From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress

Overview

Journal Front Plant Sci

Date 2021 Jan 25

PMID 33488652

Citations 22

Authors

Maria Clara de Oliveira Urquiaga

Flavia Thiebaut

Adriana Silva Hemerly

Paulo Cavalcanti Gomes Ferreira

Affiliations

Soon will be listed here.

Abstract

Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.

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References

Chen R, Li M, Zhang H, Duan L, Sun X, Jiang Q . Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. BMC Genomics. 2019; 20(1):730. PMC: 6790039. DOI: 10.1186/s12864-019-6101-7. View

Vieira L, Grativol C, Thiebaut F, Carvalho T, Hardoim P, Hemerly A . PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants. Noncoding RNA. 2018; 3(1). PMC: 5831995. DOI: 10.3390/ncrna3010011. View

Szczesniak M, Rosikiewicz W, Makalowska I . CANTATAdb: A Collection of Plant Long Non-Coding RNAs. Plant Cell Physiol. 2015; 57(1):e8. PMC: 4722178. DOI: 10.1093/pcp/pcv201. View

Kim D, Xi Y, Sung S . Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet. 2017; 13(7):e1006939. PMC: 5552341. DOI: 10.1371/journal.pgen.1006939. View

Cagirici H, Alptekin B, Budak H . RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats. Sci Rep. 2017; 7(1):10670. PMC: 5587677. DOI: 10.1038/s41598-017-11170-8. View

Lang Z, Wang Y, Tang K, Tang D, Datsenka T, Cheng J . Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci U S A. 2017; 114(22):E4511-E4519. PMC: 5465898. DOI: 10.1073/pnas.1705233114. View

Secco D, Wang C, Shou H, Schultz M, Chiarenza S, Nussaume L . Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife. 2015; 4. PMC: 4534844. DOI: 10.7554/eLife.09343. View

Tan X, Li S, Hu L, Zhang C . Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering. BMC Plant Biol. 2020; 20(1):81. PMC: 7032001. DOI: 10.1186/s12870-020-2286-9. View

Karlik E, Gozukirmizi N . Expression analysis of lncRNA AK370814 involved in the barley vitamin B6 salvage pathway under salinity. Mol Biol Rep. 2018; 45(6):1597-1609. DOI: 10.1007/s11033-018-4289-2. View

10.

Mosher R, Schwach F, Studholme D, Baulcombe D . PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A. 2008; 105(8):3145-50. PMC: 2268599. DOI: 10.1073/pnas.0709632105. View

11.

Unver T, Tombuloglu H . Barley long non-coding RNAs (lncRNA) responsive to excess boron. Genomics. 2019; 112(2):1947-1955. DOI: 10.1016/j.ygeno.2019.11.007. View

12.

Yan H, Bombarely A, Xu B, Frazier T, Wang C, Chen P . siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. Biotechnol Biofuels. 2018; 11:208. PMC: 6058383. DOI: 10.1186/s13068-018-1202-0. View

13.

Fukuda M, Nishida S, Kakei Y, Shimada Y, Fujiwara T . Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen. Plant Cell Physiol. 2019; 60(9):1961-1973. DOI: 10.1093/pcp/pcz048. View

14.

Yamada K, Lim J, Dale J, Chen H, Shinn P, Palm C . Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003; 302(5646):842-6. DOI: 10.1126/science.1088305. View

15.

Ding J, Shen J, Mao H, Xie W, Li X, Zhang Q . RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Mol Plant. 2012; 5(6):1210-6. DOI: 10.1093/mp/sss095. View

16.

Heo J, Sung S . Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science. 2010; 331(6013):76-9. DOI: 10.1126/science.1197349. View

17.

Li M, Li X, Zhou Z, Wu P, Fang M, Pan X . Reassessment of the Four Yield-related Genes Gn1a, DEP1, GS3, and IPA1 in Rice Using a CRISPR/Cas9 System. Front Plant Sci. 2016; 7:377. PMC: 4811884. DOI: 10.3389/fpls.2016.00377. View

18.

Csorba T, Questa J, Sun Q, Dean C . Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci U S A. 2014; 111(45):16160-5. PMC: 4234544. DOI: 10.1073/pnas.1419030111. View

19.

Yan Q, Wu F, Yan Z, Li J, Ma T, Zhang Y . Differential co-expression networks of long non-coding RNAs and mRNAs in Cleistogenes songorica under water stress and during recovery. BMC Plant Biol. 2019; 19(1):23. PMC: 6330494. DOI: 10.1186/s12870-018-1626-5. View

20.

Swiezewski S, Liu F, Magusin A, Dean C . Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature. 2009; 462(7274):799-802. DOI: 10.1038/nature08618. View