Long noncoding RNA transcriptome of plants

Plant Biotechnology Journal

Volumn 13, Issue 3, 2015, Pages 319-328

  Liu, Jun ^a,b   Wang, Huan ^a   Chua, Nam Hai ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Long noncoding RNA; Post translational regulation; Transcriptional regulation

Indexed keywords

ANIMALIA; EMBRYOPHYTA;

LONG UNTRANSLATED RNA; PLANT RNA; TRANSCRIPTOME;

CLASSIFICATION; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; PLANT;

GENE EXPRESSION REGULATION, PLANT; PLANTS; RNA, LONG NONCODING; RNA, PLANT; TRANSCRIPTOME;

EID: 84926287259     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/pbi.12336     Document Type: Article

References (171)

1. Akua, T. and 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.
2. Ariel, F., Jegu, T., Latrasse, D., Romero-Barrios, N., Christ, A., Benhamed, M. and Crespi, M. (2014) Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol. Cell, 55, 383-396.
3. Audas, T.E., Jacob, M.D. and Lee, S. (2012) Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA. Mol. Cell, 45, 147-157.
4. Aung, K., Lin, S.I., Wu, C.C., Huang, Y.T., Su, C.L. and Chiou, T.J. (2006) pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol. 141, 1000-1011.
5. Axtell, M.J. (2013) Classification and comparison of small RNAs from plants. Annu. Rev. Plant Biol. 64, 137-159.
6. Bardou, F., Ariel, F., Simpson, C.G., Romero-Barrios, N., Laporte, P., Balzergue, S., Brown, J.W. and Crespi, M. (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev. Cell, 30, 166-176.
7. Bateman, A., Agrawal, S., Birney, E., Bruford, E.A., Bujnicki, J.M., Cochrane, G., Cole, J.R., Dinger, M.E., Enright, A.J., Gardner, P.P., Gautheret, D., Griffiths-Jones, S., Harrow, J., Herrero, J., Holmes, I.H., Huang, H.D., Kelly, K.A., Kersey, P., Kozomara, A., Lowe, T.M., Marz, M., Moxon, S., Pruitt, K.D., Samuelsson, T., Stadler, P.F., Vilella, A.J., Vogel, J.H., Williams, K.P., Wright, M.W. and Zwieb, C. (2011) RNAcentral: a vision for an international database of RNA sequences. RNA, 17, 1941-1946.
8. Batista, P.J. and Chang, H.Y. (2013) Cytotopic localization by long noncoding RNAs. Curr. Opin. Cell Biol. 25, 195-199.
9. Baurle, I. and Dean, C. (2008) Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets. PLoS One, 3, e2733.
10. Baurle, I., Smith, L., Baulcombe, D.C. and Dean, C. (2007) Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing. Science, 318, 109-112.
11. Belmonte, M.F., Kirkbride, R.C., Stone, S.L., Pelletier, J.M., Bui, A.Q., Yeung, E.C., Hashimoto, M., Fei, J., Harada, C.M., Munoz, M.D., Le, B.H., Drews, G.N., Brady, S.M., Goldberg, R.B. and Harada, J.J. (2013) Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc. Natl Acad. Sci. USA, 110, E435-E444.
12. Ben Amor, B., Wirth, S., Merchan, F., Laporte, P., d'Aubenton-Carafa, Y., Hirsch, J., Maizel, A., Mallory, A., Lucas, A., Deragon, J.M., Vaucheret, H., Thermes, C. and Crespi, M. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 19, 57-69.
13. Benson, D.A., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2014) GenBank. Nucleic Acids Res. 42, D32-D37.
14. Blevins, T., Pontvianne, F., Cocklin, R., Podicheti, R., Chandrasekhara, C., Yerneni, S., Braun, C., Lee, B., Rusch, D., Mockaitis, K., Tang, H. and Pikaard, C.S. (2014) A two-step process for epigenetic inheritance in Arabidopsis. Mol. Cell, 54, 30-42.
15. Boerner, S. and McGinnis, K.M. (2012) Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS One, 7, e43047.
16. Bologna, N.G. and Voinnet, O. (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu. Rev. Plant Biol. 65, 473-503.
17. Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R. and Zhu, J.K. (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell, 123, 1279-1291.
18. Bove, J., Kim, C.Y., Gibson, C.A. and Assmann, S.M. (2008) Characterization of wound-responsive RNA-binding proteins and their splice variants in Arabidopsis. Plant Mol. Biol. 67, 71-88.
19. Brown, C.J., Hendrich, B.D., Rupert, J.L., Lafreniere, R.G., Xing, Y., Lawrence, J. and Willard, H.F. (1992) The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell, 71, 527-542.
20. Brown, J.B., Boley, N., Eisman, R., May, G.E., Stoiber, M.H., Duff, M.O., Booth, B.W., Wen, J., Park, S., Suzuki, A.M., Wan, K.H., Yu, C., Zhang, D., Carlson, J.W., Cherbas, L., Eads, B.D., Miller, D., Mockaitis, K., Roberts, J., Davis, C.A., Frise, E., Hammonds, A.S., Olson, S., Shenker, S., Sturgill, D., Samsonova, A.A., Weiszmann, R., Robinson, G., Hernandez, J., Andrews, J., Bickel, P.J., Carninci, P., Cherbas, P., Gingeras, T.R., Hoskins, R.A., Kaufman, T.C., Lai, E.C., Oliver, B., Perrimon, N., Graveley, B.R. and Celniker, S.E. (2014) Diversity and dynamics of the Drosophila transcriptome. Nature, 512, 393-399.
21. Campalans, A., Kondorosi, A. and 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, 16, 1047-1059.
22. Capel, B., Swain, A., Nicolis, S., Hacker, A., Walter, M., Koopman, P., Goodfellow, P. and Lovell-Badge, R. (1993) Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell, 73, 1019-1030.
23. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V.B., Brenner, S.E., Batalov, S., Forrest, A.R., Zavolan, M., Davis, M.J., Wilming, L.G., Aidinis, V., Allen, J.E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R.N., Bailey, T.L., Bansal, M., Baxter, L., Beisel, K.W., Bersano, T., Bono, H., Chalk, A.M., Chiu, K.P., Choudhary, V., Christoffels, A., Clutterbuck, D.R., Crowe, M.L., Dalla, E., Dalrymple, B.P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C.F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T.R., Gojobori, T., Green, R.E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T.K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S.P., Kruger, A., Kummerfeld, S.K., Kurochkin, I.V., Lareau, L.F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K.C., Pavan, W.J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J.F., Ring, B.Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S.L., Sandelin, A., Schneider, C., Schonbach, C., Sekiguchi, K., Semple, C.A., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S.L., Tang, S., Taylor, M.S., Tegner, J., Teichmann, S.A., Ueda, H.R., van Nimwegen, E., Verardo, R., Wei, C.L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S.M., Teasdale, R.D., Liu, E.T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J.S., Hume, D.A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J. and Hayashizaki, Y. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
24. Casson, S., Spencer, M., Walker, K. and Lindsey, K. (2005) Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. Plant J. 42, 111-123.
25. Chekanova, J.A., Gregory, B.D., Reverdatto, S.V., Chen, H., Kumar, R., Hooker, T., Yazaki, J., Li, P., Skiba, N., Peng, Q., Alonso, J., Brukhin, V., Grossniklaus, U., Ecker, J.R. and Belostotsky, D.A. (2007) Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell, 131, 1340-1353.
26. Chen, L.L. and Carmichael, G.G. (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.
27. Chen, D., Yuan, C., Zhang, J., Zhang, Z., Bai, L., Meng, Y., Chen, L.L. and Chen, M. (2012) PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Res. 40, D1187-D1193.
28. Chew, G.L., Pauli, A., Rinn, J.L., Regev, A., Schier, A.F. and Valen, E. (2013) Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development, 140, 2828-2834.
29. Chodroff, R.A., Goodstadt, L., Sirey, T.M., Oliver, P.L., Davies, K.E., Green, E.D., Molnar, Z. and Ponting, C.P. (2010) Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 11, R72.
30. Christie, M., Croft, L.J. and Carroll, B.J. (2011) Intron splicing suppresses RNA silencing in Arabidopsis. Plant J. 68, 159-167.
31. Chung, B.Y., Simons, C., Firth, A.E., Brown, C.M. and Hellens, R.P. (2006) Effect of 5'UTR introns on gene expression in Arabidopsis thaliana. BMC Genom. 7, 120.
32. Cocquerelle, C., Mascrez, B., Hetuin, D. and Bailleul, B. (1993) Mis-splicing yields circular RNA molecules. FASEB J. 7, 155-160.
33. Cold, G.E. (1990) Cerebral blood flow in acute head injury. The regulation of cerebral blood flow and metabolism during the acute phase of head injury, and its significance for therapy. Acta Neurochir. Suppl. (Wien), 49, 1-64.
34. Comings, D.E. (1972) The structure and function of chromatin. Adv. Hum. Genet. 3, 237-431.
35. Crevillen, P., Yang, H., Cui, X., Greeff, C., Trick, M., Qiu, Q., Cao, X. and Dean, C. (2014) Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature, 515 (7528), 587-590.
36. Csorba, T., Questa, J.I., Sun, Q. and Dean, C. (2014) Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc. Natl Acad. Sci. USA, 111, 16160-16165.
37. Dey, M., Complainville, A., Charon, C., Torrizo, L., Kondorosi, A., Crespi, M. and Datta, S. (2004) Phytohormonal responses in enod40-overexpressing plants of Medicago truncatula and rice. Physiol. Plant. 120, 132-139.
38. Di, C., Yuan, J., Wu, Y., Li, J., Lin, H., Hu, L., Zhang, T., Qi, Y., Gerstein, M.B., Guo, Y. and Lu, Z.J. (2014) Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J. 80 (5), 848-861.
39. van Dijk, E.L., Chen, C.L., d'Aubenton-Carafa, Y., Gourvennec, S., Kwapisz, M., Roche, V., Bertrand, C., Silvain, M., Legoix-Ne, P., Loeillet, S., Nicolas, A., Thermes, C. and Morillon, A. (2011) XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature, 475, 114-117.
40. Ding, J., Lu, Q., Ouyang, Y., Mao, H., Zhang, P., Yao, J., Xu, C., Li, X., Xiao, J. and 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.
41. Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G.K., Khatun, J., Williams, B.A., Zaleski, C., Rozowsky, J., Roder, M., Kokocinski, F., Abdelhamid, R.F., Alioto, T., Antoshechkin, I., Baer, M.T., Bar, N.S., 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, M.J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O.J., Park, E., Persaud, K., Preall, J.B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L.H., Shahab, A., Skancke, J., Suzuki, A.M., 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, S.E., Hannon, G., Giddings, M.C., Ruan, Y., Wold, B., Carninci, P., Guigo, R. and Gingeras, T.R. (2012) Landscape of transcription in human cells. Nature, 489, 101-108.
42. Dunoyer, P., Brosnan, C.A., Schott, G., Wang, Y., Jay, F., Alioua, A., Himber, C. and Voinnet, O. (2010) An endogenous, systemic RNAi pathway in plants. EMBO J. 29, 1699-1712.
43. ENCODE_Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
44. Esch, J.J., Chen, M., Sanders, M., Hillestad, M., Ndkium, S., Idelkope, B., Neizer, J. and Marks, M.D. (2003) A contradictory GLABRA3 allele helps define gene interactions controlling trichome development in Arabidopsis. Development, 130, 5885-5894.
45. Fang, Y. and Spector, D.L. (2007) Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr. Biol. 17, 818-823.
46. Feng, J., Bi, C., Clark, B.S., Mady, R., Shah, P. and Kohtz, J.D. (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 20, 1470-1484.
47. Flynn, R.A., Almada, A.E., Zamudio, J.R. and Sharp, P.A. (2011) Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc. Natl Acad. Sci. USA, 108, 10460-10465.
48. Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A. and Paz-Ares, J. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39, 1033-1037.
49. Goodrich, J.A. and Kugel, J.F. (2006) Non-coding-RNA regulators of RNA polymerase II transcription. Nat. Rev. Mol. Cell Biol. 7, 612-616.
50. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P., Cabili, M.N., Jaenisch, R., Mikkelsen, T.S., Jacks, T., Hacohen, N., Bernstein, B.E., Kellis, M., Regev, A., Rinn, J.L. and Lander, E.S. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
51. Guttman, M., Russell, P., Ingolia, N.T., Weissman, J.S. and Lander, E.S. (2013) Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell, 154, 240-251.
52. Gy, I., Gasciolli, V., Lauressergues, D., Morel, J.B., Gombert, J., Proux, F., Proux, C., Vaucheret, H. and Mallory, A.C. (2007) Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell, 19, 3451-3461.
53. Ha, M. and Kim, V.N. (2014) Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 15, 509-524.
54. Haag, J.R., Ream, T.S., Marasco, M., Nicora, C.D., Norbeck, A.D., Pasa-Tolic, L. and Pikaard, C.S. (2012) In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol. Cell, 48, 811-818.
55. Haudry, A., Platts, A.E., Vello, E., Hoen, D.R., Leclercq, M., Williamson, R.J., Forczek, E., Joly-Lopez, Z., Steffen, J.G., Hazzouri, K.M., Dewar, K., Stinchcombe, J.R., Schoen, D.J., Wang, X., Schmutz, J., Town, C.D., Edger, P.P., Pires, J.C., Schumaker, K.S., Jarvis, D.E., Mandakova, T., Lysak, M.A., van den Bergh, E., Schranz, M.E., Harrison, P.M., Moses, A.M., Bureau, T.E., Wright, S.I. and Blanchette, M. (2013) An atlas of over 90, 000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891-898.
56. He, Y. (2012) Chromatin regulation of flowering. Trends Plant Sci. 17, 556-562.
57. He, Y. and Amasino, R.M. (2005) Role of chromatin modification in flowering-time control. Trends Plant Sci. 10, 30-35.
58. Heo, J.B. and Sung, S. (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science, 331, 76-79.
59. Herzog, V.A., Lempradl, A., Trupke, J., Okulski, H., Altmutter, C., Ruge, F., Boidol, B., Kubicek, S., Schmauss, G., Aumayr, K., Ruf, M., Pospisilik, A., Dimond, A., Senergin, H.B., Vargas, M.L., Simon, J.A. and Ringrose, L. (2014) A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element. Nat. Genet. 46, 973-981.
60. Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A. and Yoshiki, A. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature, 423, 91-96.
61. Ivashuta, S., Banks, I.R., Wiggins, B.E., Zhang, Y., Ziegler, T.E., Roberts, J.K. and Heck, G.R. (2011) Regulation of gene expression in plants through miRNA inactivation. PLoS One, 6, e21330.
62. Iyer-Pascuzzi, A.S., Zurek, P.R. and Benfey, P.N. (2013) High-throughput, noninvasive imaging of root systems. Methods Mol. Biol. 959, 177-187.
63. Jensen, T.H., Jacquier, A. and Libri, D. (2013) Dealing with pervasive transcription. Mol. Cell, 52, 473-484.
64. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science, 293, 1074-1080.
65. Jin, J., Liu, J., Wang, H., Wong, L. and Chua, N.H. (2013) PLncDB: plant long non-coding RNA database. Bioinformatics, 29, 1068-1071.
66. Kanaoka, M.M., Pillitteri, L.J., Fujii, H., Yoshida, Y., Bogenschutz, N.L., Takabayashi, J., Zhu, J.K. and Torii, K.U. (2008) SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation. Plant Cell, 20, 1775-1785.
67. Kapusta, A., Kronenberg, Z., Lynch, V.J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M. and Feschotte, C. (2013) Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 9, e1003470.
68. Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A. and Carrington, J.C. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5, e57.
69. Katiyar-Agarwal, S., Morgan, R., Dahlbeck, D., Borsani, O., Villegas, A. Jr, Zhu, J.K., Staskawicz, B.J. and Jin, H. (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl Acad. Sci. USA, 103, 18002-18007.
70. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A., Regev, A., Lander, E.S. and Rinn, J.L. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA, 106, 11667-11672.
71. Kim, S.H., Koroleva, O.A., Lewandowska, D., Pendle, A.F., Clark, G.P., Simpson, C.G., Shaw, P.J. and Brown, J.W. (2009) Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2 and UPF3 are enriched in the Arabidopsis nucleolus. Plant Cell, 21, 2045-2057.
72. Kim, T.K., Hemberg, M., Gray, J.M., Costa, A.M., Bear, D.M., Wu, J., Harmin, D.A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., Markenscoff-Papadimitriou, E., Kuhl, D., Bito, H., Worley, P.F., Kreiman, G. and Greenberg, M.E. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182-187.
73. Kim, Y.J., Zheng, B., Yu, Y., Won, S.Y., Mo, B. and Chen, X. (2011) The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J. 30, 814-822.
74. Kim, Y.J., Maizel, A. and Chen, X. (2014) Traffic into silence: endomembranes and post-transcriptional RNA silencing. EMBO J. 33, 968-980.
75. Kos, A., Dijkema, R., Arnberg, A.C., van der Meide, P.H. and Schellekens, H. (1986) The hepatitis delta (delta) virus possesses a circular RNA. Nature, 323, 558-560.
76. Kouchi, H. and Hata, S. (1993) Isolation and characterization of novel nodulin cDNAs representing genes expressed at early stages of soybean nodule development. Mol. Gen. Genet. 238, 106-119.
77. Kung, J.T., Colognori, D. and Lee, J.T. (2013) Long noncoding RNAs: past, present, and future. Genetics, 193, 651-669.
78. Kurihara, Y., Matsui, A., Hanada, K., Kawashima, M., Ishida, J., Morosawa, T., Tanaka, M., Kaminuma, E., Mochizuki, Y., Matsushima, A., Toyoda, T., Shinozaki, K. and Seki, M. (2009) Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc. Natl Acad. Sci. USA, 106, 2453-2458.
79. Kurihara, Y., Schmitz, R.J., Nery, J.R., Schultz, M.D., Okubo-Kurihara, E., Morosawa, T., Tanaka, M., Toyoda, T., Seki, M. and Ecker, J.R. (2012) Surveillance of 3' noncoding transcripts requires FIERY1 and XRN3 in Arabidopsis. G3: Genes - Genomes - Genetics, 2, 487-498.
80. Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K. and Gage, F.H. (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell, 116, 779-793.
81. Lai, F., Orom, U.A., Cesaroni, M., Beringer, M., Taatjes, D.J., Blobel, G.A. and Shiekhattar, R. (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature, 494, 497-501.
82. Lam, M.T., Li, W., Rosenfeld, M.G. and Glass, C.K. (2014) Enhancer RNAs and regulated transcriptional programs. Trends Biochem. Sci. 39, 170-182.
83. Lambermon, M.H., Fu, Y., Wieczorek Kirk, D.A., Dupasquier, M., Filipowicz, W. and Lorkovic, Z.J. (2002) UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants. Mol. Cell. Biol. 22, 4346-4357.
84. Lamesch, P., Berardini, T.Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D.L., Garcia-Hernandez, M., Karthikeyan, A.S., Lee, C.H., Nelson, W.D., Ploetz, L., Singh, S., Wensel, A. and Huala, E. (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40, D1202-D1210.
85. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J.C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R.H., Wilson, R.K., Hillier, L.W., McPherson, J.D., Marra, M.A., Mardis, E.R., Fulton, L.A., Chinwalla, A.T., Pepin, K.H., Gish, W.R., Chissoe, S.L., Wendl, M.C., Delehaunty, K.D., Miner, T.L., Delehaunty, A., Kramer, J.B., Cook, L.L., Fulton, R.S., Johnson, D.L., Minx, P.J., Clifton, S.W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J.F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R.A., Muzny, D.M., Scherer, S.E., Bouck, J.B., Sodergren, E.J., Worley, K.C., Rives, C.M., Gorrell, J.H., Metzker, M.L., Naylor, S.L., Kucherlapati, R.S., Nelson, D.L., Weinstock, G.M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D.R., Doucette-Stamm, L., Rubenfield, M., Weinstock, K., Lee, H.M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R.W., Federspiel, N.A., Abola, A.P., Proctor, M.J., Myers, R.M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D.R., Olson, M.V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G.A., Athanasiou, M., Schultz, R., Roe, B.A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W.R., de la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J.A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D.G., Burge, C.B., Cerutti, L., Chen, H.C., Church, D., Clamp, M., Copley, R.R., Doerks, T., Eddy, S.R., Eichler, E.E., Furey, T.S., Galagan, J., Gilbert, J.G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L.S., Jones, T.A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W.J., Kitts, P., Koonin, E.V., Korf, I., Kulp, D., Lancet, D., Lowe, T.M., McLysaght, A., Mikkelsen, T., Moran, J.V., Mulder, N., Pollara, V.J., Ponting, C.P., Schuler, G., Schultz, J., Slater, G., Smit, A.F., Stupka, E., Szustakowski, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y.I., Wolfe, K.H., Yang, S.P., Yeh, R.F., Collins, F., Guyer, M.S., Peterson, J., Felsenfeld, A., Wetterstrand, K.A., Patrinos, A., Morgan, M.J., de Jong, P., Catanese, J.J., Osoegawa, K., Shizuya, H., Choi, S. and Chen, Y.J. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
86. Lanz, R.B., McKenna, N.J., Onate, S.A., Albrecht, U., Wong, J., Tsai, S.Y., Tsai, M.J. and O'Malley, B.W. (1999) A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell, 97, 17-27.
87. Laubinger, S., Sachsenberg, T., Zeller, G., Busch, W., Lohmann, J.U., Ratsch, G. and 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. USA, 105, 8795-8800.
88. Lee, J.T. (2012) Epigenetic regulation by long noncoding RNAs. Science, 338, 1435-1439.
89. Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A.Y., Merkurjev, D., Zhang, J., Ohgi, K., Song, X., Oh, S., Kim, H.S., Glass, C.K. and Rosenfeld, M.G. (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature, 498, 516-520.
90. 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., Evans, M.M., Scanlon, M.J., Yu, J., Schnable, P.S., Timmermans, M.C., Springer, N.M. and Muehlbauer, G.J. (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol. 15, R40.
91. Liu, F., Quesada, V., Crevillen, P., Baurle, I., Swiezewski, S. and Dean, C. (2007) The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Mol. Cell, 28, 398-407.
92. Liu, J., Jung, C., Xu, J., Wang, H., Deng, S., Bernad, L., Arenas-Huertero, C. and Chua, N.H. (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell, 24, 4333-4345.
93. Liu, T.T., Zhu, D., Chen, W., Deng, W., He, H., He, G., Bai, B., Qi, Y., Chen, R. and Deng, X.W. (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.
94. Lorkovic, Z.J. (2009) Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci. 14, 229-236.
95. Lu, T., Zhu, C., Lu, G., Guo, Y., Zhou, Y., Zhang, Z., Zhao, Y., Li, W., Lu, Y., Tang, W., Feng, Q. and Han, B. (2012) Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice. BMC Genom. 13, 721.
96. MacIntosh, G.C., Wilkerson, C. and Green, P.J. (2001) Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol. 127, 765-776.
97. Macknight, R., Bancroft, I., Page, T., Lister, C., Schmidt, R., Love, K., Westphal, L., Murphy, G., Sherson, S., Cobbett, C. and Dean, C. (1997) FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell, 89, 737-745.
98. Managadze, D., Rogozin, I.B., Chernikova, D., Shabalina, S.A. and Koonin, E.V. (2011) Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol. Evol. 3, 1390-1404.
99. Maris, C., Dominguez, C. and Allain, F.H. (2005) The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J. 272, 2118-2131.
100. Marker, C., Zemann, A., Terhorst, T., Kiefmann, M., Kastenmayer, J.P., Green, P., Bachellerie, J.P., Brosius, J. and Huttenhofer, A. (2002) Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr. Biol. 12, 2002-2013.
101. Marquardt, S., Raitskin, O., Wu, Z., Liu, F., Sun, Q. and Dean, C. (2014) Functional consequences of splicing of the antisense transcript COOLAIR on FLC transcription. Mol. Cell, 54, 156-165.
102. Marques, A.C. and Ponting, C.P. (2009) Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol. 10, R124.
103. Martianov, I., Ramadass, A., Serra Barros, A., Chow, N. and Akoulitchev, A. (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature, 445, 666-670.
104. Matsui, A., Ishida, J., Morosawa, T., Mochizuki, Y., Kaminuma, E., Endo, T.A., Okamoto, M., Nambara, E., Nakajima, M., Kawashima, M., Satou, M., Kim, J.M., Kobayashi, N., Toyoda, T., Shinozaki, K. and Seki, M. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol. 49, 1135-1149.
105. Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S.D., Gregersen, L.H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F. and Rajewsky, N. (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495, 333-338.
106. Meng, Y., Shao, C., Wang, H. and Jin, Y. (2012) Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants. BMC Genom. 13, 197.
107. Moussaieff, A., Rogachev, I., Brodsky, L., Malitsky, S., Toal, T.W., Belcher, H., Yativ, M., Brady, S.M., Benfey, P.N. and Aharoni, A. (2013) High-resolution metabolic mapping of cell types in plant roots. Proc. Natl Acad. Sci. USA, 110, E1232-E1241.
108. Munroe, S.H. and Lazar, M.A. (1991) Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J. Biol. Chem. 266, 22083-22086.
109. Mylona, P., Pawlowski, K. and Bisseling, T. (1995) Symbiotic nitrogen fixation. Plant Cell, 7, 869-885.
110. Natoli, G. and Andrau, J.C. (2012) Noncoding transcription at enhancers: general principles and functional models. Annu. Rev. Genet. 46, 1-19.
111. Neil, H., Malabat, C., d'Aubenton-Carafa, Y., Xu, Z., Steinmetz, L.M. and Jacquier, A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature, 457, 1038-1042.
112. Ntini, E., Jarvelin, A.I., Bornholdt, J., Chen, Y., Boyd, M., Jorgensen, M., Andersson, R., Hoof, I., Schein, A., Andersen, P.R., Andersen, P.K., Preker, P., Valen, E., Zhao, X., Pelechano, V., Steinmetz, L.M., Sandelin, A. and Jensen, T.H. (2013) Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat. Struct. Mol. Biol. 20, 923-928.
113. Ohno, S. (1972) So much "junk" DNA in our genome. Brookhaven Symp. Biol. 23, 366-370.
114. Okamoto, M., Tatematsu, K., Matsui, A., Morosawa, T., Ishida, J., Tanaka, M., Endo, T.A., Mochizuki, Y., Toyoda, T., Kamiya, Y., Shinozaki, K., Nambara, E. and Seki, M. (2010) Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J. 62, 39-51.
115. O'Nell, T.D. and Mitchell, C.M. (1996) Alcohol use among American Indian adolescents: the role of culture in pathological drinking. Soc. Sci. Med. 42, 565-578.
116. Paige, J.S., Wu, K.Y. and Jaffrey, S.R. (2011) RNA mimics of green fluorescent protein. Science, 333, 642-646.
117. Panganiban, G. and Rubenstein, J.L. (2002) Developmental functions of the Distal-less/Dlx homeobox genes. Development, 129, 4371-4386.
118. Ponjavic, J., Ponting, C.P. and Lunter, G. (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 17, 556-565.
119. Preker, P., Nielsen, J., Kammler, S., Lykke-Andersen, S., Christensen, M.S., Mapendano, C.K., Schierup, M.H. and Jensen, T.H. (2008) RNA exosome depletion reveals transcription upstream of active human promoters. Science, 322, 1851-1854.
120. Quek, X.C., Thomson, D.W., Maag, J.L., Bartonicek, N., Signal, B., Clark, M.B., Gloss, B.S. and Dinger, M.E. (2014) lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. pii: gku988.
121. Riera, M., Redko, Y. and Leung, J. (2006) Arabidopsis RNA-binding protein UBA2a relocalizes into nuclear speckles in response to abscisic acid. FEBS Lett. 580, 4160-4165.
122. Rinn, J.L., Kertesz, M., Wang, J.K., Squazzo, S.L., Xu, X., Brugmann, S.A., Goodnough, L.H., Helms, J.A., Farnham, P.J., Segal, E. and Chang, H.Y. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129, 1311-1323.
123. Rose, A.B. (2002) Requirements for intron-mediated enhancement of gene expression in Arabidopsis. RNA, 8, 1444-1453.
124. Rymarquis, L.A., Kastenmayer, J.P., Huttenhofer, A.G. and Green, P.J. (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci. 13, 329-334.
125. Salmena, L., Poliseno, L., Tay, Y., Kats, L. and Pandolfi, P.P. (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell, 146, 353-358.
126. Salzman, J., Gawad, C., Wang, P.L., Lacayo, N. and Brown, P.O. (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One, 7, e30733.
127. Salzman, J., Chen, R.E., Olsen, M.N., Wang, P.L. and Brown, P.O. (2013) Cell-type specific features of circular RNA expression. PLoS Genet. 9, e1003777.
128. Sanger, H.L., Klotz, G., Riesner, D., Gross, H.J. and Kleinschmidt, A.K. (1976) Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl Acad. Sci. USA, 73, 3852-3856.
129. Shamovsky, I., Ivannikov, M., Kandel, E.S., Gershon, D. and Nudler, E. (2006) RNA-mediated response to heat shock in mammalian cells. Nature, 440, 556-560.
130. Sheldon, C.C., Rouse, D.T., Finnegan, E.J., Peacock, W.J. and Dennis, E.S. (2000) The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc. Natl Acad. Sci. USA, 97, 3753-3758.
131. Shuai, P., Liang, D., Tang, S., Zhang, Z., Ye, C.Y., Su, Y., Xia, X. and Yin, W. (2014) Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J. Exp. Bot. 65, 4975-4983.
132. Simpson, G.G. (2004) The autonomous pathway: epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time. Curr. Opin. Plant Biol. 7, 570-574.
133. Simpson, G.G., Dijkwel, P.P., Quesada, V., Henderson, I. and Dean, C. (2003) FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell, 113, 777-787.
134. Song, W., Strack, R.L. and Jaffrey, S.R. (2013) Imaging bacterial protein expression using genetically encoded RNA sensors. Nat. Methods, 10, 873-875.
135. Sonmez, C., Baurle, I., Magusin, A., Dreos, R., Laubinger, S., Weigel, D. and Dean, C. (2011) RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription. Proc. Natl Acad. Sci. USA, 108, 8508-8513.
136. Strack, R.L. and Jaffrey, S.R. (2013) New approaches for sensing metabolites and proteins in live cells using RNA. Curr. Opin. Chem. Biol. 17, 651-655.
137. Strack, R.L., Song, W. and Jaffrey, S.R. (2014) Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nat. Protoc. 9, 146-155.
138. Sun, Q., Csorba, T., Skourti-Stathaki, K., Proudfoot, N.J. and Dean, C. (2013) R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science, 340, 619-621.
139. Swiezewski, S., Liu, F., Magusin, A. and Dean, C. (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature, 462, 799-802.
140. Tay, Y., Kats, L., Salmena, L., Weiss, D., Tan, S.M., Ala, U., Karreth, F., Poliseno, L., Provero, P., Di Cunto, F., Lieberman, J., Rigoutsos, I. and Pandolfi, P.P. (2011) Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell, 147, 344-357.
141. Tilsner, J., Linnik, O., Christensen, N.M., Bell, K., Roberts, I.M., Lacomme, C. and Oparka, K.J. (2009) Live-cell imaging of viral RNA genomes using a Pumilio-based reporter. Plant J. 57, 758-770.
142. Ulitsky, I. and Bartel, D.P. (2013) lincRNAs: genomics, evolution, and mechanisms. Cell, 154, 26-46.
143. Ulitsky, I., Shkumatava, A., Jan, C.H., Sive, H. and Bartel, D.P. (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell, 147, 1537-1550.
144. Valencia, P., Dias, A.P. and Reed, R. (2008) Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc. Natl Acad. Sci. USA, 105, 3386-3391.
145. Veley, K.M. and Michaels, S.D. (2008) Functional redundancy and new roles for genes of the autonomous floral-promotion pathway. Plant Physiol. 147, 682-695.
146. Wahba, L. and Koshland, D. (2013) The Rs of biology: R-loops and the regulation of regulators. Mol. Cell, 50, 611-612.
147. Wang, Q.Q., Liu, F., Chen, X.S., Ma, X.J., Zeng, H.Q. and Yang, Z.M. (2010) Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics, 96, 369-376.
148. Wang, K.C., Yang, Y.W., Liu, B., Sanyal, A., Corces-Zimmerman, R., Chen, Y., Lajoie, B.R., Protacio, A., Flynn, R.A., Gupta, R.A., Wysocka, J., Lei, M., Dekker, J., Helms, J.A. and Chang, H.Y. (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature, 472, 120-124.
149. Wang, H., Chung, P.J., Liu, J., Jang, I.C., Kean, M.J., Xu, J. and Chua, N.H. (2014a) Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res. 24, 444-453.
150. Wang, P., Xue, Y., Han, Y., Lin, L., Wu, C., Xu, S., Jiang, Z., Xu, J., Liu, Q. and Cao, X. (2014b) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science, 344, 310-313.
151. Wang, Y., Fan, X., Lin, F., He, G., Terzaghi, W., Zhu, D. and Deng, X.W. (2014c) Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc. Natl Acad. Sci. USA, 111, 10359-10364.
152. Wang, Y., Wang, X., Deng, W., Fan, X., Liu, T.T., He, G., Chen, R., Terzaghi, W., Zhu, D. and Deng, X.W. (2014d) Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis. Mol. Plant, 7, 514-527.
153. Wang, Z.W., Wu, Z., Raitskin, O., Sun, Q. and Dean, C. (2014e) Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor. Proc. Natl Acad. Sci. USA, 111, 7468-7473.
154. Wei, T., Huang, T.S., McNeil, J., Laliberte, J.F., Hong, J., Nelson, R.S. and Wang, A. (2010) Sequential recruitment of the endoplasmic reticulum and chloroplasts for plant potyvirus replication. J. Virol. 84, 799-809.
155. Wen, J., Parker, B.J. and Weiller, G.F. (2007) In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biol. 7, 485-505.
156. Willingham, A.T., Orth, A.P., Batalov, S., Peters, E.C., Wen, B.G., Aza-Blanc, P., Hogenesch, J.B. and Schultz, P.G. (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science, 309, 1570-1573.
157. Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q.Q. and Hunt, A.G. (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Natl Acad. Sci. USA, 108, 12533-12538.
158. Wu, H.J., Wang, Z.M., Wang, M. and Wang, X.J. (2013) Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol. 161, 1875-1884.
159. Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.C., Dufour, M.E., Boulay, J., Regnault, B., Devaux, F., Namane, A., Seraphin, B., Libri, D. and Jacquier, A. (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell, 121, 725-737.
160. Xin, M., Wang, Y., Yao, Y., Song, N., Hu, Z., Qin, D., Xie, C., Peng, H., Ni, Z. and Sun, Q. (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.
161. Yang, L., Lin, C., Liu, W., Zhang, J., Ohgi, K.A., Grinstein, J.D., Dorrestein, P.C. and Rosenfeld, M.G. (2011) ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell, 147, 773-788.
162. Yang, F., Zhang, H., Mei, Y. and Wu, M. (2014a) Reciprocal regulation of HIF-1alpha and lincRNA-p21 modulates the Warburg effect. Mol. Cell, 53, 88-100.
163. Yang, L., Froberg, J.E. and Lee, J.T. (2014b) Long noncoding RNAs: fresh perspectives into the RNA world. Trends Biochem. Sci. 39, 35-43.
164. Zhang, F. and Simon, A.E. (2003) A novel procedure for the localization of viral RNAs in protoplasts and whole plants. Plant J. 35, 665-673.
165. Zhang, Y., Liu, J., Jia, C., Li, T., Wu, R., Wang, J., Chen, Y., Zou, X., Chen, R., Wang, X.J. and Zhu, D. (2010) Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. BMC Genom. 11, 61.
166. Zhang, X., Xia, J., Lii, Y.E., Barrera-Figueroa, B.E., Zhou, X., Gao, S., Lu, L., Niu, D., Chen, Z., Leung, C., Wong, T., Zhang, H., Guo, J., Li, Y., Liu, R., Liang, W., Zhu, J.K., Zhang, W. and Jin, H. (2012) Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol. 13, R20.
167. Zhang, X.O., Wang, H.B., Zhang, Y., Lu, X., Chen, L.L. and Yang, L. (2014a) Complementary sequence-mediated exon circularization. Cell, 159, 134-147.
168. Zhang, Y., Liao, J., Li, Z., Yu, Y., Zhang, J., Li, Q., Qu, L., Shu, W. and Chen, Y. (2014b) Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol. 15, 512.
169. Zhou, X., Sunkar, R., Jin, H., Zhu, J.K. and Zhang, W. (2009) Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res. 19, 70-78.
170. Zhou, P., Silverstein, K.A., Gao, L., Walton, J.D., Nallu, S., Guhlin, J. and Young, N.D. (2013) Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). BMC Bioinformatics, 14, 335.
171. Ziemienowicz, A., Haasen, D., Staiger, D. and Merkle, T. (2003) Arabidopsis transportin1 is the nuclear import receptor for the circadian clock-regulated RNA-binding protein AtGRP7. Plant Mol. Biol. 53, 201-212.