[1]Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M(2015).Battles and hijacks: noncoding transcription in plants.Trends Plant Sci, 20:362-371.
[2]Aung K, Lin SI, Wu CC, Huang YT, Su CL, Chiou TJ(2006).pho2,a phosphate overaccumulator,is caused by a nonsense mutation in a microRNA399 target gene.Plant Physiol, 141:1000-1011.
[3]Beló A, Beatty MK, Hondred D, Fengler KA, Li B, Rafalski A(2010).Allelic genome structural variations in maize detected by array comparative genome hybridization.Theor Appl Genet, 120:355-367.
[4]Boerner S, McGinnis KM(2012).Computational identification and functional predictions of long noncoding RNA in Zea mays..PLoS One, 7:e43047-e43047.
[5]Brannan CI, Dees EC, Ingram RS, Tilghman SM(1990).The product of the H19 gene may function as an RNA.Mol Cell Biol, 10:28-36.
[6]Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL(2006).Regulation of phosphate homeostasis by microRNA in Arabidopsis.Plant Cell, 18:412-421.
[7]Csorba T, Questa JI, Sun Q, Dean C(2014).Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization.Proc Natl Acad Sci USA, 111:16160-16165.
[8]Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q(2012).A long noncoding RNA regulates photoperiod-sensitive male sterility,an essential component of hybrid rice.Proc Natl Acad Sci USA, 109:2654-2659.
[9]Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, R?der M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR(2012).Landscape of transcription in human cells.Nature, 489:101-108.
[10]Downes BP, Stupar RM, Gingerich DJ,Vierstra RD(2003).The HECT ubiquitin-protein ligase (UPL) family in Arabidopsis: UPL3 has a specific role in trichome development.Plant J, 35:729-742.
[11]Du Q, Wang K, Zou C, Xu C, Li WX(2018).The PILNCR1-miR399 regulatory module is important for low phosphate tolerance in maize.Plant Physiol, 177:1743-1753.
[12]Du Toit A(2013).Non-coding RNA: RNA stability control by Pol II..Nat Rev Mol Cell Bio, 14:128-129.
[13]Fan Y, Yang J, Mathioni SM, Yu J, Shen J, Yang X, Wang L, Zhang Q, Cai Z, Xu C, Li X, Xiao J, Meyers BC, Zhang Q(2016).PMS1T,producing phased small-interfering RNAs,regulates photoperiod-sensitive male sterility in rice.Proc Natl Acad Sci USA, 113:15144-15149.
[14]Fang X, Wu Z, Raitskin O, Webb K, Voigt P, Lu T, Howard M, Dean C(2020).The 3' processing of antisense RNAs physically links to chromatin-based transcriptional control.Proc Natl Acad Sci USA, 117:15316-15321.
[15]Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J(2007).Target mimicry provides a new mechanism for regulation of microRNA activity.Nat Genet, 39:1033-1037.
[16]Friedman WE(1994).The evolution of embryogeny in seed plants and the developmental origin and early history of endosperm.Am J Bot, 81:1468-1486.
[17]Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK(2005).A miRNA involved in phosphate-starvation response in Arabidopsis.Curr Biol, 15:2038-2043.
[18]Guo G, Liu X, Sun F, Cao J, Huo N, Wuda B, Xin M, Hu Z, Du J, Xia R, Rossi V, Peng H, Ni Z, Sun Q, Yao Y(2018).Wheat miR9678 affects seed germination by generating phased siRNAs and modulating abscisic acidgibberellin signaling.Plant Cell, 30:796-814.
[19]Han L, Mu Z, Luo Z, Pan Q, Li L(2019).New lncRNA annotation reveals extensive functional divergence of the transcriptome in maize.J Integr Plant Biol, 61:394-405.
[20]Heo JB, Sung S(2011).Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.Science, 331:76-79.
[21]Hermans-Beijnsberger S, van Bilsen M, Schroen B(2018).Long non-coding RNAs in the failing heart and vasculature.Noncoding RNA Res, 3:118-130.
[22]Hu B, Zhu C, Li F, Tang J, Wang Y, Lin A, Liu L, Che R, Chu C(2011).LEAF TIP NECROSIS1 plays a pivotal role in the regulation of multiple phosphate starvation responses in rice.Plant Physiol, 156:1101-1115.
[23]Hu X, Wei Q, Wu H, Huang Y, Peng X, Han G, Ma Q, Zhao Y(2022).Identification and characterization of heat-responsive lncRNAs in maize inbred line CM1.BMC Genomics, 23:208-208.
[24]Huang D, Feurtado JA, Smith MA, Flatman LK, Koh C, Cutler AJ(2017).Long noncoding miRNA gene represses wheat β-diketone waxes.Proc Natl Acad Sci USA, 114:E3149-E3158.
[25]Huang TK, Han CL, Lin SI, Chen YJ, Tsai YC, Chen YR, Chen JW, Lin WY, Chen PM, Liu TY, Chen YS, Sun CM, Chiou TJ(2013).Identification of downstream components of ubiquitin-conjugating enzyme PHOSPHATE2 by quantitative membrane proteomics in Arabidopsis roots.Plant Cell, 25:4044-4060.
[26]Jabnoune M, Secco D, Lecampion C, Robaglia C, Shu Q, Poirier Y(2013).A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness.Plant Cell, 25:4166-4182.
[27]Kim DH, Sung S(2017).Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs.Dev Cell, 40:302-312.
[28]Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J(2010).Genome-wide patterns of genetic variation among elite maize inbred lines.Nat Genet, 42:1027-1030.
[29]Lauressergues D, Couzigou JM, Clemente HS, Martinez Y, Dunand C, Bécard G, Combier JP(2015).Primary transcripts of microRNAs encode regulatory peptides.Nature, 520:90-93.
[30]Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ(2014).Genome-wide discovery and characterization of maize long non-coding RNAs.Genome Biol, 15:R40-R40.
[31]Li W, Chen Y, Wang Y, Zhao J, Wang Y(2022).Gypsy retrotransposon-derived maize lncRNA GARR2 modulates gibberellin response.Plant J, 110:1433-1446.
[32]Li X, Chen W, Lu S, Fang J, Zhu H, Zhang X, Qi Y(2022).Full-length transcriptome analysis of maize root tips reveals the molecular mechanism of cold stress during the seedling stage.BMC Plant Biol, 22:398-398.
[33]Lin SI, Chiang SF, Lin WY, Chen JW, Tseng CY, Wu PC, Chiou TJ(2008).Regulatory network of microRNA399 and PHO2 by systemic signaling.Plant Physiol, 147:732-746.
[34]Liu P, Zhang Y, Zou C, Yang C, Pan G, Ma L, Shen Y(2022).Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress.BMC Genomics, 23:50-50.
[35]Lu J, Zhen S, Zhang J, Xie Y, He C, Wang X, Wang Z, Zhang S, Li Y, Cui Y, Wang G, Wang J, Liu J, Li L, Gu R, Zheng X, Fu J(2023).Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize.Theor Appl Genet, 136:16-16.
[36]Lv Y, Liang Z, Ge M, Qi W, Zhang T, Lin F, Peng Z, Zhao H(2016).Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).BMC Genomics, 17:350-350.
[37]Ma J, Yan B, Qu Y, Qin F, Yang Y, Hao X, Yu J, Zhao Q, Zhu D, Ao G(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.
[38]Mao Y, Xu J, Wang Q, Li G, Tang X, Liu T, Feng X, Wu F, Li M, Xie W, Lu Y(2021).A natural antisense transcript acts as a negative regulator for the maize drought stress response gene ZmNAC48.J Exp Bot, 72:2790-2806.
[39]Melé M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL(2017).Chromatin environment,transcriptional regulation,and splicing distinguish lincRNAs and mRNAs.Genome Res, 27:27-37.
[40]Palazzo AF, Koonin EV(2020).Functional long non-coding RNAs evolve from junk transcripts.Cell, 183:1151-1161.
[41]Ponting CP, Oliver PL, Reik W(2009).Evolution and functions of long noncoding RNAs.Cell, 136:629-641.
[42]Qin T, Zhao H, Cui P, Albesher N, Xiong L(2017).A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance.Plant Physiol, 175:1321-1336.
[43]Ratcliffe OJ, Kumimoto RW, Wong BJ, Riechmann JL(2003).Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold.Plant Cell, 15:1159-1169.
[44]Rohrig H, Schmidt J, Miklashevichs E, Schell J, John M(2002).Soybean ENOD40 encodes two peptides that bind to sucrose synthase.Proc Natl Acad Sci USA, 99:1915-1920.
[45]Sharma A, Badola PK, Bhatia C, Sharma D, Trivedi PK(2020).Primary transcript of miR858 encodes regulatory peptide and controls flavonoid biosynthesis and development in Arabidopsis.Nat Plants, 6:1262-1274.
[46]Shi X, Sun M, Liu H, Yao Y, Song Y(2013).Long non-coding RNAs: a new frontier in the study of human diseases.Cancer Lett, 339:159-166.
[47]Song Y, Xuan A, Bu C, Ci D, Tian M, Zhang D(2019).Osmotic stress-responsive promoter upstream transcripts (s) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii.Plant Biotechnol J, 17:164-177.
[48]Statello L, Guo CJ, Chen LL, Huarte M(2020).Gene regulation by long non-coding RNAs and its biological functions.Nat Rev Mol Cell Biol, 22:96-118.
[49]Sun Q, Liu X, Yang J, Liu W, Du Q, Wang H, Fu C, Li WX(2018).MicroRNA528 affects lodging resistance of maize by regulating lignin biosynthesis under nitrogen-luxury conditions.Mol Plant, 11:806-814.
[50]Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Guo W, Wu F, Feng X, Wang Q, Lu Y, Xu J(2023).Identification and functional analysis of drought-responsive long noncoding RNAs in maize roots.Int J Mol Sci, 24:15039-.
[51]Tian Y, Zheng H, Zhang F, Wang S, Ji X, Xu C, He Y, Ding Y(2019).PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR.Sci Adv, 5:eaau7246-.
[52]Wang H, Niu QW, Wu HW, Liu J, Ye J, Yu N, Chua NH(2015).Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits.Plant J, 84:404-416.
[53]Wang KC, Chang HY(2011).Molecular mechanisms of long noncoding RNAs.Mol Cell, 43:904-914.
[54]Wang Y, Fan X, Lin F, He G, Terzaghi W, Zhu D, Deng XW(2014).Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light.Proc Natl Acad Sci USA, 111:10359-10364.
[55]Wang Y, Luo X, Sun F, Hu J, Zha X, Su W, Yang J(2018).Overexpressing lncRNA LAIR increases grain yield and regulates neighboring gene cluster expression in rice.Nat Commun, 9:3516-.
[56]Wang Y, Wang Z, Du Q, Wang K, Zou C, Li WX(2023).The long non-coding RNA PILNCR2 increases low phosphate tolerance in maize by interfering with miRNA399-guided cleavage of ZmPHT1s.Mol Plant, 16:1146-1159.
[57]Wierzbicki AT, Haag JR, Pikaard CS(2008).Noncoding transcription by RNA polymerase Pol IVbPol V mediates transcriptional silencing of overlapping and adjacent genes.Cell, 135:635-648.
[58]Xing L, Zhu M, Luan M, Zhang M, Jin L, Liu Y, Zou J, Wang L, Xu M(2022).miR169q and NUCLEAR FACTOR YA8 enhance salt tolerance by activating PEROXIDASE1 expression in response to ROS.Plant Physiol, 188:608-623.
[59]Yang J, Wei H, Hou M, Chen L, Zou T, Ding H, Jing Y, Zhang X, Zhao Y, Liu Q, Heng Y, Wu H, Wang B, Kong D, Wang H(2023).ZmSPL13 and ZmSPL29 act together to promote vegetative and reproductive transition in maize.New Phytol, 239:1505-1520.
[60]Zhao S, Zhang Y, Gordon W, Quan J, Xi H, Du S, von Schack D, Zhang B(2015).Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap.BMC Genomics, 16:675-.
[61]Zhao X, Li J, Lian B, Gu H, Li Y, Qi Y(2018).Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA.Nat Commun, 9:5056-.
[62]Zhao Y, Zhu P, Hepworth J, Bloomer R, Antoniou-Kourounioti RL, Doughty J, Heckmann A, Xu C, Yang H, Dean C(2021).Natural temperature fluctuations promote COOLAIR regulation of FLC.Genes Dev, 35:888-898.
[63]Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, Yang YW, Lian JP, Feng YZ, Zhang Z, Yang L, He RR, Huang JH, Cheng Y, Liu YW, Chen YQ(2021).The parent-of-origin lncRNA MISSEN regulates rice endosperm development.Nat Commun, 12:6525-6525.