1 |
Aubert, D., Chen, L., Moon, Y. H., Martin, D., Castle, L. A., Yang, C. H. and Sung, Z. R. 2001. EMF1, a novel protein involved in the control of shoot architecture and flowering in Arabidopsis. Plant Cell 13, 1865-1875.
DOI
|
2 |
Bastow, R., Mylne, J. S., Lister, C., Lippman, Z., Martienssen, R. A. and Dean, C. 2004. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427, 164-167.
DOI
|
3 |
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.
|
4 |
Bi, X. 2012. Functions of chromatin remodeling factors in heterochromatin formation and maintenance. Sci. China Life Sci. 55, 89-96.
DOI
|
5 |
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.
DOI
|
6 |
Birney, E., et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816.
DOI
|
7 |
Boerner, S. and McGinnis, K. M. 2012. Computational identification and functional predictions of long noncoding RNA in Zea mays. PloS one 7, e43047.
DOI
|
8 |
Cabili, M. N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J. L. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes. Dev. 25, 1915-1927.
DOI
|
9 |
Chen, L. L. and Carmichael, G. G. 2010. Decoding the function of nuclear long non-coding RNAs. Curr. Opin. Cell Biol. 22, 357-364.
DOI
|
10 |
Chen, X. 2009. Small RNAs and their roles in plant development. Annu. Rev. Cell. Dev. Biol. 25, 21-44.
DOI
|
11 |
Crespi, M. D., Jurkevitch, E., Poiret, M., d′Aubenton-Carafa, Y., Petrovics, G., Kondorosi, E. and Kondorosi, A. 1994. enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. EMBO J. 13, 5099-5112.
|
12 |
Ding, J., Shen, J., Mao, H., Xie, W., Li, X. and Zhang, Q. 2012a. RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Mol. plant 5, 1210-1216.
DOI
|
13 |
Ding, J., Lu, Q., Ouyang, Y., Mao, H., Zhang, P., Yao, J., Xu, C., Li, X., Xiao, J. and Zhang, Q. 2012b. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc. Natl. Acad. Sci. USA 109, 2654-2659.
DOI
|
14 |
Guttman, M., Donaghey, J., Carey, B. W., Garber, M., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R., Bruhn, L., Yang, X., Amit, I., Meissner, A., Regev, A., Rinn, J. L., Root, D. E. and Lander, E. S. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295-300.
DOI
|
15 |
Dinger, M. E., Pang, K. C., Mercer, T. R. and Mattick, J. S. 2008. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput. Biol. 4, e1000176.
DOI
|
16 |
Dinger, M. E., Pang, K. C., Mercer, T. R., Crowe, M. L., Grimmond, S. M. and Mattick, J. S. 2009. NRED: a database of long noncoding RNA expression. Nucleic Acids Res. 37, D122-126.
DOI
|
17 |
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. Nature Genet. 39, 1033-1037.
DOI
|
18 |
Helliwell, C. A., Robertson, M., Finnegan, E. J., Buzas, D. M. and Dennis, E. S. 2011. Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts. PloS One 6, e21513.
DOI
|
19 |
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.
DOI
|
20 |
Hangauer, M. J., Vaughn, I. W. and McManus, M. T. 2013. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9, e1003569.
DOI
|
21 |
Heo, J. B. and Sung, S. 2011. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331, 76-79.
DOI
|
22 |
Kaneko, S., Li, G., Son, J., Xu, C. F., Margueron, R., Neubert, T. A. and Reinberg, D. 2010. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev. 24, 2615-2620.
DOI
|
23 |
Hirsch, J., Lefort, V., Vankersschaver, M., Boualem, A., Lucas, A., Thermes, C., d′Aubenton-Carafa, Y. and Crespi, M. 2006. Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol. 140, 1192-1204.
DOI
|
24 |
Huang, H. and Jiao, R. 2012. Roles of chromatin assembly factor 1 in the epigenetic control of chromatin plasticity. Sci. China Life Sci. 55, 15-19.
DOI
|
25 |
Jia, H., Osak, M., Bogu, G. K., Stanton, L. W., Johnson, R. and Lipovich, L. 2010. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16, 1478-1487.
DOI
|
26 |
Liu, J., Wang, H. and Chua, N. H. 2015. Long noncoding RNA transcriptome of plants. Plant Biotechnol. J. 13, 319-328.
DOI
|
27 |
Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermuller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H. and Gingeras, T. R. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488.
DOI
|
28 |
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.
DOI
|
29 |
Kim, E. D. and Sung, S. 2012. Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci. 17, 16-21.
DOI
|
30 |
Lee, Y., Kim, M., Han, J., Yeom, K. H., Lee, S., Baek, S. H. and Kim, V. N. 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051-4060.
DOI
|
31 |
Li, L., Wang, X., Stolc, V., Li, X., Zhang, D., Su, N., Tongprasit, W., Li, S., Cheng, Z., Wang, J. and Deng, X. W. 2006. Genome-wide transcription analyses in rice using tiling microarrays. Nature Genet. 38, 124-129.
DOI
|
32 |
Liu, C., Muchhal, U. S. and Raghothama, K. G. 1997. Differential expression of TPS11, a phosphate starvation-induced gene in tomato. Plant Mol. Biol. 33, 867-874.
DOI
|
33 |
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.
DOI
|
34 |
Nagano, T. and Fraser, P. 2011. No-nonsense functions for long noncoding RNAs. Cell 145, 178-181.
DOI
|
35 |
Ma, J., Yan, B., Qu, Y., Qin, F., Yang, Y., Hao, X., Yu, J., Zhao, Q., Zhu, D. and Ao, G. 2008. Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize. J. Cell Biochem. 105, 136-146.
DOI
|
36 |
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.
DOI
|
37 |
Martin, A. C., del Pozo, J. C., Iglesias, J., Rubio, V., Solano, R., de La Pena, A., Leyva, A. and Paz-Ares, J. 2000. Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. Plant J. 24, 559-567.
DOI
|
38 |
Matsui, A., Ishida, J., Morosawa, T., Okamoto, M., Kim, J. M., Kurihara, Y., Kawashima, M., Tanaka, M., To, T. K., Nakaminami, K., Kaminuma, E., Endo, T. A., Mochizuki, Y., Kawaguchi, S., Kobayashi, N., Shinozaki, K., Toyoda, T. and Seki, M. 2010. Arabidopsis tiling array analysis to identify the stress-responsive genes. Methods Mol. Biol. 639, 141-155.
|
39 |
Matvienko, M., Van de Sande, K., Yang, W. C., van Kammen, A., Bisseling, T. and Franssen, H. 1994. Comparison of soybean and pea ENOD40 cDNA clones representing genes expressed during both early and late stages of nodule development. Plant Mol. Biol. 26, 487-493.
DOI
|
40 |
Mylne, J. S., Barrett, L., Tessadori, F., Mesnage, S., Johnson, L., Bernatavichute, Y. V., Jacobsen, S. E., Fransz, P. and Dean, C. 2006. LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc. Natl. Acad. Sci. USA 103, 5012-5017.
DOI
|
41 |
Nam, J. W. and Bartel, D. P. 2012. Long noncoding RNAs in C. elegans. Genome Res. 22, 2529-2540.
DOI
|
42 |
Shin, H., Shin, H. S., Chen, R. and Harrison, M. J. 2006. Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation. Plant J. 45, 712-726.
DOI
|
43 |
Ng, J. H. and Ng, H. H. 2010. LincRNAs join the pluripotency alliance. Nature Genet. 42, 1035-1036.
DOI
|
44 |
Okazaki, Y., et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573.
DOI
|
45 |
Orom, U. A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., Guigo, R. and Shiekhattar, R. 2010. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46-58.
DOI
|
46 |
Pauli, A., Valen, E., Lin, M. F., Garber, M., Vastenhouw, N. L., Levin, J. Z., Fan, L., Sandelin, A., Rinn, J. L., Regev, A. and Schier, A. F. 2012. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22, 577-591.
DOI
|
47 |
Rehrauer, H., Aquino, C., Gruissem, W., Henz, S. R., Hilson, P., Laubinger, S., Naouar, N., Patrignani, A., Rombauts, S., Shu, H., Van de Peer, Y., Vuylsteke, M., Weigel, D., Zeller, G. and Hennig, L. 2010. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol. 152, 487-499.
DOI
|
48 |
Rohrig, H., Schmidt, J., Miklashevichs, E., Schell, J. and John, M. 2002. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc. Natl. Acad. Sci. USA 99, 1915-1920.
DOI
|
49 |
Shuai, P., Liang, D., Zhang, Z., Yin, W. and Xia, X. 2013. Identification of drought-responsive and novel Populus trichocarpa microRNAs by high-throughput sequencing and their targets using degradome analysis. BMC Genomics 14, 233.
DOI
|
50 |
Sung, S., He, Y., Eshoo, T. W., Tamada, Y., Johnson, L., Nakahigashi, K., Goto, K., Jacobsen, S. E. and Amasino, R. M. 2006. Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat. Genet. 38, 706-710.
DOI
|
51 |
Tang, L., Zhang, W., Su, B. and Yu, B. 2013. Long noncoding RNA HOTAIR is associated with motility, invasion and metastatic potential of metastatic melanoma. Biomed. Res. Int. 2013, 251098.
|
52 |
Wang, Y., Fan, X., Lin, F., He, G., Terzaghi, W., Zhu, D. and Deng, X. W. 2014b. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc. Natl. Acad. Sci. USA 111, 10359-10364.
DOI
|
53 |
Turck, F., Roudier, F., Farrona, S., Martin-Magniette, M. L., Guillaume, E., Buisine, N., Gagnot, S., Martienssen, R. A., Coupland, G. and Colot, V. 2007. Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet. 3, e86.
DOI
|
54 |
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.
DOI
|
55 |
Wang, K. C. and Chang, H. Y. 2011. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904-914.
DOI
|
56 |
Wierzbicki, A. T., Haag, J. R. and Pikaard, C. S. 2008. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135, 635-648.
DOI
|
57 |
Wilhelm, B. T., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C. J., Rogers, J. and Bahler, J. 2008. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243.
DOI
|
58 |
Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J. and Lee, J. T. 2008. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750-756.
DOI
|
59 |
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.
DOI
|
60 |
Wu, J., Okada, T., Fukushima, T., Tsudzuki, T., Sugiura, M. and Yukawa, Y. 2012. A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis. RNA Biol. 9, 302-313.
DOI
|
61 |
Yang, W. C., Katinakis, P., Hendriks, P., Smolders, A., de Vries, F., Spee, J., van Kammen, A., Bisseling, T. and Franssen, H. 1993. Characterization of GmENOD40, a gene showing novel patterns of cell-specific expression during soybean nodule development. Plant J. 3, 573-585.
DOI
|
62 |
Zhang, X., Germann, S., Blus, B. J., Khorasanizadeh, S., Gaudin, V. and Jacobsen, S. E. 2007. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat. Struct. Mol. Biol 14, 869-871.
DOI
|
63 |
Zhang, Y. C. and Chen, Y. Q. 2013. Long noncoding RNAs: new regulators in plant development. Biochem. Biophys. Res. Commun. 436, 111-114.
DOI
|
64 |
Zhu, Q. H., Stephen, S., Taylor, J., Helliwell, C. A. and Wang, M. B. 2014. Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. New Phytol. 201, 574-584.
DOI
|