Abstract
Plants must adapt to multiple biotic and abiotic stresses ; thus, sensing and responding to environmental signals is imperative for their survival. Moreover, understanding these responses is imperative for efforts to improve plant yield and consistency. Regulation of transcript levels is a key aspect of the plant response to environmental signals. Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years with the advance of high-throughput sequencing technologies. As important biological regulators, lncRNAs have been implicated in a wide range of developmental processes and diseases in animals. However, knowledge of the role that lncRNAs play in plant stress tolerance remains limited. Here, we review recent studies on the identification, characteristics, classification, and biological functions of lncRNAs in response to various stresses, including bacterial pathogens, excess light, drought, salinity, hypoxia, extreme temperatures, and nitrogen/phosphate deficiency. We also discuss possible directions for future research.
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References
Ashraf M, Harris PJC (2013) Photosynthesis under stressful environments: an overview. Photosynthetica 51:163–190
Wang WX, Vinocur B, Shoseyov O, Altman A (2001) Biotechnology of plant osmotic stress tolerance: physiological and molecular considerations. Acta Hort 560:285–292
Wani SH, Sah SK, Hussain MA, Kumar V, Balachandra SM (2016) Transgenic approaches for abiotic stress tolerance in crop plants. In: Al-Khayri JM, Jain SM, Johnson DV (eds) Advances in plant breeding strategies, vol 2. Agronomic, abiotic and biotic stress traits. Springer, Gewerbestrasse, pp 345–396
Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17(4):196–203
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61(6):1041–1052
Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10:155–159
Brosnan CA, Voinnet O (2009) The long and the short of noncoding RNAs. Curr Opin Cell Biol 21:416–425
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 4(16):1047–1059
Swiezewski S, Liu FQ, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462(7274):799–802
Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629–641
Ma L, Bajic VB, Zhang Z (2013) On the classification of long non-coding RNAs. RNA Biol 10:925–933
Zheng B, Wang Z, Li S, Yu B, Liu JY, Chen X (2009) Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev 23:2850–2860
Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24:4333–4345
Herr AJ, Jensen MB, Dalmay T, Baulcombe DC (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308:118–120
Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJ (2005b) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37:761–765
Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 19:2030–2040
Wierzbicki AT, Ream TS, Haag JR, Pikaard CS (2009) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 41:630–634
Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS (2012) Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev 26(16):1825–1836
Liu X, Hao LL, Li DY, Zhu LH, Hu SN (2015) Long non-coding RNAs and their biological roles in plants. Genomics Proteomics Bioinformatics 13:137–147
Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y, Lu ZJ (2014) Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J 80(5):848–861
Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76–79
Wang ZW, Wu Z, Raitskin O, Sun Q, Dean C (2014) Antisense mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor. Proc Natl Acad Sci U S A 111:7468–7473
Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46
Wang H, Chung PJ, Liu J, Jang IC, Kean MJ, Xu J, Chua NH (2014) Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res 24:444–453
Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Ratsch G, Weigel D (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 105:8795–8800
Rose AB (2002) Requirements for intron-mediated enhancement of gene expression in Arabidopsis. RNA 8:1444–1453
Christie M, Croft LJ, Carroll BJ (2011) Intron splicing suppresses RNA silencing in Arabidopsis. Plant J 68:159–167
Akua T, Shaul O (2013) The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5′ UTR intron. J Exp Bot 64:4255–4270
Kim SH, Koroleva OA, Lewandowska D, Pendle AF, Clark GP, Simpson CG, Shaw PJ, Brown JW (2009) Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Plant Cell 21:2045–2057
Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, Tanaka M, Kaminuma E, Mochizuki Y, Matsushima A, Toyoda T, Shinozaki K, Seki M (2009) Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci U S A 106:2453–2458
Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA (2007) Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131:1340–1353
Gy I, Gasciolli V, Lauressergues D, Morel JB, Gombert J, Proux F, Proux C, Vaucheret H, Mallory AC (2007) Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 19:3451–3461
Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Okubo-Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR (2012) Surveillance of 3′ noncoding transcripts requires FIERY1 and XRN3 in Arabidopsis. G3 2:487–498
Liu TT, Zhu D, Chen W, Deng W, He H, He G, Bai B, Qi Y, Chen R, Deng XW (2013) A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. Mol Plant 6:830–846
Wang Y, Wang X, Deng W, Fan X, Liu TT, He G, Chen R, Terzaghi W, Zhu D, Deng XW (2014) Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis. Mol Plant 7:514–527
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–338
Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO (2013) Cell-type specific features of circular RNA expression. PLoS Genet 9:e1003777
Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL, Yang L (2014a) Complementary sequence-mediated exon circularization. Cell 159:134–147
Lee JT (2012) Epigenetic regulation by long noncoding RNAs. Science 338:1435–1439
Yang L, Froberg JE, Lee JT (2014) Long noncoding RNAs: fresh perspectives into the RNA world. Trends Biochem Sci 39:35–43
Shuai P, Liang D, Tang S, Zhang Z, Ye CY, Su Y, Xia X, Yin W (2014) Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot 65(17):4975–4983
Xin MM, Wang Y, Yao YY, Song N, Hu ZR, Qin DD, Xie CJ, Peng HR, Ni ZF, Sun QX (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
Bari R, Datt Pant B, Stitt M, Scheible WR (2006) PHO2, micro-RNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141:988–999
Cruz de Carvalho MH, Sun HX, Bowler C, Chua NH (2016) Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations. New Phytol 210(2):497–510
Joshi RK, Megha S, Basu U, Rahman MH, Kav NN (2016) Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus. PLoS One 11(7):e0158784
Wang J, Yu W, Yang Y, Li X, Chen T, Liu T, Ma N, Yang X, Liu R, Zhang B (2015) Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection. Sci Rep 5:16946
Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, Zhu JK, Staskawicz BJ, Jin H (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A 103:18002–18007
Song YP, Ci D, Tian M, Zhang DQ (2016) Stable methylation of a non-coding RNA gene regulates gene expression in response to abiotic stress in Populus simonii. J Exp Bot 67(5):1477–1492
Liu J, Wang H, Chua NH (2015) Long noncoding RNA transcriptome of plants. Plant Biotechnol J 13:319–328
Aung K, Lin SI, Wu CC, Huang YT, Su CL, Chiou TJ (2006) pho2, a phosphate over accumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol 141:1000–1011
Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033–1037
Wunderlich M, Gross-Hardt R, Schöffl F (2014) Heat shock factor HSFB2a involved in gametophyte development of Arabidopsis thaliana and its expression is controlled by a heat-inducible long non-coding antisense RNA. Plant Mol Biol 85(6):541–550
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 U S A 111:16160–16165
Marquardt S, Raitskin O, Wu Z, Liu F, Sun Q, Dean C (2014) Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Mol Cell 54:156–165
Jabnoune M, Secco D, Lecampion C, Robaglia C, Shu QY, 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
Listerman I, Bledau AS, Grishina I, Neugebauer KM (2007) Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet 3:e212
Wu J, Okada T, Fukushima T, Tsudzuki T, Sugiura M, Yukawa Y (2012) A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis. RNA Biol 9(3):302–313
Zhu QH, Stephen S, Taylor J, Helliwell CA, Wang MB (2014) Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol 201(2):574–584
Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a noncoding interfering transcript. Nature 445:666–670
Sun Q, Csorba T, Skourti-Stathaki K, Proudfoot NJ, Dean C (2013) Rloop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 340:619–621
Wahba L, Koshland D (2013) The Rs of biology: R-loops and the regulation of regulators. Mol Cell 50:611–612
Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, Jiang Z, Xu J, Liu Q, Cao X (2014) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344:310–313
Yang F, Zhang H, Mei Y, Wu M (2014) Reciprocal regulation of HIF-1alpha and lincRNA-p21 modulates the Warburg effect. Mol Cell 53:88–100
Chen LL, Carmichael GG (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 35:467–478
Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, Dorrestein PC, Rosenfeld MG (2011) ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147:773–788
Audas TE, Jacob MD, Lee S (2012) Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA. Mol Cell 45:147–157
Batista PJ, Chang HY (2013) Cytotopic localization by long noncoding RNAs. Curr Opin Cell Biol 25:195–199
Dey M, Complainville A, Charon C, Torrizo L, Kondorosi A, Crespi M, Datta S (2004) Phytohormonal responses in enod40-overexpressing plants of Medicago truncatula and rice. Physiol Plant 120:132–139
Lorkovic ZJ (2009) Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci 14:229–236
Matzke M, Kanno T, Huettel B, Jaligot E, Mette MF, Kreil DP, Daxinger L, Rovina P, Aufsatz W, Matzke AJM (2005) RNA-directed DNA methylation. In: Meyer P (ed) Plant epigenetics. Blackwell Publishing, Oxford, pp 69–96
Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123(7):1279–1291
Zhang Q, Wang D, Lang Z, He L, Yang L, Zeng L, Li Y, Zhao C, Huang H, Zhang H, Zhang H, Zhu JK (2016) Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proc Natl Acad Sci U S A 113(29):E4248–E4256
Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, Alioua A, Himber C, Voinnet O (2010) An endogenous, systemic RNAi pathway in plants. EMBO J 29:1699–1712
Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C (2013) Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 9:e1003470
Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080
Crevillen P, Yang H, Cui X, Greeff C, Trick M, Qiu Q, Cao X, Dean C (2014) Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature 515(7528):587–590
He Y (2012) Chromatin regulation of flowering. Trends Plant Sci 17:556–562
He Y, Amasino RM (2005) Role of chromatin modification in flowering time control. Trends Plant Sci 10:30–35
Liu F, Quesada V, Crevillen P, Baurle I, Swiezewski S, Dean C (2007) The Arabidopsis RNA-binding protein FCA requires a lysine specific demethylase 1 homolog to downregulate FLC. Mol Cell 28:398–407
Simpson GG (2004) The autonomous pathway: epigenetic and posttranscriptional gene regulation in the control of Arabidopsis flowering time. Curr Opin Plant Biol 7:570–574
Maris C, Dominguez C, Allain FH (2005) The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 272:2118–2131
Baurle I, Dean C (2008) Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets. PLoS One 3:e2733
Baurle I, Smith L, Baulcombe DC, Dean C (2007) Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing. Science 318:109–112
Veley KM, Michaels SD (2008) Functional redundancy and new roles for genes of the autonomous floral-promotion pathway. Plant Physiol 147:682–695
Song XM, Liu GF, Huang ZN, Duan WK, Tan HW, Li Y, Hou XL (2016) Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage. BMC Genomics 17:297
Hamburger D, Rezzonico E, MacDonald-Comber Petetot J, Somerville C, Poirier Y (2002) Identification and characterization of the Arabidopsis PHO1 gene involved in phosphate loading to the xylem. Plant Cell 14:889–902
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(1):350
Qi X, Xie S, Liu Y, Yi F, Yu J (2013) Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Mol Biol 83(4–5):459–473
Seki M, Narusaka M, Abe H, Kasuga M, Yamaguchi-Shinozaki K, Carninci P, Hayashizaki Y, Shinozaki K (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13(1):61–72
Salleh FM, Evans K, Goodall B, Machin H, Mowla SB, Mur LA, Runions J, Theodoulou FL, Foyer CH, Rogers HJ (2012) A novel function for a redox-related LEA protein (SAG21/AtLEA5) in root development and biotic stress responses. Plant Cell Environ 35(2):418–429
Deepak S, Shailasree S, Kini RK, Hause B, Shetty SH, Mithofer A (2007) Role of hydroxyproline-rich glycoproteins in resistance of pearl millet against downy mildew pathogen Sclerospora graminicola. Planta 226(2):323–333
Wang TZ, Liu M, Zhao MG, Chen R, Zhang WH (2015) Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing. BMC Plant Biol 15:131
Xiong LM, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:S165–S183
Yamaguchi T, Aharon GS, Sottosanto JB, Blumwald E (2005) Vacuolar Na+/H+ antiporter cation selectivity is regulated by calmodulin from within the vacuole in a Ca2+- and pH-dependent manner. Proc Natl Acad Sci U S A 102(44):16107–16112
Belmonte MF, Kirkbride RC, Stone SL, Pelletier JM, Bui AQ, Yeung EC, Hashimoto M, Fei J, Harada CM, Munoz MD, Le BH, Drews GN, Brady SM, Goldberg RB, Harada JJ (2013) Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc Natl Acad Sci U S A 110:E435–E444
Iyer-Pascuzzi AS, Zurek PR, Benfey PN (2013) High-throughput, noninvasive imaging of root systems. Methods Mol Biol 959:177–187
Moussaieff A, Rogachev I, Brodsky L, Malitsky S, Toal TW, Belcher H, Yativ M, Brady SM, Benfey PN, Aharoni A (2013) High-resolution metabolic mapping of cell types in plant roots. Proc Natl Acad Sci U S A 110:E1232–E1241
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C (2011) RNAcentral: a vision for an international database of RNA sequences. RNA 17:1941–1946
Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen LL, Chen M (2012) PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res 40:D1187–D1193
Jin J, Liu J, Wang H, Wong L, Chua NH (2013) PLncDB: plant long non-coding RNA database. Bioinformatics 29:1068–1071
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210
Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME (2014) lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 43:168–173
Goodrich JA, Kugel JF (2006) Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 7:612–616
Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG (2005) A strategy for probing the functionof noncoding RNAs finds a repressor of NFAT. Science 309:1570–1573
Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494:497–501
Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, Crespi M (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell 55:383–396
Lam MT, Li W, Rosenfeld MG, Glass CK (2014) Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 39:170–182
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380
Zeng S, Baillargeat D, Ho HP, Yong KT (2014) Nanomaterials enhanced surface plasmon resonance for biological and chemical sensing applications. Chem Soc Rev 43(10):3426–3452
Law GL, Raney A, Heusner C, Morris DR (2001) Polyamine regulation of ribosome pausing at the upstream open reading frame of S adenosylmethionine decarboxylase. J Biol Chem 276:38036–38043
Andrews SJ, Rothnagel JA (2014) Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 15:193–204
Röhrig H, Schmidt J, Miklashevichs E, Schell J, John M (2002) Soybean ENDO40 encodes two peptides that bind sucrose synthase. Proc Natl Acad Sci 99(4):1915–1920
Frank MJ, Smith LG (2002) A small, novel protein highly conserved in plants and animals promotes the polarized growth and division of maize leaf epidermal cells. Curr Biol 12:849–853
Casson SA, Chilley PM, Topping JF, Evans M, Souter MA, Lindsey K (2002) The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning. Plant Cell 14:1705–1721
Narita NN, Moore S, Horiguchi G, Kubo M, Demura T, Fukuda H, Goodrich J, Tsukaya H (2004) Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters leaf shape in Arabidopsis thaliana. Plant J 38:699–713
Buratti E, Muro AF, Giombi M, Gherbassi D, Iaconcig A, Baralle FE (2004) RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon. Mol Cell Biol 24:1387–1400
Cruz JA, Westhof E (2009) The dynamic landscapes of RNA architecture. Cell 136:604–609
Kozak M (2005) Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361:13–37
Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM (2013) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505:696–700
Gong J, Liu W, Zhang JY, Miao XP, Guo AY (2015) lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 43:D181–D186
Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, Brown JW, Crespi M (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell 30:166–176
Rearick D, Prakash A, McSweeny A, Shepard SS, Fedorova L, Fedorov A (2011) Critical association of ncRNA with introns. Nucleic Acids Res 39:2357–2366
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7:e30733
Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL (2011) Genome wide characterization of non-polyadenylated RNAs. Genome Biol 12:R16
Yin QF, Yang L, Zhang Y, Xiang JF, Wu YW, Carmichael GG, Chen LL (2012) Long noncoding RNAs with snoRNA ends. Mol Cell 48(2):219–230
Chang CY, Lin WD, Tu SL (2014) Genome-wide analysis of heat-sensitive alternative splicing in Physcomitrella patens. Plant Physiol 165(2):826–840
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Song, Y., Zhang, D. (2017). The Role of Long Noncoding RNAs in Plant Stress Tolerance. In: Sunkar, R. (eds) Plant Stress Tolerance. Methods in Molecular Biology, vol 1631. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7136-7_3
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