Non-coding RNAs and Their Roles in Stress Response in Plants
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摘要
Eukaryotic genomes encode thousands of non-coding RNAs(ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially micro RNAs(miRNAs) and long ncRNAs(lncRNAs),have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification,characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA-and lncRNA-mediated plant stress tolerance.
Eukaryotic genomes encode thousands of non-coding RNAs(ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially micro RNAs(miRNAs) and long ncRNAs(lncRNAs),have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification,characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA-and lncRNA-mediated plant stress tolerance.
Eukaryotic genomes encode thousands of non-coding RNAs(ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially micro RNAs(miRNAs) and long ncRNAs(lncRNAs),have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification,characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA-and lncRNA-mediated plant stress tolerance.
引文
[1]Rajagopalan R,Vaucheret H,Trejo J,Bartel DP.A diverse and evolutionarily fluid set of micrornas in Arabidopsis thaliana.Genes Dev 2006;20:3407-25.
[2]Liu X,Hao L,Li D,Zhu L,Hu S.Long non-coding RNAs and their biological roles in plants.Genomics Proteomics Bioinformatics 2015;13:137-47.
[3]Liu J,Wang H,Chua NH.Long noncoding RNA transcriptome of plants.Plant Biotechnol J 2015;13:319-28.
[4]Chekanova JA.Long non-coding RNAs and their functions in plants.Curr Opin Plant Biol 2015;27:207-16.
[5]Shafiq S,Li J,Sun Q.Functions of plants long non-coding RNAs.Biochim Biophys Acta 2016;1859:155-62.
[6]Xu XW,Zhou XH,Wang RR,Peng WL,An Y,Chen LL.Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network.Sci Rep 2016;6:20715.
[7]Lv Y,Liang Z,Ge M,Qi W,Zhang T,Lin F,et al.Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize(Zea mays L.).BMC Genomics 2016;17:350.
[8]Chen M,Wang C,Bao H,Chen H,Wang Y.Genome-wide identification and characterization of novel lnc RNAs in populus under nitrogen deficiency.Mol Genet Genomics2016;291:1663-80.
[9]Di C,Yuan J,Wu Y,Li J,Lin H,Hu L,et al.Characterization of stress-responsive lnc RNAs in Arabidopsis thaliana by integrating expression,epigenetic and structural features.Plant J2014;80:848-61.
[10]Gan ES,Huang J,Ito T.Functional roles of histone modification,chromatin remodeling and micrornas in Arabidopsis flower development.Int Rev Cell Mol Biol 2013;305:115-61.
[11]Zhang S,Xie M,Ren G,Yu B.CDC5,a DNA binding protein,positively regulates posttranscriptional processing and/or transcription of primary micro RNA transcripts.Proc Natl Acad Sci U S A 2013;110:17588-93.
[12]Zhang S,Liu Y,Yu B.PRL1,an RNA-binding protein,positively regulates the accumulation of mi RNAs and si RNAs in Arabidopsis.PLo S Genet 2014;10:e1004841.
[13]Wang L,Song X,Gu L,Li X,Cao S,Chu C,et al.NOT2proteins promote polymerase II-dependent transcription and interact with multiple micro RNA biogenesis factors in Arabidopsis.Plant Cell 2013;25:715-27.
[14]Ren G,Xie M,Dou Y,Zhang S,Zhang C,Yu B.Regulation of mi RNA abundance by RNA binding protein TOUGH in Arabidopsis.Proc Natl Acad Sci U S A 2012;109:12817-21.
[15]Machida S,Yuan YA.Crystal structure of Arabidopsis thaliana Dawdle forkhead-associated domain reveals a conserved phospho-threonine recognition cleft for dicer-like 1 binding.Mol Plant 2013;6:1290-300.
[16]Fang X,Cui Y,Li Y,Qi Y.Transcription and processing of primary micro RNAs are coupled by Elongator complex in Arabidopsis.Nat Plants 2015;1:15075.
[17]Achkar NP,Cambiagno DA,Manavella PA.mi RNA biogenesis:a dynamic pathway.Trends Plant Sci 2016;21:1034-44.
[18]An J,Lai J,Sajjanhar A,Lehman ML,Nelson CC.mi RPlant:an integrated tool for identification of plant mi RNA from RNAsequencing data.BMC Bioinformatics 2014;15:275.
[19]Hackenberg M,Sturm M,Langenberger D,Falco′n-Pe′rez JM,Aransay AM.mi Ranalyzer:a micro RNA detection and analysis tool for next-generation sequencing experiments.Nucleic Acids Res 2009;37:W68-76.
[20]Evers M,Huttner M,Dueck A,Meister G,Engelmann JC.mi Ra:adaptable novel mi RNA identification in plants using small RNA sequencing data.BMC Bioinformatics 2015;16:370.
[21]Yang X,Li L.mi RDeep-P:a computational tool for analyzing the micro RNA transcriptome in plants.Bioinformatics2011;27:2614-5.
[22]Munoz-Me′rida A,Perkins JR,Viguera E,Thode G,Bejarano ER,Pe′rez-pulido AJ.Semirna:searching for plant mi RNAs using target sequences.OMICS 2012;16:168-77.
[23]Bonnet E,He Y,Billiau K,Van de Peer Y.TAPIR,a web server for the prediction of plant micro RRNA targets,including target mimics.Bioinformatics 2010;26:1566-8.
[24]Dai X,Zhao PX.ps RNATarget:a plant small RNA target analysis server.Nucleic Acids Res 2011;39:W155-9.
[25]Zhang Y.mi RU:an automated plant mi RNA target prediction server.Nucleic Acids Res 2005;33:W701-4.
[26]Mhuantong W,Wichadakul D.Micro PC(micro PC):a comprehensive resource for predicting and comparing plant microRNAs.BMC Genomics 2009;10:366.
[27]Numnark S,Mhuantong W,Ingsriswang S,Wichadakul D.C-mii:a tool for plant mi RNA and target identification.BMCGenomics 2012;13:S16.
[28]Zhang Z,Jiang L,Wang J,Gu P,Chen M.MTide:an integrated tool for the identification of mi RNA-target interaction in plants.Bioinformatics 2015;31:290-1.
[29]Rhee S,Chae H,Kim S.Plant Mirna T:mi RNA and m NAintegrated analysis fully utilizing characteristics of plant sequencing data.Methods 2015;83:80-7.
[30]Chae H,Rhee S,Nephew KP,Kim S.Bio VLAB-MMIA-NGS:micro RNA-m RNA integrated analysis using high-throughput sequencing data.Bioinformatics 2015;31:265-7.
[31]Xu J,Li CX,Li YS,Lv JY,Ma Y,Shao TT,et al.Mi RNA-mi RNA synergistic network:construction via co-regulating functional modules and disease mirna topological features.Nucleic Acids Res 2011;39:825-36.
[32]Lin MF,Jungreis I,Kellis M.Phylo CSF:a comparative genomics method to distinguish protein coding and non-coding regions.Bioinformatics 2011;27:i275-82.
[33]Kong L,Zhang Y,Ye ZQ,Liu XQ,Zhao SQ,Wei L,et al.CPC:assess the protein-coding potential of transcripts using sequence features and support vector machine.Nucleic Acids Res 2007;35:W345-9.
[34]Sun L,Luo H,Bu D,Zhao G,Yu K,Zhang C,et al.Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.Nucleic Acids Res 2013;41:e166.
[35]Wang L,Park HJ,Dasari S,Wang S,Kocher JP,Li W.CPAT:Coding-Potential Assessment Tool using an alignment-free logistic regression model.Nucleic Acids Res 2013;41:e74.
[36]Tripathi R,Patel S,Kumari V,Chakraborty P,Varadwaj PK.Deep LNC,a long non-coding RNA prediction tool using deep neural network.Netw Model Anal Health Inform Bioinform2016;5:21.
[37]Sun K,Chen X,Jiang P,Song X,Wang H,Sun H.i See RNA:identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data.BMC Genomics 2013;14:S7.
[38]Hu R,Sun X.lnc RNATargets:a platform for lnc RNA target prediction based on nucleic acid thermodynamics.J Bioinform Comput Biol 2016;14:1650016.
[39]Furio′-Tar?′P,Tarazona S,Gabaldo′n T,Enright AJ,Conesa A.sponge Scan:a web for detecting micro RNA binding elements in lnc RNA sequences.Nucleic Acids Res 2016;44:W176-80.
[40]Jiang Q,Wang J,Wang Y,Ma R,Wu X,Li Y.TF2Lnc RNA:identifying common transcription factors for a list of lnc RNAgenes from CHIP-Seq data.Biomed Res Int 2014;2014:1-5.
[41]Huang HY,Chien CH,Jen KH,Huang HD.Reg RNA:an integrated web server for identifying regulatory RNA motifs and elements.Nucleic Acids Res 2006;34:W429-34.
[42]Friedlander MR,Mackowiak SD,Li N,Chen W,Rajewsky N.mi RDeep2 accurately identifies known and hundreds of novel micro RNA genes in seven animal clades.Nucleic Acids Res2012;40:37-52.
[43]Addo-Quaye C,Miller W,Axtell MJ.Cleave Land:a pipeline for using degradome data to find cleaved small RNA targets.Bioinformatics 2009;25:130-1.
[44]Kozomara A,Griffiths-Jones S.mi RBase:annotating high confidence micro RNAs using deep sequencing data.Nucleic Acids Res 2014;42:d68-73.
[45]Nawrocki EP,Burge SW,Bateman A,Daub J,Eberhardt RY,Eddy SR,et al.Rfam 12.0:updates to the RNA families database.Nucleic Acids Res 2015;43:D130-7.
[46]Chiang K,Shu J,Zempleni J,Cui J.Dietary micro RNAdatabase(DMD):an archive database and analytic tool for food-borne micro RNAs.PLo S One 2015;10:e0128089.
[47]Meng Y,Gou L,Chen D,Mao C,Jin Y,Wu P,et al.Pmi RKB:a plant micro RNA knowledge base.Nucleic Acids Res 2011;39:D181-7.
[48]Zhang Z,Yu J,Li D,Zhang Z,Liu F,Zhou X,et al.PMRD:plant micro RNA database.Nucleic Acids Res 2010;38:D806-13.
[49]R Lorenzetti AP,A de Antonio GY,Paschoal AR,Domingues DS.Plan TE-MIR DB:a database for transposable elementrelated micro RNAs in plant genomes.Funct Integr Genomics2016;16:235-42.
[50]Backman TW,Sullivan CM,Cumbie JS,Miller ZA,Chapman EJ,Fahlgren N,et al.Update of ASRP:the Arabidopsis small RNA project database.Nucleic Acids Res 2008;36:D982-5.
[51]Hsu SD,Lin FM,Wu WY,Liang C,Huang WC,Chan WL,et al.mi RTar Base:a database curates experimentally validated micro RNA-target interactions.Nucleic Acids Res 2011;39:D163-9.
[52]Liu H,Jin T,Liao R,Wan L,Xu B,Zhou S,et al.mi RFANs:an integrated database for Arabidopsis thaliana micro RNA function annotations.BMC Plant Biol 2012;12:68.
[53]Zhang S,Yue Y,Sheng L,Wu Y,Fan G,Li A,et al.PASmi R:a literature-curated database for mi RNA molecular regulation in plant response to abiotic stress.BMC Plant Biol 2013;13:33.
[54]Remita MA,Lord E,Agharbaoui Z,Leclercq M,Badawi M,Makarenkov V,et al.WMP:a novel comprehensive wheat mirna database,including related bioinformatics software.Biorxiv2015,024893.
[55]Zhao Y,Li H,Fang S,Kang Y,Wu W,Hao Y,et al.NONCODE 2016:an informative and valuable data source of long non-coding RNAs.Nucleic Acids Res 2016;44:D203-8.
[56]Paytuv?′Gallart A,Hermoso Pulido A,Anzar Mart?′nez de Lagra′n I,Sanseverino W,Aiese Cigliano R.GREENC:a Wikibased database of plant lnc RNAs.Nucleic Acids Res 2016;44:D1161-6.
[57]Quek XC,Thomson DW,Maag JL,Bartonicek N,Signal B,Clark MB,et al.lnc RNAdb v2.0:expanding the reference database for functional long noncoding RNAs.Nucleic Acids Res 2015;43:D168-73.
[58]Jin J,Liu J,Wang H,Wong L,Chua NH.PLnc DB:plant long non-coding RNA database.Bioinformatics 2013;29:1068-71.
[59]Yi X,Zhang Z,Ling Y,Xu W,Su Z.PNRD:a plant non-coding RNA database.Nucleic Acids Res 2015;43:D982-9.
[60]Szczes′niak MW,Rosikiewicz W,Makalowska I.CANTATAdb:a collection of plant long non-coding RNAs.Plant Cell Physiol2016;57:e8.
[61]Xuan H,Zhang L,Liu X,Han G,Li J,Li X,et al.PLNlnc Rbase:a resource for experimentally identified lnc RNAs in plants.Gene 2015;573:328-32.
[62]Ng SY,Lin L,Soh BS,Stanton LW.Long noncoding RNAs in development and disease of the central nervous system.Trends Genet 2013;29:461-8.
[63]Rohrig H,Schmidt J,Miklashevichs E,Schell J,John M.Soybean ENOD40 encodes two peptides that bind to sucrose synthase.Proc Natl Acad Sci U S A 2002;99:1915-20.
[64]Wu J,Okada T,Fukushima T,Tsudzuki T,Sugiura M,Yukawa Y.A novel hypoxic stress-responsive long non-coding RNAtranscribed by RNA polymerase III in Arabidopsis.RNA Biol2012;9:302-13.
[65]Shin JH,Chekanova JA.Arabidopsis RRP6l1 and RRP6l2function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis.PLo S Genet 2014;10:e1004612.
[66]Mattick JS,Rinn JL.Discovery and annotation of long noncoding RNAs.Nat Struct Mol Biol 2015;22:5-7.
[67]Shriram V,Kumar V,Devarumath RM,Khare TS,Wani SH.Micro RNAs as potential targets for abiotic stress tolerance in plants.Front Plant Sci 2016;7:817.
[68]Mittal D,Sharma N,Sharma V,Sopory SK,Sanan-Mishra N.Role of micro RNAs in rice plant under salt stress.Ann Appl Biol2016;168:2-18.
[69]Koroban NV,Kudryavtseva AV,Krasnov GS,Sadritdinova AF,Fedorova MS,Snezhkina AV,et al.The role of micro RNAin abiotic stress response in plants.Mol Bio(Mosk)2016;50:387-94.
[70]Schmidt U,Keck ME,Buell DR.mi RNAs and other non-coding RNAs in posttraumatic stress disorder:a systematic review of clinical and animal studies.J Psychiatr Res 2015;65:1-8.
[71]Panda SK,Sunkar R.Nutrient-and other stress-responsive micro RNAs in plants:role for thiol-based redox signaling.Plant Signal Behav 2015;10:e1010916.
[72]Budak H,Kantar M,Bulut R,Akpinar BA.Stress responsive mi RNAs and isomi Rs in cereals.Plant Sci 2015;235:1-13.
[73]Nguyen GN,Rothstein SJ,Spangenberg G,Kant S.Role of micro RNAs involved in plant response to nitrogen and phosphorous limiting conditions.Front Plant Sci 2015;6:629.
[74]Liang G,He H,Yu D.Identification of nitrogen starvationresponsive micro RNAs in Arabidopsis thaliana.PLo S One2012;7:e48951.
[75]Zhao M,Ding H,Zhu JK,Zhang F,Li WX.Involvement of mi R169 in the nitrogen-starvation responses in Arabidopsis.New Phytol 2011;190:906-15.
[76]Zhao Y,Xu Z,Mo Q,Zou C,Li W,Xu Y,et al.Combined small RNA and degradome sequencing reveals novel mi RNAs and their targets in response to low nitrate availability in maize.Ann Bot 2013;112:633-42.
[77]Contreras-Cubas C,Palomar M,Arteaga-Va′zquez M,Reyes JL,Covarrubias AA.Non-coding RNAs in the plant response to abiotic stress.Planta 2012;236:943-58.
[78]Sunkar R,Li YF,Jagadeeswaran G.Functions of micro RNAs in plant stress responses.Trends Plant Sci 2012;17:196-203.
[79]Akdogan G,Tufekci ED,Uranbey S,Unver T.mi RNA-based drought regulation in wheat.Funct Integr Genomics2016;16:221-33.
[80]Franco-Zorrilla JM,Valli A,Todesco M,Mateos I,Puga MI,Rubio-Somoza I,et al.Target mimicry provides a new mechanism for regulation of micro RNA activity.Nat Genetics2007;39:1033-7.
[81]Wang J,Yu W,Yang Y,Li X,Chen T,Liu T,et al.Genomewide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for micro RNA in response to TYLCV infection.Sci Rep 2015;5:16946.
[82]Joshi RK,Megha S,Basu U,Rahman MH,Kav NN.Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus.PLo S One 2016;11:e0158784.
[83]Xin M,Wang Y,Yao Y,Song N,Hu Z,Qin D,et al.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.BMCPlant Biol 2011;11:61.
[84]Chen D,Yuan C,Zhang J,Zhang Z,Bai L,Meng Y,et al.Plant NATs DB:a comprehensive database of plant natural antisense transcripts.Nucleic Acids Res 2012;40:D1187-93.
[85]Yuan C,Wang J,Harrison AP,Meng X,Chen D,Chen M.Genome-wide view of natural antisense transcripts in Arabidopsis thaliana.DNA Res 2015;22:233-43.
[86]Wight M,Werner A.The functions of natural antisense transcripts.Essays Biochem 2013;54:91-101.
[87]Zhang X,Lii Y,Wu Z,Polishko A,Zhang H,Chinnusamy V,et al.Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues.Mol Plant2013;6:704-15.
[88]Zhang W,Han Z,Guo Q,Liu Y,Zheng Y,Wu F,et al.Identification of maize long non-coding RNAs responsive to drought stress.PLo S One 2014;9:e98958.
[89]Zhang H,Chen X,Wang C,Xu Z,Wang Y,Liu X,et al.Long non-coding genes implicated in response to stripe rust pathogen stress in wheat(Triticum aestivum L.).Mol Biol Rep2013;40:6245-53.
[90]Wang H,Chung PJ,Liu J,Jang IC,Kean MJ,Xu J,et al.Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis.Genome Res 2014;24:444-53.
[91]Wang J,Meng X,Yuan C,Harrison AP,Chen M.The roles of cross-talk epigenetic patterns in Arabidopsis thaliana.Brief Funct Genomics 2016;15:278-87.
[92]Csorba T,Questa JI,Sun Q,Dean C.Antisense COOLAIRmediates the coordinated switching of chromatin states at FLCduring vernalization.Proc Natl Acad Sci U S A2014;111:16160-5.
[93]Heo JB,Sung S.Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.Science 2011;331:76-9.
[94]Michaels SD,Amasino RM.FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering.Plant Cell 1999;11:949-56.
[95]Marquardt S,Raitskin O,Wu Z,Liu F,Sun Q,Dean C.Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription.Mol Cell 2014;54:156-65.
[96]Matzke MA,Mosher RA.RNA-directed DNA methylation:an epigenetic pathway of increasing complexity.Nat Rev Genet2014;15:394-408.
[97]Wierzbicki AT.The role of long non-coding RNA in transcriptional gene silencing.Curr Opin Plant Biol 2012;15:517-22.
[98]Movahedi A,Sun W,Zhang J,Wu X,Mousavi M,Mohammadi K,et al.RNA-directed DNA methylation in plants.Plant Cell Rep 2015;34:1857-62.
[99]Huang W,Xian Z,Hu G,Li Z.SLAGO4A,a core factor of RNA-directed DNA methylation(Rd DM)pathway,plays an important role under salt and drought stress in tomato.Mol Breed 2016;36:28.
[100]Steward N,Kusano T,Sano H.Expression of Zmmet1,a gene encoding a DNA methyltransferase from maize,is associated not only with DNA replication in actively proliferating cells,but also with altered DNA methylation status in cold-stressed quiescent cells.Nucleic Acids Res 2000;28:3250-9.
[101]Le TN,Schumann U,Smith NA,Tiwari S,Au PC,Zhu QH,et al.DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis.Genome Biol 2014;15:458.
[102]Popova OV,Dinh HQ,Aufsatz W,Jonak C.The Rd DMpathway is required for basal heat tolerance in Arabidopsis.Mol Plant 2013;6:396-410.
[103]Xu R,Wang Y,Zheng H,Lu W,Wu C,Huang J,et al.Saltinduced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis.J Exp Bot2015;66:5997-6008.
[104]Wibowo A,Becker C,Marconi G,Durr J,Price J,Hagmann J,et al.Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity.Elife 2016;5:e13546.
[105]Baldrich P,Kakar K,Sire′C,Moreno AB,Berger A,Garc?′aChapa M,et al.Small RNA profiling reveals regulation of Arabidopsis mi R168 and heterochromatic si RNA415 in response to fungal elicitors.BMC Genomics 2014;15:1083.
[106]Axtell MJ.Classification and comparison of small RNAs from plants.Annu Rev Plant Biol 2013;64:137-59.
[107]Sunkar R,Zhu JK.Novel and stress-regulated micro RNAs and other small RNAs from Arabidopsis.Plant Cell2004;16:2001-19.
[108]Borsani O,Zhu J,Verslues PE,Sunkar R,Zhu JK.Endogenous si RNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis.Cell 2005;123:1279-91.
[109]Guleria P,Mahajan M,Bhardwaj J,Yadav SK.Plant small RNAs:biogenesis,mode of action and their roles in abiotic stresses.Genomics Proteomics Bioinformatics 2011;9:183-99.
[110]Wierzbicki AT,Haag JR,Pikaard CS.Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes.Cell2008;135:635-48.
[111]Xia J,Zeng C,Chen Z,Zhang K,Chen X,Zhou Y,et al.Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava.BMC Genomics2014;15:634.
[112]Taft RJ,Glazov EA,Lassmann T,Hayashizaki Y,Carninci P,Mattick JS.Small RNAs derived from sno RNAs.RNA2009;15:1233-40.
[113]Lee YS,Shibata Y,Malhotra A,Dutta A.A novel class of small RNAs:t RNA-derived RNA fragments(t RFs).Genes Dev2009;23:2639-49.
[114]Wang Y,Wang X,Deng W,Fan X,Liu TT,He G,et al.Genomic features and regulatory roles of intermediate-sized noncoding RNAs in Arabidopsis.Mol Plant 2014;7:514-27.
[115]Bilichak A,Ilnytskyy Y,Wo′ycicki R,Kepeshchuk N,Fogen D,Kovalchuk I.The elucidation of stress memory inheritance in Brassica rapa plants.Front Plant Sci 2015;6:5.
[116]Wang Y,Li H,Sun Q,Yao Y.Characterization of small RNAs derived from t RNAs,r RNAs and sno RNAs and their response to heat stress in wheat seedlings.PLo S One 2016;11:e0150933.
[117]Visser M,Maree HJ,Rees DJ,Burger JT.High-throughput sequencing reveals small RNAs involved in ASGV infection.BMC Genomics 2014;15:568.
[118]Asha S,Soniya EV.Transfer RNA derived small RNAs targeting defense responsive genes are induced during Phytophthora capsici infection in black pepper(Piper nigrum L.).Front Plant Sci 2016;7:767.
[119]Hsieh LC,Lin SI,Kuo HF,Chiou TJ.Abundance of t RNA-derived small RNAs in phosphate-starved Arabidopsis roots.Plant Signal Behav 2010;5:537-9.
[120]Vandivier LE,Anderson SJ,Foley SW,Gregory BD.The conservation and function of RNA secondary structure in plants.Annu Rev Plant Biol 2016;67:463-88.
[2]Liu X,Hao L,Li D,Zhu L,Hu S.Long non-coding RNAs and their biological roles in plants.Genomics Proteomics Bioinformatics 2015;13:137-47.
[3]Liu J,Wang H,Chua NH.Long noncoding RNA transcriptome of plants.Plant Biotechnol J 2015;13:319-28.
[4]Chekanova JA.Long non-coding RNAs and their functions in plants.Curr Opin Plant Biol 2015;27:207-16.
[5]Shafiq S,Li J,Sun Q.Functions of plants long non-coding RNAs.Biochim Biophys Acta 2016;1859:155-62.
[6]Xu XW,Zhou XH,Wang RR,Peng WL,An Y,Chen LL.Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network.Sci Rep 2016;6:20715.
[7]Lv Y,Liang Z,Ge M,Qi W,Zhang T,Lin F,et al.Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize(Zea mays L.).BMC Genomics 2016;17:350.
[8]Chen M,Wang C,Bao H,Chen H,Wang Y.Genome-wide identification and characterization of novel lnc RNAs in populus under nitrogen deficiency.Mol Genet Genomics2016;291:1663-80.
[9]Di C,Yuan J,Wu Y,Li J,Lin H,Hu L,et al.Characterization of stress-responsive lnc RNAs in Arabidopsis thaliana by integrating expression,epigenetic and structural features.Plant J2014;80:848-61.
[10]Gan ES,Huang J,Ito T.Functional roles of histone modification,chromatin remodeling and micrornas in Arabidopsis flower development.Int Rev Cell Mol Biol 2013;305:115-61.
[11]Zhang S,Xie M,Ren G,Yu B.CDC5,a DNA binding protein,positively regulates posttranscriptional processing and/or transcription of primary micro RNA transcripts.Proc Natl Acad Sci U S A 2013;110:17588-93.
[12]Zhang S,Liu Y,Yu B.PRL1,an RNA-binding protein,positively regulates the accumulation of mi RNAs and si RNAs in Arabidopsis.PLo S Genet 2014;10:e1004841.
[13]Wang L,Song X,Gu L,Li X,Cao S,Chu C,et al.NOT2proteins promote polymerase II-dependent transcription and interact with multiple micro RNA biogenesis factors in Arabidopsis.Plant Cell 2013;25:715-27.
[14]Ren G,Xie M,Dou Y,Zhang S,Zhang C,Yu B.Regulation of mi RNA abundance by RNA binding protein TOUGH in Arabidopsis.Proc Natl Acad Sci U S A 2012;109:12817-21.
[15]Machida S,Yuan YA.Crystal structure of Arabidopsis thaliana Dawdle forkhead-associated domain reveals a conserved phospho-threonine recognition cleft for dicer-like 1 binding.Mol Plant 2013;6:1290-300.
[16]Fang X,Cui Y,Li Y,Qi Y.Transcription and processing of primary micro RNAs are coupled by Elongator complex in Arabidopsis.Nat Plants 2015;1:15075.
[17]Achkar NP,Cambiagno DA,Manavella PA.mi RNA biogenesis:a dynamic pathway.Trends Plant Sci 2016;21:1034-44.
[18]An J,Lai J,Sajjanhar A,Lehman ML,Nelson CC.mi RPlant:an integrated tool for identification of plant mi RNA from RNAsequencing data.BMC Bioinformatics 2014;15:275.
[19]Hackenberg M,Sturm M,Langenberger D,Falco′n-Pe′rez JM,Aransay AM.mi Ranalyzer:a micro RNA detection and analysis tool for next-generation sequencing experiments.Nucleic Acids Res 2009;37:W68-76.
[20]Evers M,Huttner M,Dueck A,Meister G,Engelmann JC.mi Ra:adaptable novel mi RNA identification in plants using small RNA sequencing data.BMC Bioinformatics 2015;16:370.
[21]Yang X,Li L.mi RDeep-P:a computational tool for analyzing the micro RNA transcriptome in plants.Bioinformatics2011;27:2614-5.
[22]Munoz-Me′rida A,Perkins JR,Viguera E,Thode G,Bejarano ER,Pe′rez-pulido AJ.Semirna:searching for plant mi RNAs using target sequences.OMICS 2012;16:168-77.
[23]Bonnet E,He Y,Billiau K,Van de Peer Y.TAPIR,a web server for the prediction of plant micro RRNA targets,including target mimics.Bioinformatics 2010;26:1566-8.
[24]Dai X,Zhao PX.ps RNATarget:a plant small RNA target analysis server.Nucleic Acids Res 2011;39:W155-9.
[25]Zhang Y.mi RU:an automated plant mi RNA target prediction server.Nucleic Acids Res 2005;33:W701-4.
[26]Mhuantong W,Wichadakul D.Micro PC(micro PC):a comprehensive resource for predicting and comparing plant microRNAs.BMC Genomics 2009;10:366.
[27]Numnark S,Mhuantong W,Ingsriswang S,Wichadakul D.C-mii:a tool for plant mi RNA and target identification.BMCGenomics 2012;13:S16.
[28]Zhang Z,Jiang L,Wang J,Gu P,Chen M.MTide:an integrated tool for the identification of mi RNA-target interaction in plants.Bioinformatics 2015;31:290-1.
[29]Rhee S,Chae H,Kim S.Plant Mirna T:mi RNA and m NAintegrated analysis fully utilizing characteristics of plant sequencing data.Methods 2015;83:80-7.
[30]Chae H,Rhee S,Nephew KP,Kim S.Bio VLAB-MMIA-NGS:micro RNA-m RNA integrated analysis using high-throughput sequencing data.Bioinformatics 2015;31:265-7.
[31]Xu J,Li CX,Li YS,Lv JY,Ma Y,Shao TT,et al.Mi RNA-mi RNA synergistic network:construction via co-regulating functional modules and disease mirna topological features.Nucleic Acids Res 2011;39:825-36.
[32]Lin MF,Jungreis I,Kellis M.Phylo CSF:a comparative genomics method to distinguish protein coding and non-coding regions.Bioinformatics 2011;27:i275-82.
[33]Kong L,Zhang Y,Ye ZQ,Liu XQ,Zhao SQ,Wei L,et al.CPC:assess the protein-coding potential of transcripts using sequence features and support vector machine.Nucleic Acids Res 2007;35:W345-9.
[34]Sun L,Luo H,Bu D,Zhao G,Yu K,Zhang C,et al.Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.Nucleic Acids Res 2013;41:e166.
[35]Wang L,Park HJ,Dasari S,Wang S,Kocher JP,Li W.CPAT:Coding-Potential Assessment Tool using an alignment-free logistic regression model.Nucleic Acids Res 2013;41:e74.
[36]Tripathi R,Patel S,Kumari V,Chakraborty P,Varadwaj PK.Deep LNC,a long non-coding RNA prediction tool using deep neural network.Netw Model Anal Health Inform Bioinform2016;5:21.
[37]Sun K,Chen X,Jiang P,Song X,Wang H,Sun H.i See RNA:identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data.BMC Genomics 2013;14:S7.
[38]Hu R,Sun X.lnc RNATargets:a platform for lnc RNA target prediction based on nucleic acid thermodynamics.J Bioinform Comput Biol 2016;14:1650016.
[39]Furio′-Tar?′P,Tarazona S,Gabaldo′n T,Enright AJ,Conesa A.sponge Scan:a web for detecting micro RNA binding elements in lnc RNA sequences.Nucleic Acids Res 2016;44:W176-80.
[40]Jiang Q,Wang J,Wang Y,Ma R,Wu X,Li Y.TF2Lnc RNA:identifying common transcription factors for a list of lnc RNAgenes from CHIP-Seq data.Biomed Res Int 2014;2014:1-5.
[41]Huang HY,Chien CH,Jen KH,Huang HD.Reg RNA:an integrated web server for identifying regulatory RNA motifs and elements.Nucleic Acids Res 2006;34:W429-34.
[42]Friedlander MR,Mackowiak SD,Li N,Chen W,Rajewsky N.mi RDeep2 accurately identifies known and hundreds of novel micro RNA genes in seven animal clades.Nucleic Acids Res2012;40:37-52.
[43]Addo-Quaye C,Miller W,Axtell MJ.Cleave Land:a pipeline for using degradome data to find cleaved small RNA targets.Bioinformatics 2009;25:130-1.
[44]Kozomara A,Griffiths-Jones S.mi RBase:annotating high confidence micro RNAs using deep sequencing data.Nucleic Acids Res 2014;42:d68-73.
[45]Nawrocki EP,Burge SW,Bateman A,Daub J,Eberhardt RY,Eddy SR,et al.Rfam 12.0:updates to the RNA families database.Nucleic Acids Res 2015;43:D130-7.
[46]Chiang K,Shu J,Zempleni J,Cui J.Dietary micro RNAdatabase(DMD):an archive database and analytic tool for food-borne micro RNAs.PLo S One 2015;10:e0128089.
[47]Meng Y,Gou L,Chen D,Mao C,Jin Y,Wu P,et al.Pmi RKB:a plant micro RNA knowledge base.Nucleic Acids Res 2011;39:D181-7.
[48]Zhang Z,Yu J,Li D,Zhang Z,Liu F,Zhou X,et al.PMRD:plant micro RNA database.Nucleic Acids Res 2010;38:D806-13.
[49]R Lorenzetti AP,A de Antonio GY,Paschoal AR,Domingues DS.Plan TE-MIR DB:a database for transposable elementrelated micro RNAs in plant genomes.Funct Integr Genomics2016;16:235-42.
[50]Backman TW,Sullivan CM,Cumbie JS,Miller ZA,Chapman EJ,Fahlgren N,et al.Update of ASRP:the Arabidopsis small RNA project database.Nucleic Acids Res 2008;36:D982-5.
[51]Hsu SD,Lin FM,Wu WY,Liang C,Huang WC,Chan WL,et al.mi RTar Base:a database curates experimentally validated micro RNA-target interactions.Nucleic Acids Res 2011;39:D163-9.
[52]Liu H,Jin T,Liao R,Wan L,Xu B,Zhou S,et al.mi RFANs:an integrated database for Arabidopsis thaliana micro RNA function annotations.BMC Plant Biol 2012;12:68.
[53]Zhang S,Yue Y,Sheng L,Wu Y,Fan G,Li A,et al.PASmi R:a literature-curated database for mi RNA molecular regulation in plant response to abiotic stress.BMC Plant Biol 2013;13:33.
[54]Remita MA,Lord E,Agharbaoui Z,Leclercq M,Badawi M,Makarenkov V,et al.WMP:a novel comprehensive wheat mirna database,including related bioinformatics software.Biorxiv2015,024893.
[55]Zhao Y,Li H,Fang S,Kang Y,Wu W,Hao Y,et al.NONCODE 2016:an informative and valuable data source of long non-coding RNAs.Nucleic Acids Res 2016;44:D203-8.
[56]Paytuv?′Gallart A,Hermoso Pulido A,Anzar Mart?′nez de Lagra′n I,Sanseverino W,Aiese Cigliano R.GREENC:a Wikibased database of plant lnc RNAs.Nucleic Acids Res 2016;44:D1161-6.
[57]Quek XC,Thomson DW,Maag JL,Bartonicek N,Signal B,Clark MB,et al.lnc RNAdb v2.0:expanding the reference database for functional long noncoding RNAs.Nucleic Acids Res 2015;43:D168-73.
[58]Jin J,Liu J,Wang H,Wong L,Chua NH.PLnc DB:plant long non-coding RNA database.Bioinformatics 2013;29:1068-71.
[59]Yi X,Zhang Z,Ling Y,Xu W,Su Z.PNRD:a plant non-coding RNA database.Nucleic Acids Res 2015;43:D982-9.
[60]Szczes′niak MW,Rosikiewicz W,Makalowska I.CANTATAdb:a collection of plant long non-coding RNAs.Plant Cell Physiol2016;57:e8.
[61]Xuan H,Zhang L,Liu X,Han G,Li J,Li X,et al.PLNlnc Rbase:a resource for experimentally identified lnc RNAs in plants.Gene 2015;573:328-32.
[62]Ng SY,Lin L,Soh BS,Stanton LW.Long noncoding RNAs in development and disease of the central nervous system.Trends Genet 2013;29:461-8.
[63]Rohrig H,Schmidt J,Miklashevichs E,Schell J,John M.Soybean ENOD40 encodes two peptides that bind to sucrose synthase.Proc Natl Acad Sci U S A 2002;99:1915-20.
[64]Wu J,Okada T,Fukushima T,Tsudzuki T,Sugiura M,Yukawa Y.A novel hypoxic stress-responsive long non-coding RNAtranscribed by RNA polymerase III in Arabidopsis.RNA Biol2012;9:302-13.
[65]Shin JH,Chekanova JA.Arabidopsis RRP6l1 and RRP6l2function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis.PLo S Genet 2014;10:e1004612.
[66]Mattick JS,Rinn JL.Discovery and annotation of long noncoding RNAs.Nat Struct Mol Biol 2015;22:5-7.
[67]Shriram V,Kumar V,Devarumath RM,Khare TS,Wani SH.Micro RNAs as potential targets for abiotic stress tolerance in plants.Front Plant Sci 2016;7:817.
[68]Mittal D,Sharma N,Sharma V,Sopory SK,Sanan-Mishra N.Role of micro RNAs in rice plant under salt stress.Ann Appl Biol2016;168:2-18.
[69]Koroban NV,Kudryavtseva AV,Krasnov GS,Sadritdinova AF,Fedorova MS,Snezhkina AV,et al.The role of micro RNAin abiotic stress response in plants.Mol Bio(Mosk)2016;50:387-94.
[70]Schmidt U,Keck ME,Buell DR.mi RNAs and other non-coding RNAs in posttraumatic stress disorder:a systematic review of clinical and animal studies.J Psychiatr Res 2015;65:1-8.
[71]Panda SK,Sunkar R.Nutrient-and other stress-responsive micro RNAs in plants:role for thiol-based redox signaling.Plant Signal Behav 2015;10:e1010916.
[72]Budak H,Kantar M,Bulut R,Akpinar BA.Stress responsive mi RNAs and isomi Rs in cereals.Plant Sci 2015;235:1-13.
[73]Nguyen GN,Rothstein SJ,Spangenberg G,Kant S.Role of micro RNAs involved in plant response to nitrogen and phosphorous limiting conditions.Front Plant Sci 2015;6:629.
[74]Liang G,He H,Yu D.Identification of nitrogen starvationresponsive micro RNAs in Arabidopsis thaliana.PLo S One2012;7:e48951.
[75]Zhao M,Ding H,Zhu JK,Zhang F,Li WX.Involvement of mi R169 in the nitrogen-starvation responses in Arabidopsis.New Phytol 2011;190:906-15.
[76]Zhao Y,Xu Z,Mo Q,Zou C,Li W,Xu Y,et al.Combined small RNA and degradome sequencing reveals novel mi RNAs and their targets in response to low nitrate availability in maize.Ann Bot 2013;112:633-42.
[77]Contreras-Cubas C,Palomar M,Arteaga-Va′zquez M,Reyes JL,Covarrubias AA.Non-coding RNAs in the plant response to abiotic stress.Planta 2012;236:943-58.
[78]Sunkar R,Li YF,Jagadeeswaran G.Functions of micro RNAs in plant stress responses.Trends Plant Sci 2012;17:196-203.
[79]Akdogan G,Tufekci ED,Uranbey S,Unver T.mi RNA-based drought regulation in wheat.Funct Integr Genomics2016;16:221-33.
[80]Franco-Zorrilla JM,Valli A,Todesco M,Mateos I,Puga MI,Rubio-Somoza I,et al.Target mimicry provides a new mechanism for regulation of micro RNA activity.Nat Genetics2007;39:1033-7.
[81]Wang J,Yu W,Yang Y,Li X,Chen T,Liu T,et al.Genomewide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for micro RNA in response to TYLCV infection.Sci Rep 2015;5:16946.
[82]Joshi RK,Megha S,Basu U,Rahman MH,Kav NN.Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus.PLo S One 2016;11:e0158784.
[83]Xin M,Wang Y,Yao Y,Song N,Hu Z,Qin D,et al.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.BMCPlant Biol 2011;11:61.
[84]Chen D,Yuan C,Zhang J,Zhang Z,Bai L,Meng Y,et al.Plant NATs DB:a comprehensive database of plant natural antisense transcripts.Nucleic Acids Res 2012;40:D1187-93.
[85]Yuan C,Wang J,Harrison AP,Meng X,Chen D,Chen M.Genome-wide view of natural antisense transcripts in Arabidopsis thaliana.DNA Res 2015;22:233-43.
[86]Wight M,Werner A.The functions of natural antisense transcripts.Essays Biochem 2013;54:91-101.
[87]Zhang X,Lii Y,Wu Z,Polishko A,Zhang H,Chinnusamy V,et al.Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues.Mol Plant2013;6:704-15.
[88]Zhang W,Han Z,Guo Q,Liu Y,Zheng Y,Wu F,et al.Identification of maize long non-coding RNAs responsive to drought stress.PLo S One 2014;9:e98958.
[89]Zhang H,Chen X,Wang C,Xu Z,Wang Y,Liu X,et al.Long non-coding genes implicated in response to stripe rust pathogen stress in wheat(Triticum aestivum L.).Mol Biol Rep2013;40:6245-53.
[90]Wang H,Chung PJ,Liu J,Jang IC,Kean MJ,Xu J,et al.Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis.Genome Res 2014;24:444-53.
[91]Wang J,Meng X,Yuan C,Harrison AP,Chen M.The roles of cross-talk epigenetic patterns in Arabidopsis thaliana.Brief Funct Genomics 2016;15:278-87.
[92]Csorba T,Questa JI,Sun Q,Dean C.Antisense COOLAIRmediates the coordinated switching of chromatin states at FLCduring vernalization.Proc Natl Acad Sci U S A2014;111:16160-5.
[93]Heo JB,Sung S.Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.Science 2011;331:76-9.
[94]Michaels SD,Amasino RM.FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering.Plant Cell 1999;11:949-56.
[95]Marquardt S,Raitskin O,Wu Z,Liu F,Sun Q,Dean C.Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription.Mol Cell 2014;54:156-65.
[96]Matzke MA,Mosher RA.RNA-directed DNA methylation:an epigenetic pathway of increasing complexity.Nat Rev Genet2014;15:394-408.
[97]Wierzbicki AT.The role of long non-coding RNA in transcriptional gene silencing.Curr Opin Plant Biol 2012;15:517-22.
[98]Movahedi A,Sun W,Zhang J,Wu X,Mousavi M,Mohammadi K,et al.RNA-directed DNA methylation in plants.Plant Cell Rep 2015;34:1857-62.
[99]Huang W,Xian Z,Hu G,Li Z.SLAGO4A,a core factor of RNA-directed DNA methylation(Rd DM)pathway,plays an important role under salt and drought stress in tomato.Mol Breed 2016;36:28.
[100]Steward N,Kusano T,Sano H.Expression of Zmmet1,a gene encoding a DNA methyltransferase from maize,is associated not only with DNA replication in actively proliferating cells,but also with altered DNA methylation status in cold-stressed quiescent cells.Nucleic Acids Res 2000;28:3250-9.
[101]Le TN,Schumann U,Smith NA,Tiwari S,Au PC,Zhu QH,et al.DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis.Genome Biol 2014;15:458.
[102]Popova OV,Dinh HQ,Aufsatz W,Jonak C.The Rd DMpathway is required for basal heat tolerance in Arabidopsis.Mol Plant 2013;6:396-410.
[103]Xu R,Wang Y,Zheng H,Lu W,Wu C,Huang J,et al.Saltinduced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis.J Exp Bot2015;66:5997-6008.
[104]Wibowo A,Becker C,Marconi G,Durr J,Price J,Hagmann J,et al.Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity.Elife 2016;5:e13546.
[105]Baldrich P,Kakar K,Sire′C,Moreno AB,Berger A,Garc?′aChapa M,et al.Small RNA profiling reveals regulation of Arabidopsis mi R168 and heterochromatic si RNA415 in response to fungal elicitors.BMC Genomics 2014;15:1083.
[106]Axtell MJ.Classification and comparison of small RNAs from plants.Annu Rev Plant Biol 2013;64:137-59.
[107]Sunkar R,Zhu JK.Novel and stress-regulated micro RNAs and other small RNAs from Arabidopsis.Plant Cell2004;16:2001-19.
[108]Borsani O,Zhu J,Verslues PE,Sunkar R,Zhu JK.Endogenous si RNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis.Cell 2005;123:1279-91.
[109]Guleria P,Mahajan M,Bhardwaj J,Yadav SK.Plant small RNAs:biogenesis,mode of action and their roles in abiotic stresses.Genomics Proteomics Bioinformatics 2011;9:183-99.
[110]Wierzbicki AT,Haag JR,Pikaard CS.Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes.Cell2008;135:635-48.
[111]Xia J,Zeng C,Chen Z,Zhang K,Chen X,Zhou Y,et al.Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava.BMC Genomics2014;15:634.
[112]Taft RJ,Glazov EA,Lassmann T,Hayashizaki Y,Carninci P,Mattick JS.Small RNAs derived from sno RNAs.RNA2009;15:1233-40.
[113]Lee YS,Shibata Y,Malhotra A,Dutta A.A novel class of small RNAs:t RNA-derived RNA fragments(t RFs).Genes Dev2009;23:2639-49.
[114]Wang Y,Wang X,Deng W,Fan X,Liu TT,He G,et al.Genomic features and regulatory roles of intermediate-sized noncoding RNAs in Arabidopsis.Mol Plant 2014;7:514-27.
[115]Bilichak A,Ilnytskyy Y,Wo′ycicki R,Kepeshchuk N,Fogen D,Kovalchuk I.The elucidation of stress memory inheritance in Brassica rapa plants.Front Plant Sci 2015;6:5.
[116]Wang Y,Li H,Sun Q,Yao Y.Characterization of small RNAs derived from t RNAs,r RNAs and sno RNAs and their response to heat stress in wheat seedlings.PLo S One 2016;11:e0150933.
[117]Visser M,Maree HJ,Rees DJ,Burger JT.High-throughput sequencing reveals small RNAs involved in ASGV infection.BMC Genomics 2014;15:568.
[118]Asha S,Soniya EV.Transfer RNA derived small RNAs targeting defense responsive genes are induced during Phytophthora capsici infection in black pepper(Piper nigrum L.).Front Plant Sci 2016;7:767.
[119]Hsieh LC,Lin SI,Kuo HF,Chiou TJ.Abundance of t RNA-derived small RNAs in phosphate-starved Arabidopsis roots.Plant Signal Behav 2010;5:537-9.
[120]Vandivier LE,Anderson SJ,Foley SW,Gregory BD.The conservation and function of RNA secondary structure in plants.Annu Rev Plant Biol 2016;67:463-88.