1 Khalil A M, Rinn J L. RNA-protein interactions in human health and disease. Semin Cell Dev Biol, 2011, 22: 359-365
[2]
2 Mercer T R, Dinger M E, Mattick J S. Long non-coding RNAs: Insights into functions. Nat Rev Genet, 2009, 10: 155-159
[3]
3 Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 2009, 458: 223-227
[4]
6 Cesana M, Cacchiarelli D, Legnini I, et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 2011, 147: 358-369
[5]
7 Ponting C P, Oliver P L, Reik W. Evolution and functions of long noncoding RNAs. Cell, 2009, 136: 629-641
[6]
9 Brockdorff N, Ashworth A, Kay G F, et al. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature, 1991, 351: 329-331
[7]
10 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
[8]
12 Guttman M, Donaghey J, Carey B W, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 2011, 477: 295-300
[9]
13 Khalil A M, Guttman M, Huarte M, 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
[10]
16 Wapinski O, Chang H Y. Long noncoding RNAs and human disease. Trends Cell Biol, 2011, 21: 354-361
[11]
19 Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60770 full-length cDNAs. Nature, 2022, 420: 563-573
[12]
20 Li L, Wang X, Stolc V, et al. Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet, 2005, 38: 124-129
[13]
21 Hung T, Wang Y, Lin M F, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet, 2011, 43: 621-629
[14]
22 Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Nat Genet, 2010, 20: 646-654
[15]
23 Zhao J, Ohsumi T K, Kung J T, et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell, 2010, 40: 939-953
[16]
25 Mikkelsen T S, Ku M, Jaffe D B, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 2007, 448: 553-560
[17]
26 Cabili M N, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 2011, 25: 1915-1927
[18]
27 Kong L, Zhang Y, Ye Z Q, et al. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007, 35: W345-W349
[19]
28 Lin M F, Carlson J W, Crosby M A, et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res, 2007, 17: 1823-1836
[20]
29 Lin M F, Jungreis I, Kellis M, et al. PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics, 2011, 27: i275-i282
[21]
30 Prensner J R, Iyer M K, Balbin O A, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol, 2011, 29: 742-749
[22]
33 Ulveing D, Francastel C, Hubé F. When one is better than two: RNA with dual fuction. Biochime, 2011, 93: 633-644
[23]
34 Hershberg R, Petrov D A. Selection on codon bias. Annu Rev Genet, 2008, 42: 287-299
[24]
37 Yang Z H, Nielsen R, Goldman N, et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 2000, 155: 431-449
[25]
38 Endo T, Ikeo K, Gojobori T. Large-scale search for genes on which positive selection may operate. Mol Biol Evol, 1996, 13: 685-690
[26]
39 Ponjavic J, Ponting C P, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res, 2007, 17: 556-565
[27]
41 Maenner S, Blaud M, Fouillen L, et al. 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol, 2010, 8: e1000276
[28]
43 Mercer T R, Dinger M E, Sunkin S M, et al. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA, 2008, 105: 716
[29]
44 Amaral P P, Mattick J S. Mattick. Noncoding RNA in development. Mamm Genome, 2008, 19: 454-492
[30]
49 Gupta R A, Shah N, Wang K C, et al. Long non-coding RNA hotair reprograms chromatin state to promote cancer metastasis. Nature, 2010, 464: 1071-1076
[31]
4 Bu D, Yu K, Sun S, et al. Noncode v3.0: Integrative annotation of long noncoding RNAs. Nucleic Acids Res, 2012, 40: D210-D215
[32]
5 Huarte M, Guttman M, Feldser D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 2010, 142: 409-419
[33]
8 Bartolomei M S, Zemel S, Tilghman S M. Parental imprinting of the mouse H19 gene. Nature, 1991, 351: 153-155
[34]
11 Redrup L, Branco M R, Perdeaux E R, et al. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development, 2009, 136: 525-530
[35]
14 Guttman M, Rinn J L. Modular regulatory principles of large non-coding RNAs. Nature, 2012, 482: 339-346
[36]
15 Tsai M C, Spitale R C, Chang H Y. Long intergenic noncoding RNAs: New links in cancer progression. Cancer Res, 2011, 71: 3-7
[37]
17 Hiller M, Findeiss S, Lein S, et al. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res, 2009, 19: 1289-1300
[38]
18 Rose D, Hiller M, Schutt K, et al. Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics, 2011, 27: 1894-1900
[39]
24 Jia H, Osak M, Bogu G K, et al. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA, 2010, 16: 1478-1487
[40]
31 Nordstr?m K J, Mirza M A, Almén M S, et al. Critical evaluation of the FANTOM3 non-coding RNA transcripts. Genomics, 2009, 94: 169-176
[41]
32 Dinger M E, Pang K C, Mercer T R, et al. Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLoS Comput Biol, 2008, 4: e1000176
[42]
35 Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics, 1991, 129: 897-907
[43]
36 Niazi F, Valadkhan S. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3′ UTRs. RNA, 2012, 18: 825-843
[44]
40 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
[45]
42 Liao Q, Liu C, Yuan X, et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res, 2011, 39: 3864-3878
[46]
45 Wilusz J E, Sunwoo H, Spector D L. Long noncoding RNAs: Functional surprises from the RNA world. Genes Dev, 2009, 23: 1494-1504
[47]
46 Clark M B, Johnston R L, Inostroza-Ponta M, et al. Genome-wide analysis of long noncoding RNA stability. Genome Res, 2012, 22: 885-898
[48]
47 Khaitan D, Dinger M E, Mazar J, et al. The melanoma-upregulated long noncoding RNA spry4-it1 modulates apoptosis and invasion. Cancer Res, 2011, 71: 3852
[49]
48 Faghihi M A, Modarresi F, Khalil A M, et al. 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
[50]
50 Gibb E A, Vucic E A, Enfield K S S, et al. Human cancer long non-coding RNA transcriptomes. PLoS One, 2011, 6: e25915