbstractDNA methylation is an important epigenetic mark in many eukaryotes. In plants, 24-nucleotide small interfering RNAs (siRNAs) bound to the effector protein, Argonaute 4 (AGO4), can direct de novo DNA methylation by the methyltransferase DRM2 (refs 2, 4-6). Here we report a new regulator of RNA-directed DNA methylation (RdDM) in Arabidopsis: RDM1. Loss-of-function mutations in the RDM1 gene impair the accumulation of 24-nucleotide siRNAs, reduce DNA methylation, and release transcriptional gene silencing at RdDM target loci. RDM1 encodes a small protein that seems to bind single-stranded methyl DNA, and associates and co-localizes with RNA polymerase II (Pol II, also known as NRPB), AGO4 and DRM2 in the nucleus. Our results indicate that RDM1 is a component of the RdDM effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation. Our results also indicate that, although RDM1 and Pol V (also known as NRPE) may function together at some RdDM target sites in the peri-nucleolar siRNA processing centre, Pol II rather than Pol V is associated with the RdDM effector complex at target sites in the nucleoplasm. © 2010 Macmillan Publishers Limited. All rights reserved.
CitationGao Z, Liu H-L, Daxinger L, Pontes O, He X, et al. (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465: 106-109. doi:10.1038/nature09025.
PubMed Central IDPMC2865564
- The ability to form homodimers is essential for RDM1 to function in RNA-directed DNA methylation.
- Authors: Sasaki T, Lorković ZJ, Liang SC, Matzke AJ, Matzke M
- Issue date: 2014
- DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
- Authors: Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, Cai T, Tang K, Liu R, Shi X, He XJ, Zhu JK
- Issue date: 2013 May 14
- A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis.
- Authors: Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE
- Issue date: 2010 May 25
- AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana.
- Authors: Wang F, Axtell MJ
- Issue date: 2017 Apr
- NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation.
- Authors: He XJ, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, Pikaard C, Wang CS, Zhu JK
- Issue date: 2009 Feb 1
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The human interactome knowledge base (hint-kb): An integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid techniqueTheofilatos, Konstantinos A.; Dimitrakopoulos, Christos M.; Likothanassis, Spiridon D.; Kleftogiannis, Dimitrios A.; Moschopoulos, Charalampos N.; Alexakos, Christos; Papadimitriou, Stergios; Mavroudi, Seferina P. (Artificial Intelligence Review, Springer Nature, 2013-07-12) [Article]Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about experimentally and computationally detected human PPIs as well as their corresponding annotation data. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (http://biotools.ceid.upatras.gr/hint-kb/), a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, cal-culatesasetoffeaturesofinterest and computesaconfidence score for every candidate protein interaction. This confidence score is essential for filtering the false positive interactions which are present in existing databases, predicting new protein interactions and measuring the frequency of each true protein interaction. For this reason, a novel machine learning hybrid methodology, called (Evolutionary Kalman Mathematical Modelling—EvoKalMaModel), was used to achieve an accurate and interpretable scoring methodology. The experimental results indicated that the proposed scoring scheme outperforms existing computational methods for the prediction of PPIs.
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