Abstract
Non-coding RNAs (ncRNAs) are a family of regulatory RNAs, which do not encode mRNA, rRNA or tRNA, found in a variety of organisms including plants. Different classes of ncRNAs have been identified based on their length and their position in the genome, including small ncRNAs (microRNAs and small-interfering RNAs), natural antisense transcripts (NATs), and long intronic/intergenic ncRNAs (lncRNAs, 200nt or longer). Recent advances in next-generation sequencing technologies and computational analysis for transcriptome profiling have led to the genome-wide identification of ncRNAs. Functional characterization of these ncRNAs has implicated them to play a role in a wide range of cellular functions, such as epigenetic silencing, transcriptional regulation, and RNA metabolism. Emerging evidence suggest that several lncRNAs play important roles in many fundamental biological processes including growth and development as well as abiotic stress responses. Recent findings on the roles of lncRNAs in the aforementioned plant processes are summarized in this chapter.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63:3523–3543
Aung K, Lin SI, Wu CC et al (2006) pho2, a phosphate over-accumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol 141:1000–1011
Bari R, Datt Pant B, Stitt M et al (2006) PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141:988–999
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism and function. Cell 116:281–297
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233
Ben Amor B, Wirth S, Merchan F et al (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19:57–69
Brodersen P, Sakvarelidze-Achard L, Brunn-Rasmussen M et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 30:1185–1190
Burleigh SH, Harrison MJ (1999) The down-regulation of Mt4-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots. Plant Physiol 119:241–248
Campalans A, Kondorosi A, Crespi M (2004) Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 16:1047–1059
Chiou TJ (2007) The role of microRNAs in sensing nutrient stress. Plant Cell Environ 30:323–332
Chiou TJ, Aung K, Lin SI et al (2006) Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell 18:412–421
Cho J, Koo DH, Nam Y et al (2005) Isolation and characterization of cDNA clones expressed under male sex expression conditions in a monoecious cucumber plant (Cucumis sativus L. cv. winter long). Euphytica 146:271–281
Clamp M, Fry B, Kamal M et al (2007) Distinguishing protein coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A 104:19428–19433
Conley B, Jordan IK (2012) Epigenetic regulation of human cis-natural antisense transcripts. Nucleic Acids Res 40:1438–1445
Contreras-Cubas C, Palomar M, Arteaga-Vazquez M et al (2012) Non-coding RNAs in the plant response to abiotic stress. Planta 236:943–958
Crespi MD, Jurkevitch E, Poiret M et al (1994) Enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. EMBO J 13:5099–5112
Dai XY, Yu JI, Zhao Q et al (2004) Non-coding RNA for ZM401, a pollen-specific gene of Zea Mays. Acta Bot Sin 46:497–504
de Alba AEM, Parent J-S et al (2013) Small RNA-mediated control of development in plants. In: Grafi G, Ohad N (eds) Epigenetic memory and control in plants. Springer, Heidelberg, pp 177–199
de Lucia F, Crevillen P, Jones AM et al (2008) A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci U S A 105:16831–16836
Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789
Dieci G, Fiorino G, Castelnuova M et al (2007) The expanding RNA polymerase III transcriptome. Trends Genet 23:614–622
Ding J, Lu Q, Ouyang Y et al (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A 109:2654–2659
Ebert MS, Neilson JR, Sharp PA (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4:721–726
Franco-Zorrilla JM, Valli A, Todesco M et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033–1037
Fujii H, Chiou TJ, Lin SI et al (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15:2038–2043
Geisler S, Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 12:699–712
Gibb EA, Vucic EA, Enfield KS et al (2011) Human cancer long non-coding RNA transcriptomes. PLoS One 6:e25915
Grant-Downton R, Rodriguez-Enriquez J (2012) Emerging roles for non-coding RNAs in male reproductive development in flowering plants. Biomolecules 2:608–621
Grennan AK (2008) Phosphate accumulation in plants: signaling. Plant Physiol 148:3–5
Guttman M, Amit I, Garber M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227
Henz SR, Cumbie JS, Kasschau KD et al (2007) Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol 144:1247–1255
Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76–79
Ho L, Crabtree GR (2010) Chromatin remodelling during development. Nature 463:474–484
Huang W, Long N, Khatib H (2012) Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data. Anim Genet 43:674–682
Ingram J, Bartels D (1996) The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biol 47:377–403
Jia H, Osak M, Bogu GK et al (2010) Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16:1478–1487
Jian Z, Hana M, Yuxuan H et al (2013) Plant long ncRNAs: a new frontier for gene regulatory control. Am J Plant Sci 4:1038–1045
Jin J, Liu J, Wang H et al (2013) PLncDB: plant long non-coding RNA database. Bioinformatics 29:1068–1071
Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
Kim ED, Sung S (2012) Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci 17:16–21
Knowling S, Morris KV (2011) Non-coding RNA and antisense RNA. Nature’s trash or treasure? Biochimie 93:1922–1927
Kong L, Zhang Y, Ye ZQ et al (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35:W345–W349
Lapidot M, Pilpel Y (2006) Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep 7:1216–1222
Lei N, Wu HS, Hsu JM et al (2012) Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res 4:127–150
Li L, Wang X, Stolc V et al (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38:124–129
Li T, Wang S, Wu R, Zhou X, Zhu D et al (2012) Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing. Genomics 99:292–298
Lin S, Chiang SF, Chiou TJ (2008) Regulatory network of MicroRNA399 and PHO2 by systemic signaling. Plant Physiol 147:732–746
Liu C, Muchhal US, Raghothama KG (1997) Differential expression of TPS11, a phosphate starvation-induced gene in tomato. Plant Mol Biol 33:867–874
Lu ZJ, Yip KY, Wang G et al (2011) Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res 21:276–285
Luo M, Taylor JM, Spriggs A (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7:e1002125
Ma J, Yan B, Qu Y et al (2008) Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize. J Cell Biochem 105:136–146
Ma H, Hao Y, Dong X, Gong Q, Chen J et al (2012) Molecular mechanisms and function prediction of long noncoding RNA. ScientificWorldJournal 2012:541786. doi:10.1100/2012/541786
Martin AC, del Pozo JC, Iglesias J et al (2000) Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. Plant J 24:559–567
Matsui A, Ishida J, Morosawa T et al (2010) Arabidopsis tiling array analysis to identify the stress-responsive genes. Methods Mol Biol 639:141–155
Meng Y, Shao C, Wang H et al (2013) The regulatory activities of plant microRNAs: a more dynamic perspective. Plant Physiol 157:1583–1595
Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956
Michelhaugh SKL, Lipovich J, Blythe H et al (2011) Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. J Neurochem 116:459–466
Mittler R (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci 11:15–19
Nagano T, Mitchell JA, Sanz LA et al (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322:1717–1720
Nam JW, Bartel DP (2012) Long noncoding RNAs in C. elegans. Genome Res 22:2529–2540
Nie L, Wu HJ, Hsu J-M et al (2012) Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res 4:127–150
Orom UA, Dierren T, Guigo R et al (2010) Long non-coding RNAs as enhancers of gene expression. Cold Spring Harb Symp Quant Biol 75:325–331
Pandey RR, Mondal T, Mohammad F et al (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232–246
Pauli AE, Valen MF, Lin M et al (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22:577–591
Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10:645–652
Rehrauer H, Aquino C, Gruissem W et al (2010) AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol 152:487–499
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166
Rohrig H, Schmidt J, Miklashevichs E et al (2002) Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc Natl Acad Sci U S A 99:1915–1920
Rymarquis LA, Kastenmayer JP, Huttenhofer AG et al (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci 13:329–334
Sigova AA, Mullen AC, Molinie B et al (2013) Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A 110:2876–2881
Sousa C, Johansson C, Charon C et al (2001) Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex. Mol Cell Biol 21:354–366
Sunkar R (2010) MicroRNAs with macro effects on plant stress responses. Semin Cell Dev Biol 21:805–811
Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019
Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17:196–203
Swiezewski S, Liu F, Magusin A et al (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462:799–802
Verma SS, Megha S, Rahman MH, Kav NNV et al (2014) MicroRNA omics approaches to investigate biotic and abiotic stress responses. In: Benkeblia N (ed) Omics technologies and crop improvement. CRC, Boca Raton
Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687
Wasaki J, Yonetani R, Shinano T et al (2003) Expression of the OsPI1 gene, cloned from rice roots using cDNA microarray, rapidly responds to phosphorus status. New Phytol 158:239–248
Washietl S, Findeiss S, Muller SA et al (2011) RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA 17:578–594
Wierzbicki AT (2012) The role of long non-coding RNA in transcriptional gene silencing. Curr Opin Plant Biol 15:517–522
Wilhelm BT, Marguerat S, Watt S et al (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single nucleotide resolution. Nature 453:1239–1243
Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23:1494–1504
Wood CC, Robertson M, Tanner G et al (2006) The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci U S A 103:14631–14636
Wu HJ, Wang ZM, Wang M et al (2013) Wide spread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol 161:1875–1884
Xin M, Wang Y, Yao Y et al (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol 11:61
Yang WC, Katinakis P, Hendriks P et al (1993) Characterization of GmENOD40, a gene showing novel patterns of cell-specific expression during soybean nodule development. Plant J 3:573–585
Zhang YC, Chen YQ (2013) Long noncoding RNAs: new regulators in plant development. Biochem Biophys Res Commun 436:111–114
Zhang M, Zhao H, Xie S et al (2011) Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc Natl Acad Sci U S A 108:20042–20047
Zhao J, Sun BK, Erwin JA et al (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322:750–756
Zhou H, Liu Q, Li J et al (2012) Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res 22:649–660
Zhu QH, Wang MB (2012) Molecular functions of long non-coding RNAs in plants. Genes (Basel) 3:176–190
Zhu QH, Stephen S, Taylor J et al (2014) Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol 201:574–584
Acknowledgment
Work in the corresponding author’s laboratory is partially supported by a grant from the Natural Sciences and Engineering Research Council (NSERC) of Canada.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this chapter
Cite this chapter
Megha, S., Basu, U., Rahman, M.H., Kav, N.N.V. (2015). The Role of Long Non-coding RNAs in Abiotic Stress Tolerance in Plants. In: Pandey, G. (eds) Elucidation of Abiotic Stress Signaling in Plants. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2540-7_4
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2540-7_4
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4939-2539-1
Online ISBN: 978-1-4939-2540-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)