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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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 |
work_keys_str_mv |
AT philchikhangau analysisofargonaute4associatedlongnoncodingrnainarabidopsisthalianashedsnovelinsightsintogeneregulationthroughrnadirecteddnamethylation AT elizabethsdennis analysisofargonaute4associatedlongnoncodingrnainarabidopsisthalianashedsnovelinsightsintogeneregulationthroughrnadirecteddnamethylation AT mingbowang analysisofargonaute4associatedlongnoncodingrnainarabidopsisthalianashedsnovelinsightsintogeneregulationthroughrnadirecteddnamethylation |
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