Exploring the secrets of long noncoding RNAs

International Journal of Molecular Sciences

Volumn 16, Issue 3, 2015, Pages 5467-5496

  Chen, Mingyang ^a   Chen, Jinhui ^a   Zhang, Deqiang ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

Epigenetics; Functional genomics; LncRNAs; LncRNAs in plants; Post transcriptional regulation; Transcriptional regulation

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; CYCLIN D1; DIHYDROFOLATE REDUCTASE; LONG UNTRANSLATED RNA; MICRORNA; TRANSCRIPTION FACTOR;

ABIOTIC STRESS; BIOTIC STRESS; CELLULAR DISTRIBUTION; DNA METHYLATION; EPIGENETICS; FLOWERING; FOXTAIL MILLET; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENOME ANALYSIS; GENOME IMPRINTING; HIGH THROUGHPUT SEQUENCING; MALE FERTILITY; NODULATION; NONHUMAN; PHOTOPERIODICITY; PLANT GENOME; PROTEIN LOCALIZATION; REVIEW; RICE; RNA PROCESSING; RNA SEQUENCE; RNA SPLICING; SHORT INTERSPERSED REPEAT; SYMBIOSIS; TRANSCRIPTION REGULATION; X CHROMOSOME INACTIVATION; ANIMAL; GENETIC TRANSCRIPTION; GENETICS; HUMAN; MAIZE; YEAST;

ANIMALIA; ZEA MAYS;

ANIMALS; GENE EXPRESSION REGULATION, FUNGAL; GENE EXPRESSION REGULATION, PLANT; HUMANS; RNA, LONG NONCODING; TRANSCRIPTION, GENETIC; YEASTS; ZEA MAYS;

EID: 84925879764     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms16035467     Document Type: Review

References (137)

1. Ponting, C.P.; Oliver, P.L.; Reik, W. Evolution and functions of long noncoding RNAs. Cell 2009, 136, 629–641.
2. Moseley, M.L.; Zu, T.; Ikeda, Y.; Gao, W.; Mosemiller, A.K.; Daughters, R.S.; Chen, G.; Weatherspoon, M.R.; Clark, H.B.; Ebner, T.J, et al. Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8. Nat. Genet. 2006, 38, 758–769.
3. Wapinski, O.; Chang, H.Y. Long noncoding RNAs and human disease. Trends Cell Biol. 2011, 21, 354–361.
4. Ma, L.; Bajic, V.B.; Zhang, Z. On the classification of long non-coding RNAs. RNA Biol. 2013, 10, 925–933.
5. Kapranov, P.; Cheng, J.; Dike, S.; Nix, D.A.; Duttagupta, R.; Willingham, A.T.; Stadler, P.F.; Hertel, J.; Hackermuller, J.; Hofacker, I.L, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316, 1484–1488.
6. Ravasi, T.; Suzuki, H.; Pang, K.C.; Katayama, S.; Furuno, M.; Okunishi, R.; Fukuda, S.; Ru, K.; Frith, M.C.; Gongora, M.M, et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res. 2006, 16, 11–19.
7. Mercer, T.R.; Dinger, M.E.; Mattick, J.S. Long non-coding RNAs: Insights into functions. Nat. Rev. Genet. 2009, 10, 155–159.
8. Whitehead, J.; Pandey, G.K.; Kanduri, C. Regulation of the mammalian epigenome by long noncoding RNAs. Biochim. Biophys. Acta 2009, 1790, 936–947.
9. Wilusz, J.E.; Sunwoo, H.; Spector, D.L. Long noncoding RNAs: Functional surprises from the RNA world. Genes Dev. 2009, 23, 1494–1504.
10. Du Toit, A. Non-coding RNA: RNA stability control by Pol II. Nat. Rev. Mol. Cell Biol. 2013, 14, 128–129.
11. Cawley, S.; Bekiranov, S.; Ng, H.H.; Kapranov, P.; Sekinger, E.A.; Kampa, D.; Piccolboni, A.; Sementchenko, V.; Cheng, J.; Williams, A.J.; et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004, 116, 499–509.
12. Mercer, T.R.; Dinger, M.E.; Sunkin, S.M.; Mehler, M.F.; Mattick, J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. USA 2008, 105, 716–721.
13. Sone, M.; Hayashi, T.; Tarui, H.; Agata, K.; Takeichi, M.; Nakagawa, S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J. Cell Sci. 2007, 120, 2498–2506.
14. Amaral, P.P.; Mattick, J.S. Noncoding RNA in development. Mamm. Genome 2008, 19, 454–492.
15. Dinger, M.E.; Amaral, P.P.; Mercer, T.R.; Pang, K.C.; Bruce, S.J.; Gardiner, B.B.; Askarian-Amiri, M.E.; Ru, K.; Solda, G.; Simons, C, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008, 18, 1433–1445.
16. Khaitovich, P.; Kelso, J.; Franz, H.; Visagie, J.; Giger, T.; Joerchel, S.; Petzold, E.; Green, R.E.; Lachmann, M.; Paabo, S. Functionality of intergenic transcription: An evolutionary comparison. PLoS Genet. 2006, 2, e171.
17. Wang, J.; Zhang, J.; Zheng, H.; Li, J.; Liu, D.; Li, H.; Samudrala, R.; Yu, J.; Wong, G.K. Mouse transcriptome: Neutral evolution of “non-coding” complementary DNAs. Nature 2004, 431, doi:10.1038/nature03016.
18. Pang, K.C.; Frith, M.C.; Mattick, J.S. Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function. Trends Genet. 2006, 22, 1–5.
19. Carninci, P.; Kasukawa, T.; Katayama, S.; Gough, J.; Frith, M.C.; Maeda, N.; Oyama, R.; Ravasi, T.; Lenhard, B.; Wells, C., t al. The transcriptional landscape of the mammalian genome. Science 2005, 309, 1559–1563.
20. Ponjavic, J.; Ponting, C.P.; Lunter, G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 2007, 17, 556–565.
21. Martens, J.A.; Laprade, L.; Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 2004, 429, 571–574.
22. Martianov, I.; Ramadass, A.; Serra, B.A.; Chow, N.; Akoulitchev, A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007, 445, 666–670.
23. Allen, T.A.; von Kaenel, S.; Goodrich, J.A.; Kugel, J.F. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 2004, 11, 816–821.
24. Mariner, P.D.; Walters, R.D.; Espinoza, C.A.; Drullinger, L.F.; Wagner, S.D.; Kugel, J.F.; Goodrich, J.A. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 2008, 29, 499–509.
25. Wang, X.; Arai, S.; Song, X.; Reichart, D.; Du, K.; Pascual, G.; Tempst, P.; Rosenfeld, M.G.; Glass, C.K.; Kurokawa, R. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008, 454, 126–130.
26. Shamovsky, I.; Ivannikov, M.; Kandel, E.S.; Gershon, D.; Nudler, E. RNA-mediated response to heat shock in mammalian cells. Nature 2006, 440, 556–560.
27. Li, Z.; Chao, T.C.; Chang, K.Y.; Lin, N.; Patil, V.S.; Shimizu, C.; Head, S.R.; Burns, J.C.; Rana, T.M. The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. Proc. Natl. Acad. Sci. USA 2014, 111, 1002–1007.
28. Sharma, S.; Findlay, G.M.; Bandukwala, H.S.; Oberdoerffer, S.; Baust, B.; Li, Z.; Schmidt, V.; Hogan, P.G.; Sacks, D.B.; Rao, A. Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex. Proc. Natl. Acad. Sci. USA 2011, 108, 11381–11386.
29. Wan, G.; Mathur, R.; Hu, X.; Liu, Y.; Zhang, X.; Peng, G.; Lu, X. Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway. Cell Signal. 2013, 25, 1086–1095.
30. Feng, J.; Bi, C.; Clark, B.S.; Mady, R.; Shah, P.; Kohtz, J.D. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 2006, 20, 1470–1484.
31. Dinger, M.E.; Gascoigne, D.K.; Mattick, J.S. The evolution of RNAs with multiple functions. Biochimie 2011, 93, 2013–2018.
32. Johnson, R. Long non-coding RNAs in Huntington’s disease neurodegeneration. Neurobiol. Dis. 2012, 46, 245–254.
33. Dimitrova, N.; Zamudio, J.R.; Jong, R.M.; Soukup, D.; Resnick, R.; Sarma, K.; Ward, A.J.; Raj, A.; Lee, J.T.; Sharp, P.A., et al. LincRNA-p21 activates p21 in cis to promote polycomb target gene expression and to enforce the G1/S checkpoint. Mol. Cell 2014, 54, 777–790.
34. Goodrich, J.A.; Kugel, J.F. Dampening DNA binding: A common mechanism of transcriptional repression for both ncRNAs and protein domains. RNA Biol. 2010, 7, 305–309.
35. Wagner, S.D.; Kugel, J.F.; Goodrich, J.A. TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain. Mol. Cell Biol. 2010, 30, 91–97.
36. Huarte, M.; Guttman, M.; Feldser, D.; Garber, M.; Koziol, M.J.; Kenzelmann-Broz, D.; Khalil, A.M.; Zuk, O.; Amit, I.; Rabani, M, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142, 409–419.
37. Tripathi, V.; Ellis, J.D.; Shen, Z.; Song, D.Y.; Pan, Q.; Watt, A.T.; Freier, S.M.; Bennett, C.F.; Sharma, A.; Bubulya, P.A, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39, 925–938.
38. Bardou, F.; Ariel, F.; Simpson, C.G.; Romero-Barrios, N.; Laporte, P.; Balzergue, S.; Brown, J.W.; Crespi, M. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev. Cell 2014, 30, 166–176.
39. Cesana, M.; Cacchiarelli, D.; Legnini, I.; Santini, T.; Sthandier, O.; Chinappi, M.; Tramontano, A.; Bozzoni, I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011, 147, 358–369.
40. Von Roretz, C.; Beauchamp, P.; di Marco, S.; Gallouzi, I.E. HuR and myogenesis: Being in the right place at the right time. Biochim. Biophys. Acta 2011, 1813, 1663–1667.
41. Liz, J.; Portela, A.; Soler, M.; Gomez, A.; Ling, H.; Michlewski, G.; Calin, G.A.; Guil, S.; Esteller, M. Regulation of pri-miRNA processing by a long noncoding RNA transcribed from an ultraconserved region. Mol. Cell 2014, 55, 138–147.
42. Faghihi, M.A.; Modarresi, F.; Khalil, A.M.; Wood, D.E.; Sahagan, B.G.; Morgan, T.E.; Finch, C.E.; St. Laurent G III; Kenny, P.J.; Wahlestedt, C. Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of β-secretase. Nat. Med. 2008, 14, 723–730.
43. Kim, Y.K.; Furic, L.; Desgroseillers, L.; Maquat, L.E. Mammalian Staufen1 recruits Upf1 to specific mRNA 3'UTRs so as to elicit mRNA decay. Cell 2005, 120, 195–208.
44. Gong, C.; Maquat, L.E. LncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3'UTRs via Alu elements. Nature 2011, 470, 284–288.
45. Clark, M.B.; Johnston, R.L.; Inostroza-Ponta, M.; Fox, A.H.; Fortini, E.; Moscato, P.; Dinger, M.E.; Mattick, J.S. Genome-wide analysis of long noncoding RNA stability. Genome Res. 2012, 22, 885–898.
46. Blencowe, B.J. Alternative splicing: New insights from global analyses. Cell 2006, 126, 37–47.
47. Hallegger, M.; Llorian, M.; Smith, C.W. Alternative splicing: Global insights. FEBS J. 2010, 277, 856–866.
48. Licatalosi, D.D.; Darnell, R.B. RNA processing and its regulation: Global insights into biological networks. Nat. Rev. Genet. 2010, 11, 75–87.
49. Rother, S.; Meister, G. Small RNAs derived from longer non-coding RNAs. Biochimie 2011, 93, 1905–1915.
50. Tam, O.H.; Aravin, A.A.; Stein, P.; Girard, A.; Murchison, E.P.; Cheloufi, S.; Hodges, E.; Anger, M.; Sachidanandam, R.; Schultz, R.M, et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453, 534–538.
51. Watanabe, T.; Totoki, Y.; Toyoda, A.; Kaneda, M.; Kuramochi-Miyagawa, S.; Obata, Y.; Chiba, H.; Kohara, Y.; Kono, T.; Nakano, T, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453, 539–543.
52. Guhaniyogi, J.; Brewer, G. Regulation of mRNA stability in mammalian cells. Gene 2001, 265, 11–23.
53. Maccioni, R.B.; Munoz, J.P.; Barbeito, L. The molecular bases of Alzheimer’s disease and other neurodegenerative disorders. Arch. Med. Res. 2001, 32, 367–381.
54. Faghihi, M.A.; Zhang, M.; Huang, J.; Modarresi, F.; van der Brug, M.P.; Nalls, M.A.; Cookson, M.R.; St-Laurent, G.R.; Wahlestedt, C. Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol. 2010, 11, R56.
55. Mus, E.; Hof, P.R.; Tiedge, H. Dendritic BC200 RNA in aging and in Alzheimer’s disease. Proc. Natl. Acad. Sci. USA 2007, 104, 10679–10684.
56. Mattick, J.S. The genetic signatures of noncoding RNAs. PLoS Genet. 2009, 5, e1000459.
57. Di Ruscio, A.; Ebralidze, A.K.; Benoukraf, T.; Amabile, G.; Goff, L.A.; Terragni, J.; Figueroa, M.E.; de Figueiredo, P.L.; Alberich-Jorda, M.; Zhang, P, et al. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 2013, 503, 371–376.
58. Zhao, J.; Sun, B.K.; Erwin, J.A.; Song, J.J.; Lee, J.T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322, 750–756.
59. Navarro, P.; Chambers, I.; Karwacki-Neisius, V.; Chureau, C.; Morey, C.; Rougeulle, C.; Avner, P. Molecular coupling of Xist regulation and pluripotency. Science 2008, 321, 1693–1695.
60. Lee, J.T.; Bartolomei, M.S. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 2013, 152, 1308–1323.
61. Tian, D.; Sun, S.; Lee, J.T. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010, 143, 390–403.
62. Vallot, C.; Huret, C.; Lesecque, Y.; Resch, A.; Oudrhiri, N.; Bennaceur-Griscelli, A.; Duret, L.; Rougeulle, C. XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat. Genet. 2013, 45, 239–241.
63. Bell, A.C.; Felsenfeld, G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000, 405, 482–485.
64. Hark, A.T.; Schoenherr, C.J.; Katz, D.J.; Ingram, R.S.; Levorse, J.M.; Tilghman, S.M. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 2000, 405, 486–489.
65. Keniry, A.; Oxley, D.; Monnier, P.; Kyba, M.; Dandolo, L.; Smits, G.; Reik, W. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat. Cell Biol. 2012, 14, 659–665.
66. Mancini-Dinardo, D.; Steele, S.J.; Levorse, J.M.; Ingram, R.S.; Tilghman, S.M. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev. 2006, 20, 1268–1282.
67. Pandey, R.R.; Mondal, T.; Mohammad, F.; Enroth, S.; Redrup, L.; Komorowski, J.; Nagano, T.; Mancini-Dinardo, D.; Kanduri, C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 2008, 32, 232–246.
68. Braidotti, G.; Baubec, T.; Pauler, F.; Seidl, C.; Smrzka, O.; Stricker, S.; Yotova, I.; Barlow, D.P. The Air noncoding RNA: An imprinted cis-silencing transcript. Cold Spring Harb. Symp. Quant. Biol. 2004, 69, 55–66.
69. Lai, F.; Shiekhattar, R. Where long noncoding RNAs meet DNA methylation. Cell Res. 2014, 24, 263–264.
70. Lee, J.T. Epigenetic regulation by long noncoding RNAs. Science 2012, 338, 1435–1439.
71. Navarro, P.; Oldfield, A.; Legoupi, J.; Festuccia, N.; Dubois, A.; Attia, M.; Schoorlemmer, J.; Rougeulle, C.; Chambers, I.; Avner, P. Molecular coupling of Tsix regulation and pluripotency. Nature 2010, 468, 457–460.
72. Jeon, Y.; Lee, J.T. YY1 tethers Xist RNA to the inactive X nucleation center. Cell 2011, 146, 119–133.
73. Pinter, S.F.; Sadreyev, R.I.; Yildirim, E.; Jeon, Y.; Ohsumi, T.K.; Borowsky, M.; Lee, J.T. Spreading of X chromosome inactivation via a hierarchy of defined polycomb stations. Genome Res. 2012, 22, 1864–1876.
74. Engreitz, J.M.; Pandya-Jones, A.; McDonel, P.; Shishkin, A.; Sirokman, K.; Surka, C.; Kadri, S.; Xing, J.; Goren, A.; Lander, E.S, et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 2013, 341, 1237973.
75. Kaneko, S.; Bonasio, R.; Saldana-Meyer, R.; Yoshida, T.; Son, J.; Nishino, K.; Umezawa, A.; Reinberg, D. Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. Mol. Cell. 2014, 53, 290–300.
76. Pauler, F.M.; Koerner, M.V.; Barlow, D.P. Silencing by imprinted noncoding RNAs: Is transcription the answer? Trends Genet. 2007, 23, 284–292.
77. Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420, 563–573.
78. Ding, J.; Lu, Q.; Ouyang, Y.; Mao, H.; Zhang, P.; Yao, J.; Xu, C.; Li, X.; Xiao, J.; Zhang, Q. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc. Natl. Acad. Sci. USA 2012, 109, 2654–2659.
79. Ding, J.; Shen, J.; Mao, H.; Xie, W.; Li, X.; Zhang, Q. RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Mol. Plant 2012, 5, 1210–1216.
80. Zhou, H.; Liu, Q.; Li, J.; Jiang, D.; Zhou, L.; Wu, P.; Lu, S.; Li, F.; Zhu, L.; Liu, Z, et al. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res. 2012, 22, 649–660.
81. Kouchi, H.; Hata, S. Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development. Mol. Gen. Genet. 1993, 238, 106–119.
82. Yang, W.C.; Katinakis, P.; Hendriks, P.; Smolders, A.; de Vries, F.; Spee, J.; van Kammen, A.; Bisseling, T.; Franssen, H. Characterization of GmENOD40, a gene showing novel patterns of cell-specific expression during soybean nodule development. Plant J. 1993, 3, 573–585.
83. Gultyaev, A.P.; Roussis, A. Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants. Nucleic Acids Res. 2007, 35, 3144–3152.
84. Rohrig, H.; Schmidt, J.; Miklashevichs, E.; Schell, J.; John, M. Soybean enod40 encodes two peptides that bind to sucrose synthase. Proc. Natl. Acad. Sci. USA 2002, 99, 1915–1920.
85. Sousa, C.; Johansson, C.; Charon, C.; Manyani, H.; Sautter, C.; Kondorosi, A.; Crespi, M. Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex. Mol. Cell Biol. 2001, 21, 354–366.
86. Girard, G.; Roussis, A.; Gultyaev, A.P.; Pleij, C.W.; Spaink, H.P. Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean. Nucleic Acids Res. 2003, 31, 5003–5015.
87. Campalans, A.; Kondorosi, A.; Crespi, M. enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 2004, 16, 1047–1059.
88. Franco-Zorrilla, J.M.; Valli, A.; Todesco, M.; Mateos, I.; Puga, M.I.; Rubio-Somoza, I.; Leyva, A.; Weigel, D.; Garcia, J.A.; Paz-Ares, J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 2007, 39, 1033–1037.
89. Heo, J.B.; Sung, S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 2011, 331, 76–79.
90. Heo, J.B.; Sung, S. Encoding memory of winter by noncoding RNAs. Epigenetics 2011, 6, 544–547.
91. Swiezewski, S.; Liu, F.; Magusin, A.; Dean, C. Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 2009, 462, 799–802.
92. Shin, J.H.; Chekanova, J.A. Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis. PLoS Genet. 2014, 10, e1004612.
93. Wang, Y.; Fan, X.; Lin, F.; He, G.; Terzaghi, W.; Zhu, D.; Deng, X.W. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc. Natl. Acad. Sci. USA 2014, 111, 10359–10364.
94. Aung, K.; Lin, S.I.; Wu, C.C.; Huang, Y.T.; Su, C.L.; Chiou, T.J. pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol. 2006, 141, 1000–1011.
95. Csorba, T.; Questa, J.I.; Sun, Q.; Dean, C. Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc. Natl. Acad. Sci. USA 2014, 111, 16160–16165
96. Kim, D.H.; Doyle, M.R.; Sung, S.; Amasino, R.M. Vernalization: Winter and the timing of flowering in plants. Annu. Rev. Cell Dev. Biol. 2009, 25, 277–299.
97. Ietswaart, R.; Wu, Z.; Dean, C. Flowering time control: Another window to the connection between antisense RNA and chromatin. Trends Genet. 2012, 28, 445–453.
98. Liu, F.; Marquardt, S.; Lister, C.; Swiezewski, S.; Dean, C. Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 2010, 327, 94–97.
99. 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, 156–165.
100. Wang, Z.W.; Wu, Z.; Raitskin, O.; Sun, Q.; Dean, C. Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor. Proc. Natl. Acad. Sci. USA 2014, 111, 7468–7473.
101. Hornyik, C.; Duc, C; Rataj, K.; Terzi, L.C.; Simpson, G.G. Alternative polyadenylation of antisense RNAs and flowering time control. Biochem. Soc. Trans. 2010, 38, 1077–1081.
102. Sun, Q.; Csorba, T.; Skourti-Stathaki, K.; Proudfoot, N.J.; Dean, C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 2013, 340, 619–621.
103. Helliwell, C.A.; Robertson, M.; Finnegan, E.J.; Buzas, D.M.; Dennis, E.S. Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts. PLoS One 2011, 6, e21513.
104. Haag, J.R.; Pikaard, C.S. Multisubunit RNA polymerases IV and V: Purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 2011, 12, 483–492.
105. Zhang, H.; He, X.; Zhu, J.K. RNA-directed DNA methylation in plants: Where to start? RNA Biol. 2013, 10, 1593–1596.
106. Matzke, M.A.; Kanno, T.; Matzke, A.J. RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Annu. Rev. Plant Biol. 2014, doi:10.1146/annurev-arplant-043014-114633.
107. Naydenov, M.; Baev, V.; Apostolova, E.; Gospodinova, N.; Sablok, G.; Gozmanova, M.; Yahubyan, G. High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis. Plant Physiol. Biochem. 2015, 87, 102–108.
108. Alleman, M.; Sidorenko, L.; McGinnis, K.; Seshadri, V.; Dorweiler, J.E.; White, J.; Sikkink, K.; Chandler, V.L. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006, 442, 295–298.
109. Dorweiler, J.E.; Carey, C.C.; Kubo, K.M.; Hollick, J.B.; Kermicle, J.L.; Chandler, V.L. Mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. Plant Cell 2000, 12, 2101–2118.
110. McGinnis, K.M.; Springer, C.; Lin, Y.; Carey, C.C.; Chandler, V. Transcriptionally silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics 2006, 173, 1637–1647.
111. Jacquier, A. The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 2009, 10, 833–844.
112. Khachane, A.N.; Harrison, P.M. Mining mammalian transcript data for functional long non-coding RNAs. PLoS One 2010, 5, e10316.
113. Maeda, N.; Kasukawa, T.; Oyama, R.; Gough, J.; Frith, M.; Engstrom, P.G.; Lenhard, B.; Aturaliya, R.N.; Batalov, S.; Beisel, K.W, et al. Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genet. 2006, 2, e62.
114. Guttman, M.; Amit, I.; Garber, M.; French, C.; Lin, M.F.; Feldser, D.; Huarte, M.; Zuk, O.; Carey, B.W.; Cassady, J.P.; et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals van Oudenaarden, A. Nature 2009, 458, 223–227.
115. Khalil, A.M.; Guttman, M.; Huarte, M.; Garber, M.; Raj, A.; Rivea, M.D.; Thomas, K.; Presser, A.; Bernstein, B.E.;.; et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 2009, 106, 11667–11672.
116. Li, L.; Wang, X.; Stolc, V.; Li, X.; Zhang, D.; Su, N.; Tongprasit, W.; Li, S.; Cheng, Z.; Wang, J.; et al. Genome-wide transcription analyses in rice using tiling microarrays. Nat. Genet. 2006, 38, 124–129.
117. Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621–628.
118. Ben, A.B.; Wirth, S.; Merchan, F.; Laporte, P.; D’Aubenton-Carafa, Y.; Hirsch, J.; Maizel, A.; Mallory, A.; Lucas, A.; Deragon, J.M, et al. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 2009, 19, 57–69.
119. Liu, J.; Jung, C.; Xu, J.; Wang, H.; Deng, S.; Bernad, L.; Arenas-Huertero, C.; Chua, N.H. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 2012, 24, 4333–4345.
120. Tupy, J.L.; Bailey, A.M.; Dailey, G.; Evans-Holm, M.; Siebel, C.W.; Misra, S.; Celniker, S.E.; Rubin, G.M. Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 2005, 102, 5495–5500.
121. Voss, B.; Georg, J.; Schon, V.; Ude, S.; Hess, W.R. Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 2009, 10, 123.
122. Wen, J.; Parker, B.J.; Weiller, G.F. In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biol. 2007, 7, 485–505.
123. Kong, L.; Zhang, Y.; Ye, Z.Q.; Liu, X.Q.; Zhao, S.Q.; Wei, L.; Gao, G. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007, 35, W345–W349.
124. Lin, M.F.; Jungreis, I.; Kellis, M. PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 2011, 27, i275–i282.
125. Boerner, S.; McGinnis, K.M. Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS One 2012, 7, e43047.
126. Song, D.; Yang, Y.; Yu, B.; Zheng, B.; Deng, Z.; Lu, B.L.; Chen, X.; Jiang, T. Computational prediction of novel non-coding RNAs in Arabidopsis thaliana. BMC Bioinform. 2009, 10 (Suppl. 1), S36.
127. Li, L.; Eichten, S.R.; Shimizu, R.; Petsch, K.; Yeh, C.T.; Wu, W.; Chettoor, A.M.; Givan, S.A.; Cole, R.A.; Fowler, J.E, et al. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol. 2014, 15, R40.
128. Chen, J.; Quan, M.; Zhang, D. Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq. Planta 2015, 241, 125–143.
129. Charon, C.; Moreno, A.B.; Bardou, F.; Crespi, M. Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus. Mol. Plant 2010, 3, 729–739.
130. Werner, A. Natural antisense transcripts. RNA Biol. 2005, 2, 53–62.
131. Wang, H.; Chung, P.J.; Liu, J.; Jang, I.C.; Kean, M.J.; Xu, J.; Chua, N.H. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res. 2014, 24, 444–453.
132. Qi, X.; Xie, S.; Liu, Y.; Yi, F.; Yu, J. Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Mol. Biol. 2013, 83, 459–473.
133. Shuai, P.; Liang, D.; Tang, S.; Zhang, Z.; Ye, C.Y.; Su, Y.; Xia, X.; Yin, W. Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J. Exp. Bot. 2014, 65, 4975–4983.
134. Zhang, H.; Chen, X.; Wang, C.; Xu, Z.; Wang, Y.; Liu, X.; Kang, Z.; Ji, W. Long non-coding genes implicated in response to stripe rust pathogen stress in wheat (Triticum aestivum L.). Mol. Biol. Rep. 2013, 40, 6245–6253.
135. Zhu, Q.H.; Stephen, S.; Taylor, J.; Helliwell, C.A.; Wang, M.B. Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol. 2013, 201, 574–584.
136. Zhu, Q.H.; Wang, M.B. Molecular functions of long non-coding RNAs in plants. Genes (Basel) 2012, 3, 176–190.
137. Heo, J.B.; Lee, Y.S.; Sung, S. Epigenetic regulation by long noncoding RNAs in plants. Chromosome Res. 2013, 21, 685–693.