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

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 poo...

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Main Authors: Phil Chi Khang Au, Elizabeth S. Dennis, Ming-Bo Wang
Format: Article
Language:English
Published: MDPI AG 2017-08-01
Series:Genes
Subjects:
Online Access:https://www.mdpi.com/2073-4425/8/8/198
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spelling doaj-a2854048f2114711856f24e555809d0d2020-11-24T21:43:36ZengMDPI AGGenes2073-44252017-08-018819810.3390/genes8080198genes8080198Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA MethylationPhil Chi Khang Au0Elizabeth S. Dennis1Ming-Bo Wang2Commonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, AustraliaCommonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, AustraliaCommonwealth Scientific and Industrial Research Organisation Agriculture, Canberra, Australian Capital Territory 2601, AustraliaRNA-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.https://www.mdpi.com/2073-4425/8/8/198RNA-directed DNA methylationAGO4noncoding RNAplants
collection DOAJ
language English
format Article
sources DOAJ
author Phil Chi Khang Au
Elizabeth S. Dennis
Ming-Bo Wang
spellingShingle Phil Chi Khang Au
Elizabeth S. Dennis
Ming-Bo Wang
Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation
Genes
RNA-directed DNA methylation
AGO4
noncoding RNA
plants
author_facet Phil Chi Khang Au
Elizabeth S. Dennis
Ming-Bo Wang
author_sort Phil Chi Khang Au
title Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation
title_short Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation
title_full Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation
title_fullStr Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation
title_full_unstemmed Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation
title_sort analysis of argonaute 4-associated long non-coding rna in arabidopsis thaliana sheds novel insights into gene regulation through rna-directed dna methylation
publisher MDPI AG
series Genes
issn 2073-4425
publishDate 2017-08-01
description 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.
topic RNA-directed DNA methylation
AGO4
noncoding RNA
plants
url https://www.mdpi.com/2073-4425/8/8/198
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AT mingbowang analysisofargonaute4associatedlongnoncodingrnainarabidopsisthalianashedsnovelinsightsintogeneregulationthroughrnadirecteddnamethylation
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