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Role of Non-coding RNAs in Disease Resistance in Plants

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Biotechnological Advances for Disease Tolerance in Plants

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Abstract

Plants are prone to diseases caused by diverse pathogens. They respond through the modulation of molecular mechanisms at different levels. Alteration of gene expression is a major demonstration of plant defense machinery at the molecular level. In recent years, advancements in high-throughput sequencing and bioinformatic tools lead to the identification of various regulatory ncRNAs such as miRNAs, lncRNAs, and circRNAs. These ncRNAs emerged as direct or indirect regulators of gene expression through chromatin remodeling, transcriptional, and post-transcriptional regulation. Till date, studies revealed the extensive role of miRNAs and lncRNAs in providing disease resistance to plants. miRNAs target various defense-related genes and lncRNAs. Interestingly, both lncRNAs and circRNAs can also act as sponges for miRNAs and inhibit their action. Moreover, lncRNAs also act as precursors of various miRNAs. In brief, ncRNAs make complex and intermingled networks that can be exploited to enhance disease resistance in plants. However, exploration of more such networks is still needed. In this chapter, we discuss about features, discovery, and biogenesis, mechanism of action, and role of miRNAs, lncRNAs, and circRNAs in providing disease resistance to the plants.

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References

  • Abdelmohsen K, Panda AC, Munk R et al (2017) Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol 14(3):361–369

    Article  PubMed  PubMed Central  Google Scholar 

  • Akter MA, Mehraj H, Miyaji N et al (2021) Transcriptional association between mRNAs and their paired natural antisense transcripts following Fusarium oxysporum inoculation in Brassica rapa L. Horticulturae 8(1):17

    Article  Google Scholar 

  • Ariel F, Jegu T, Latrasse D, Romero-Barrios N et al (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell 55(3):383–396

    Article  CAS  PubMed  Google Scholar 

  • Ariel F, Romero-Barrios N, Jegu T et al (2015) Battles and hijacks: noncoding transcription in plants. Trends Plant Sci 20(6):362–371

    Article  CAS  PubMed  Google Scholar 

  • Ashraf MA, Ali B, Brown JK et al (2023) In silico identification of cassava genome-encoded microRNAs with predicted potential for targeting the ICMV-Kerala begomoviral pathogen of cassava. Viruses 15(2):486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ashwal-Fluss R, Meyer M, Pamudurti NR et al (2014) circRNA biogenesis competes with pre-mRNA splicing. Mol Cell 56(1):55–66

    Article  CAS  PubMed  Google Scholar 

  • Baile F, Gomez-Zambrano A, Calonje M (2021) Roles of polycomb complexes in regulating gene expression and chromatin structure in plants. Plant Commun 100267

    Google Scholar 

  • Barrett SP, Wang PL, Salzman J (2015) Circular RNA biogenesis can proceed through an exon-containing lariat precursor. elife 4:e07540

    Article  PubMed  PubMed Central  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297

    Article  CAS  PubMed  Google Scholar 

  • Bentley DL (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15(3):163–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhatia G, Upadhyay SK, Upadhyay A et al (2021) Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection. BMC Plant Biol 21(1):1–16

    Article  Google Scholar 

  • Blackledge NP, Klose RJ (2021) The molecular principles of gene regulation by polycomb repressive complexes. Nat Rev Mol Cell Biol 22(12):815–833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bonnet E, He Y, Billiau K et al (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26(12):1566–1568

    Article  CAS  PubMed  Google Scholar 

  • Borges F, Martienssen RA (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 16(12):727–741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320(5880):1185–1190

    Article  CAS  PubMed  Google Scholar 

  • Brosnan CA, Voinnet O (2009) The long and the short of noncoding RNAs. Curr Opin Cell Biol 21(3):416–425

    Article  CAS  PubMed  Google Scholar 

  • Brown CJ, Hendrich BD, Rupert JL et al (1992) The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71(3):527–542

    Article  CAS  PubMed  Google Scholar 

  • Camargo-Ramírez R, Val-Torregrosa B, San Segundo B (2018) MiR858-mediated regulation of flavonoid-specific MYB transcription factor genes controls resistance to pathogen infection in Arabidopsis. Plant Cell Physiol 59(1):190–204

    Article  PubMed  Google Scholar 

  • Cao W, Gan L, Wang C et al (2021) Genome-wide identification and characterization of potato long non-coding RNAs associated with Phytophthora infestans resistance. Front Plant Sci 12:619062

    Article  PubMed  PubMed Central  Google Scholar 

  • Cao W, Cao J, Gao J et al (2022) Genome-wide identification and association analysis for virus-responsive lncRNAs in rice (Oryza sativa L.). Plant Growth Regul 98(1):65–76

    Article  CAS  Google Scholar 

  • Cerritelli SM, Crouch RJ (2009) Ribonuclease H: the enzymes in eukaryotes. FEBS J 276(6):1494–1505

    Article  CAS  PubMed  Google Scholar 

  • Chen LL (2016) The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol 17(4):205–211

    Article  CAS  PubMed  Google Scholar 

  • Chen HM, Chen LT, Patel K et al (2010) 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 107(34):15269–15274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng C, Liu F, Tian N et al (2021) Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep 11(1):6363

    Google Scholar 

  • Chorostecki U, Palatnik JF (2014) comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants. Bioinformatics 30(14):2066–2067

    Article  CAS  PubMed  Google Scholar 

  • Chu Q, Zhang X, Zhu X et al (2017) PlantcircBase: a database for plant circular RNAs. Mol Plant 10(8):1126–1128

    Article  CAS  PubMed  Google Scholar 

  • Cui C, Wang JJ, Zhao JH et al (2020) A Brassica miRNA regulates plant growth and immunity through distinct modes of action. Mol Plant 13(2):231–245

    Article  CAS  PubMed  Google Scholar 

  • Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res 46(W1):W49–W54

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Danan M, Schwartz S, Edelheit S et al (2012) Transcriptome-wide discovery of circular RNAs in archaea. Nucleic Acids Res 40(7):3131–3142

    Article  CAS  PubMed  Google Scholar 

  • Dong Z, Han MH, Fedoroff N (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci U S A 105(29):9970–9975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong W, Ren W, Wang X et al (2021) MicroRNA319a regulates plant resistance to Sclerotinia stem rot. J Exp Bot 72(10):3540–3553

    Article  CAS  PubMed  Google Scholar 

  • Eamens AL, Smith NA, Curtin SJ et al (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 15(12):2219–2235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fabbri M, Girnita L, Varani G et al (2019) Decrypting noncoding RNA interactions, structures, and functional networks. Genome Res 29(9):1377–1388

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fahlgren N, Carrington JC (2010) miRNA target prediction in plants. In: Plant MicroRNAs: Methods and Protocols. Springer protocols, pp. 51–57

    Google Scholar 

  • Fan X, Zhang X, Wu X et al (2015) Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol 16(1):1–17

    Article  Google Scholar 

  • Fan J, Quan W, Li GB et al (2020) circRNAs are involved in the rice-Magnaporthe oryzae interaction. Plant Physiol 182(1):272–286

    Article  CAS  PubMed  Google Scholar 

  • Fei Y, Feng J, Wang R et al (2021) PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs. RNA Biol 18(11):1622–1629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng T, Zhang ZY, Gao P et al (2023) Suppression of rice Osa-miR444.2 improves the resistance to sheath blight in rice mediating through the phytohormone pathway. Int J Mol Sci 24(4):3653

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Franco-Zorrilla JM, Valli A, Todesco M et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39(8):1033–1037

    Article  CAS  PubMed  Google Scholar 

  • Ghorbani A, Izadpanah K, Tahmasebi A et al (2022) Characterization of maize miRNAs responsive to maize Iranian mosaic virus infection. 3 Biotech 12(3):69

    Article  PubMed  PubMed Central  Google Scholar 

  • Griffiths-Jones S, Saini HK, Van Dongen S et al (2007) miRBase: tools for microRNA genomics. Nucleic Acids Res 36(suppl_1):D154–D158

    Article  PubMed  PubMed Central  Google Scholar 

  • Guan Y, Wei Z, Song P (2022) MicroRNA expression profiles in response to Phytophthora infestans and Oidium neolycopersici and functional identification of sly-miR397 in tomato. Phytopathology 113(3):497–507

    Article  Google Scholar 

  • Guo Z, Kuang Z, Wang Y et al (2020) PmiREN: a comprehensive encyclopedia of plant miRNAs. Nucleic Acids Res 48(D1):D1114–D1121

    Article  CAS  PubMed  Google Scholar 

  • Haag JR, Pikaard CS (2011) Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 12(8):483–492

    Article  CAS  PubMed  Google Scholar 

  • Han G, Cheng C, Zheng Y et al (2019) Identification of long non-coding RNAs and the regulatory network responsive to arbuscular mycorrhizal fungi colonization in maize roots. Int J Mol Sci 20(18):4491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hansen TB, Jensen TI, Clausen BH et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384–388

    Article  CAS  PubMed  Google Scholar 

  • Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(6013):76–79

    Article  CAS  PubMed  Google Scholar 

  • Hong YH, Meng J, Zhang M et al (2020) Identification of tomato circular RNAs responsive to Phytophthora infestans. Gene 746:144652

    Article  CAS  PubMed  Google Scholar 

  • Hong Y, Meng J, He X et al (2021) Editing miR482b and miR482c simultaneously by CRISPR/Cas9 enhanced tomato resistance to Phytophthora infestans. Phytopathology 111(6):1008–1016

    Article  CAS  PubMed  Google Scholar 

  • Hsu MT, Coca-Prados M (1979) Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 280:339–340

    Article  CAS  PubMed  Google Scholar 

  • Hu W, Wang G, Wang S et al (2020) Co-regulation of long non-coding RNAs with allele-specific genes in wheat responding to powdery mildew infection. Agronomy 10(6):896

    Article  CAS  Google Scholar 

  • Hu G, Wang B, Jia P et al (2023) The cotton miR530-SAP6 module activated by systemic acquired resistance mediates plant defense against Verticillium dahliae. Plant Sci 330:111647

    Article  CAS  PubMed  Google Scholar 

  • Huertas P, Aguilera A (2003) Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 12(3):711–721

    Article  CAS  PubMed  Google Scholar 

  • Iki T, Yoshikawa M, Meshi T et al (2012) Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO J 31(2):267–278

    Article  CAS  PubMed  Google Scholar 

  • Ivanov A, Memczak S, Wyler E et al (2015) Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep 10(2):170–177

    Article  CAS  PubMed  Google Scholar 

  • Jacobsen SE, Running MP, Meyerowitz EM (1999) Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 126(23):5231–5243

    Article  CAS  PubMed  Google Scholar 

  • Jeck WR, Sharpless NE (2014) Detecting and characterizing circular RNAs. Nat Biotechnol 32(5):453–461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeck WR, Sorrentino JA, Wang K et al (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19(2):141–157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang N, Cui J, Shi Y et al (2019) Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction. Hortic Res 6:28

    Article  PubMed  PubMed Central  Google Scholar 

  • Jiang L, Mu R, Wang Z et al (2023) Silencing P25, HC-Pro and Brp1 of potato virus (viroid) using artificial microRNA confers resistance to PVX, PVY and PSTVd in transgenic potato. Potato Res 66(1):231–244

    Article  CAS  PubMed  Google Scholar 

  • Kamieniarz-Gdula K, Proudfoot NJ (2019) Transcriptional control by premature termination: a forgotten mechanism. Trends Genet 35(8):553–564

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang SH, Sun YD, Atallah OO et al (2019) A long non-coding RNA of Citrus tristeza virus: role in the virus interplay with the host immunity. Viruses 11(5):436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kapranov P, Cheng J, Dike S et al (2007) RNA maps reveal new and a possible classes pervasive transcription RNA function. Science 316(1486):1110–1126

    Google Scholar 

  • Kim DH, Sung S (2017) Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Dev Cell 40(3):302–312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J, Sung S (2021) Looping by RNA: dynamic control of the chromatin loop by long non-coding RNAs in plants. Mol Plant 14(9):1430–1432

    Article  CAS  PubMed  Google Scholar 

  • Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res 47(D1):D155–D162

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854

    Article  CAS  PubMed  Google Scholar 

  • Li X, Manley JL (2005) Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122(3):365–378

    Article  CAS  PubMed  Google Scholar 

  • Li Z, Huang C, Bao C et al (2015) Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 22(3):256–264

    Article  PubMed  Google Scholar 

  • Li Y, Zhao SL, Li J et al (2017) Osa-miR169 negatively regulates rice immunity against the blast fungus Magnaporthe oryzae. Front Plant Sci 8:2

    PubMed  PubMed Central  Google Scholar 

  • Li Q, Wang Y, Wu S et al (2019) CircACC1 regulates assembly and activation of AMPK complex under metabolic stress. Cell Metab 30(1):157–173

    Article  PubMed  Google Scholar 

  • Li L, Guo N, Liu T et al (2023) Genome-wide identification and characterization of long non-coding RNA in barley roots in response to Piriformospora indica colonization. Plant Sci 330:111666

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Carmell MA, Rivas FV et al (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305(5689):1437–1441

    Article  CAS  PubMed  Google Scholar 

  • Liu S, Wang Q, Li X et al (2019) Detecting of chloroplast circular RNAs in Arabidopsis thaliana. Plant Signal Behav 14(8):1621088

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu J, Liu X, Zhang S et al (2021) TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs. BMC Genomics 22(1):1–12

    Article  Google Scholar 

  • Liu W, Cui J, Luan Y (2022) Overexpression of lncRNA08489 enhances tomato immunity against Phytophthora infestans by decoying miR482e-3p. Biochem Biophys Res Commun 587:36–41

    Article  CAS  PubMed  Google Scholar 

  • Lu T, Cui L, Zhou Y et al (2015) Transcriptome-wide investigation of circular RNAs in rice. RNA 21(12):2076–2087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luan Y, Cui J, Li J et al (2018) Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum. Planta 247:127–138

    Article  CAS  PubMed  Google Scholar 

  • Lukiw WJ, Handley P, Wong L et al (1992) BC200 RNA in normal human neocortex, non-Alzheimer dementia (NAD), and senile dementia of the Alzheimer type (AD). Neurochem Res 17:591–597

    Article  CAS  PubMed  Google Scholar 

  • Luo M, Sun X, Xu M et al (2023a) Identification of miRNAs involving potato-Phytophthora infestans interaction. Plan Theory 12(3):461

    CAS  Google Scholar 

  • Luo Y, Qin C, Qiu H et al (2023b) Novel microRNAs associated with the immune response to cucumber mosaic virus in hot pepper (Capsicum annuum L.). Physiol Mol Plant Pathol 124:101963

    Article  CAS  Google Scholar 

  • Lv Y, Zhong Y, Jiang B et al (2023) MicroRNA miR171b positively regulates resistance to Huanglongbing of citrus. Int J Mol Sci 24(6):5737

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma L, Bajic VB, Zhang Z (2013) On the classification of long non-coding RNAs. RNA Biol 10(6):924–933

    Article  CAS  PubMed Central  Google Scholar 

  • Ma X, Shao C, Jin Y et al (2014) Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana. RNA Biol 11(4):373–390

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma X, Liu C, Gu L et al (2018) TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants. Bioinformatics 34(9):1574–1576

    Article  CAS  PubMed  Google Scholar 

  • MacRae IJ, Zhou K, Li F et al (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311(5758):195–198

    Article  CAS  PubMed  Google Scholar 

  • Manavella PA, Hagmann J, Ott F et al (2012) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151(4):859–870

    Article  CAS  PubMed  Google Scholar 

  • Megraw M, Baev V, Rusinov V et al (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12(9):1612–1619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mehraj H, Shea DJ, Takahashi S et al (2021) Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLoS One 16(3):e0242530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Memczak S, Jens M, Elefsinioti A et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333–338

    Article  CAS  PubMed  Google Scholar 

  • Meyers BC, Axtell MJ, Bartel B et al (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20(12):3186–3190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mi S, Cai T, Hu Y et al (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133(1):116–127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Millar AA, Waterhouse PM (2005) Plant and animal microRNAs: similarities and differences. Funct Integr Genom 5:129–135

    Article  CAS  Google Scholar 

  • Morris KV, Mattick JS (2014) The rise of regulatory RNA. Nat Rev Genet 15(6):423–437

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nie J, Wang H, Zhang W et al (2021) Characterization of lncRNAs and mRNAs involved in powdery mildew resistance in cucumber. Phytopathology 111(9):1613–1624

    Article  CAS  PubMed  Google Scholar 

  • Niu D, Lii YE, Chellappan P et al (2016) miRNA863-3p sequentially targets negative immune regulator ARLPKs and positive regulator SERRATE upon bacterial infection. Nat Commun 7(1):11324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nojima T, Proudfoot NJ (2022) Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 23(6):389–406

    Article  CAS  PubMed  Google Scholar 

  • Nowis K, Jackowiak P, Figlerowicz M et al (2021) At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format. Database 2021:baab074

    Article  PubMed  PubMed Central  Google Scholar 

  • Nozawa M, Miura S, Nei M (2012) Origins and evolution of microRNA genes in plant species. Genome Biol Evol 4(3):230–239

    Article  PubMed  PubMed Central  Google Scholar 

  • Pachnis V, Belayew A, Tilghman SM (1984) Locus unlinked to alpha-fetoprotein under the control of the murine raf and Rif genes. Proc Natl Acad Sci U S A 81(17):5523–5527

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Park MY, Wu G, Gonzalez-Sulser A (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci U S A 102(10):3691–3696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patra GK, Gupta D, Rout GR (2022) Role of long non coding RNA in plants under abiotic and biotic stresses. Plant Physiol Biochem 194:96–110

    Article  PubMed  Google Scholar 

  • Proudfoot NJ (2016) Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. Science 352(6291):aad9926

    Article  PubMed  PubMed Central  Google Scholar 

  • Rajagopalan R, Vaucheret H, Trejo J et al (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20(24):3407–3425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinhart BJ, Slack FJ, Basson M et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403(6772):901–906

    Article  CAS  PubMed  Google Scholar 

  • Reinhart BJ, Weinstein EG, Rhoades MW et al (2002) MicroRNAs in plants. Genes Dev 16(13):1616–1626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ren G, Xie M, Dou Y et al (2012) Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci U S A 109(31):12817–12821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rosli HG, Sirvent E, Bekier FN (2021) Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge. Sci Rep 11(1):24523

    Google Scholar 

  • Salvador-Guirao R, Baldrich P, Weigel D et al (2018) The microRNA miR773 is involved in the Arabidopsis immune response to fungal pathogens. Mol Plant-Microbe Interact 31(2):249–259

    Article  CAS  PubMed  Google Scholar 

  • Salzman J, Gawad C, Wang PL et al (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7(2):e30733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanchez-Sanuy F, Peris-Peris C, Tomiyama S et al (2019) Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus. BMC Plant Biol 19(1):1–16

    Article  Google Scholar 

  • Sanger HL, Klotz G, Riesner D (1976) Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci U S A 73(11):3852–3856

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seimiya T, Otsuka M, Iwata T et al (2020) Emerging roles of exosomal circular RNAs in cancer. Front Cell Dev Biol 8:568366

    Article  PubMed  PubMed Central  Google Scholar 

  • Shen Y, Guo X, Wang W (2017) Identification and characterization of circular RNAs in zebrafish. FEBS Lett 591(1):213–220

    Article  CAS  PubMed  Google Scholar 

  • Shlyueva D, Stampfel G, Stark A et al (2014) Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet 15(4):272–286

    Article  CAS  PubMed  Google Scholar 

  • Soto-Suárez M, Baldrich P, Weigel D et al (2017) The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens. Sci Rep 7(1):1–14

    Article  Google Scholar 

  • Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15(2):173–183

    Article  CAS  PubMed  Google Scholar 

  • Sun Y, Zhang H, Fan M et al (2020) Genome-wide identification of long non-coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber green mottle mosaic virus infection in watermelon. Arch Virol 165:1177–1190

    Article  CAS  PubMed  Google Scholar 

  • Swiezewski S, Liu F, Magusin A et al (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462(7274):799–802

    Article  CAS  PubMed  Google Scholar 

  • Tan-Wong SM, Dhir S, Proudfoot NJ (2019) R-loops promote antisense transcription across the mammalian genome. Mol Cell 76(4):600–616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thieffry A, Vigh ML, Bornholdt J et al (2020) Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by inactivation of nuclear RNA decay pathways. Plant Cell 32(6):1845–1867

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian J, Zhang G, Zhang F et al (2022) Genome-wide identification of powdery mildew responsive long noncoding RNAs in Cucurbita pepo. Front Genet 13:933022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomkowiak A, Bobrowska R, Kwiatek M (2023) Analysis of miRNA expression associated with gene Lr34 responsible for resistance mechanisms to wheat leaf rust. Pak J Bot 55(1):379–385

    Article  CAS  Google Scholar 

  • Wang HLV, Chekanova JA (2017) Long noncoding RNAs in plants. Adv Exp Med Biol 1008:133–154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Li J, Guo B et al (2022) Exonic circular RNAs are involved in Arabidopsis immune response against bacterial and fungal pathogens and function synergistically with corresponding linear RNAs. Phytopathology 112(3):608–619

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Wang Z (2015) Efficient backsplicing produces translatable circular mRNAs. RNA 21(2):172–179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Liu Y, Li L et al (2017) Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes. Sci Rep 7(1):4910

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Xia Y, Lin S et al (2018) Osa-miR164a targets OsNAC60 and negatively regulates rice immunity against the blast fungus Magnaporthe oryzae. Plant J 95(4):584–597

    Article  CAS  Google Scholar 

  • Wang LL, Jin JJ, Li LH et al (2020) Long non-coding RNAs responsive to blast fungus infection in rice. Rice 13(1):1–8

    Article  PubMed  PubMed Central  Google Scholar 

  • Wei X, Ke H, Wen A et al (2021) Structural basis of microRNA processing by Dicer-like 1. Nat Plants 7(10):1389–1396

    Article  CAS  PubMed  Google Scholar 

  • West S, Gromak N, Proudfoot NJ (2004) Human 5′→ 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432(7016):522–525

    Article  CAS  PubMed  Google Scholar 

  • Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75(5):855–862

    Article  CAS  PubMed  Google Scholar 

  • Wu HJ, Ma YK, Chen T et al (2012a) PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res 40(W1):W22–W28

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu J, Okada T, Fukushima T et al (2012b) A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis. RNA Biol 9(3):302–313

    Article  CAS  PubMed  Google Scholar 

  • Wu X, Shi Y, Li J et al (2013) A role for the RNA-binding protein MOS2 in microRNA maturation in Arabidopsis. Cell Res 23(5):645–657

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu J, Yang R, Yang Z et al (2017) ROS accumulation and antiviral defence control by microRNA528 in rice. Nat Plants 3(1):1–7

    Article  Google Scholar 

  • Wu M, Karadoulama E, Lloret-Llinares M et al (2020) The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res 48(15):8509–8528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiang L, Cai C, Cheng J et al (2018) Identification of circular RNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq. PeerJ 6:e4500

    Article  PubMed  PubMed Central  Google Scholar 

  • Xie Z, Allen E, Fahlgren N et al (2005) Expression of Arabidopsis miRNA genes. Plant Physiol 138(4):2145–2154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Y, Liu T, Shen D et al (2019) Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms. PLoS Pathog 15(1):e1007534

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang F, Zhao D, Fan H et al (2020) Functional analysis of long non-coding RNAs reveal their novel roles in biocontrol of bacteria-induced tomato resistance to Meloidogyne incognita. Int J Mol Sci 21(3):911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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(4):573–585

    Article  CAS  PubMed  Google Scholar 

  • Ye CY, Chen L, Liu C et al (2015) Widespread noncoding circular RNAs in plants. New Phytol 208(1):88–95

    Article  CAS  PubMed  Google Scholar 

  • Ye CY, Zhang X, Chu Q et al (2017) Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol 14(8):1055–1063

    Article  PubMed  Google Scholar 

  • Ye J, Wang L, Li S et al (2019) AtCircDB: a tissue-specific database for Arabidopsis circular RNAs. Brief Bioinform 20(1):58–65

    Article  CAS  PubMed  Google Scholar 

  • Yu B, Yang Z, Li J et al (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307(5711):932–935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu B, Bi L, Zheng B (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci U S A 105(29):10073–10078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu Y, Zhou YF, Feng YZ et al (2020) Transcriptional landscape of pathogen-responsive lncRNAs in rice unveils the role of ALEX 1 in jasmonate pathway and disease resistance. Plant Biotechnol J 18(3):679–690

    Article  CAS  PubMed  Google Scholar 

  • Yu X, Hou Y, Cao L et al (2022) MicroRNA candidate miRcand137 in apple is induced by Botryosphaeria dothidea for impairing host defense. Plant Physiol 189(3):1814–1832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang K, Shi ZM, Chang YN et al (2014a) The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene 547(1):1–9

    Article  CAS  PubMed  Google Scholar 

  • Zhang XO, Wang HB, Zhang Y et al (2014b) Complementary sequence-mediated exon circularization. Cell 159(1):134–147

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Hu W, Hao J et al (2016) Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum. BMC Genomics 17:1–11

    Article  CAS  Google Scholar 

  • Zhang P, Meng X, Chen H et al (2017) PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks. Database 2017:bax089

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang P, Fan Y, Sun X et al (2019a) A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis. Plant J 98(4):697–713

    Article  CAS  PubMed  Google Scholar 

  • Zhang R, Zheng F, Wei S et al (2019b) Evolution of disease defense genes and their regulators in plants. Int J Mol Sci 20(2):335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J, Hao Z, Yin S et al (2020a) GreenCircRNA: a database for plant circRNAs that act as miRNA decoys. Database. 2020:baaa039 2020

    Google Scholar 

  • Zhang P, Li S, Chen M (2020b) Characterization and function of circular RNAs in plants. Front Mol Biosci 7:91

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Liu J, Cheng J et al (2022a) lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt. Plant Physiol 189(1):264–284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Waseem M, Zeng Z et al (2022b) MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. New Phytol 233(5):2047–2057

    Article  CAS  PubMed  Google Scholar 

  • Zhao P, Sun J, Zou L et al (2022). Biological function research of the long non-coding RNA Malnc2310 in bananas induced by Fusarium oxysporum f. sp. cubense

    Google Scholar 

  • Zhou R, Zhu Y, Zhao J et al (2017) Transcriptome-wide identification and characterization of potato circular RNAs in response to Pectobacterium carotovorum subspecies brasiliense infection. Int J Mol Sci 19(1):71

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou X, Cui J, Cui H et al (2020) Identification of lncRNAs and their regulatory relationships with target genes and corresponding miRNAs in melon response to powdery mildew fungi. Gene 735:144403

    Article  CAS  PubMed  Google Scholar 

  • Zhou X, Cui J, Luan Y (2022) Characterization of lncRNAs in mycorrhizal tomato and elucidation of the role of lncRNA69908 in disease resistance. Biochem Biophys Res Commun 634:203–210

    Article  CAS  PubMed  Google Scholar 

  • Zhu Y, Rowley MJ, Böhmdorfer G et al (2013) A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell 49(2):298–309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhuo X, Yu Q, Russo R et al (2023) Role of long non-coding RNA in regulatory network response to Candidatus Liberibacter asiaticus in citrus. Front Plant Sci 14:1090711

    Article  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology, Panjab University, Chandigarh, India

    Nandni, Monika Bhuria, Ravneet Kaur & Kashmir Singh

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  1. Nandni
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  2. Monika Bhuria
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  3. Ravneet Kaur
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  4. Kashmir Singh
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  1. Department of Biotechnology, Panjab University, Chandigarh, India

    Kashmir Singh

  2. Department of Biotechnology, Panjab University, Chandigarh, India

    Ravneet Kaur

  3. Department of Biotechnology, Central University of Haryana, Mahendragarh, India

    Rupesh Deshmukh

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Nandni, Bhuria, M., Kaur, R., Singh, K. (2024). Role of Non-coding RNAs in Disease Resistance in Plants. In: Singh, K., Kaur, R., Deshmukh, R. (eds) Biotechnological Advances for Disease Tolerance in Plants. Springer, Singapore. https://doi.org/10.1007/978-981-99-8874-7_7

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