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Genes 2017, 8(8), 198; doi:10.3390/genes8080198

Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation

Commonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, Australia
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Received: 22 June 2017 / Revised: 1 August 2017 / Accepted: 2 August 2017 / Published: 7 August 2017
(This article belongs to the Special Issue RNA Modification)
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Abstract

RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA. Comparison of these lncRNAs with gene expression data of RdDM mutants identified novel RdDM target genes. Surprisingly, a large proportion of these target genes were repressed in RdDM mutants suggesting that they are normally activated by RdDM. These RdDM-activated genes are more enriched for gene body lncRNA than the RdDM-repressed genes. Histone modification and RNA analyses of several RdDM-activated stress response genes detected increased levels of active histone mark and short RNA transcript in the lncRNA-overlapping gene body regions in the ago4 mutant despite the repressed expression of these genes. These results suggest that RdDM, or AGO4, may play a role in maintaining or activating stress response gene expression by directing gene body chromatin modification preventing cryptic transcription. View Full-Text
Keywords: RNA-directed DNA methylation; AGO4; noncoding RNA; plants RNA-directed DNA methylation; AGO4; noncoding RNA; plants
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MDPI and ACS Style

Au, P.C.K.; Dennis, E.S.; Wang, M.-B. Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation. Genes 2017, 8, 198.

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