[1] Birney E, Stamatoyannopoulos J A, Dutta A, etal. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J]. Nature, 2007, 447(7146): 799-816.
[2] van Bakel H, Nislow C, Blencowe B J, et al.Most “dark matter” transcripts are associated with known genes [J]. PLoS Biology, 2010, 8(5): e1000371.1-8.
[3] Clark M B, Mattick J S. Long noncoding RNAs in cell biology [J]. Seminars in Cell & Developmental Biology, 2011, 22(4): 366-376.
[4] Gibb E A, Brown C J, Lam W L. The functional role of long non-coding RNA in human carcinomas [J].Molecular Cancer, 2011, 10(1): 38.1-5.
[5] Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60 770 full-length cDNAs [J]. Nature, 2002,420(6915): 563-573.
[6] Ng S Y, Johnson R, Stanton L W. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors [J]. EMBO Journal, 2012,31(3): 522-533.
[7] Zhao J, Sun B K, Erwin J A, et al. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome [J]. Science, 2008, 322(5902): 750-756.
[8] Kotake Y, Nakagawa T, Kitagawa K, et al. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene [J]. Oncogene, 2011, 30(16): 1956-1962.
[9] Dinger M E, Amaral P P, Mercer T R, et al.Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation [J]. Genome Research,2008, 18(9): 1433-1445.
[10] Gupta R A, Shah N, Wang K C, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis [J]. Nature, 2010,464(7291): 1071-1076.
[11] Atkinson S R, Marguerat S, B¨ahler J. Exploring long non-coding RNAs through sequencing [J]. Seminars in Cell & Developmental Biology, 2012, 23(2):200-205.
[12] H¨uttenhofer A, Schattner P. The principles of guiding by RNA: Chimeric RNA-protein enzymes [J].Nature Reviews Genetics, 2006, 7(6): 475-482.
[13] Tsai M C, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes [J]. Science, 2010, 329(5992): 689-693.
[14] Zhao J, Ohsumi T K, Kung J T, et al. Genomewide identification of polycomb-associated RNAs by RIP-seq [J]. Molecular Cell, 2010, 40(6): 939-953.
[15] Darnell R. CLIP (cross-linking and immunoprecipitation)identification of RNAs bound by a specific protein[J]. Cold Spring Harbor Protocols, 2012, 2012(11):1146-1160.
[16] Hafner M, Landthaler M, Burger L, et al. PARCliP:A method to identify transcriptome-wide the binding sites of RNA binding proteins [J]. Journal of Visualized Experiments, 2010(41): 2034-2037.
[17] Chu C, Qu K, Zhong F L, et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions [J]. Molecular Cell, 2011,44(4): 667-678.
[18] Rinn J L, Kertesz M, Wang J K, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs [J]. Cell, 2007,129(7): 1311-1323.
[19] Pandey R R, Mondal T, Mohammad F, et al.Kcnq1ot1 antisense noncoding RNA mediates lineagespecific transcriptional silencing through chromatinlevel regulation [J]. Molecular Cell, 2008, 32(2): 232-246.
[20] Khalil A M, Guttman M, Huarte M, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression [J]. Proceedings of the National Academy of Sciences USA, 2009, 106(28): 11667-11672.
[21] Margueron R, Reinberg D. The polycomb complex PRC2 and its mark in life [J]. Nature, 2011, 469(7330):343-349.
[22] Luo M, Li Z, WangW, et al. Long non-coding RNA H19 increases bladder cancer metastasis by associating with EZH2 and inhibiting E-cadherin expression [J].Cancer Letters, 2013, 333(2): 213-221.
[23] Yap K L, Li S, Munoz-Cabello A M, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a [J]. Molecular Cell,2010, 38(5): 662-674.
[24] Wang K C, Yang Y W, Liu B, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression [J]. Nature, 2011, 472(7341):120-124.
[25] Prensner J R, Chinnaiyan A M. The emergence of lncRNAs in cancer biology [J]. Cancer Discovery, 2011,1(5): 391-407.
[26] ?rom U A, Shiekhattar R. Noncoding RNAs and enhancers: Complications of a long-distance relationship[J]. Trends in Genetics, 2011, 27(10): 433-439.
[27] Guenther M G, Levine S S, Boyer L A, et al.A chromatin landmark and transcription initiation at most promoters in human cells [J]. Cell, 2007, 130(1):77-88.
[28] Wang X, Arai S, Song X, et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription [J]. Nature, 2008, 454(7200): 126-130.
[29] Feng J, Bi C, Clark B S, et al. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator [J]. Genes & Development, 2006, 20(11):1470-1484.
[30] Calin G A, Liu C G, Ferracin M, et al. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas [J]. Cancer Cell, 2007,12(3): 215-229.
[31] Martianov I, Ramadass A, Barros A S, et al. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript [J]. Nature, 2007,445(7128): 666-670.
[32] Go?ni J R, De La Cruz X, Orozco M. Triplexforming oligonucleotide target sequences in the human genome [J]. Nucleic Acids Research, 2004, 32(1): 354-360.
[33] Mercer T R, Dinger M E, Mattick J S. Long non-coding RNAs: Insights into functions [J]. Nature Reviews Genetics, 2009, 10(3): 155-159.
[34] Katayama S, Tomaru Y, Kasukawa T, et al. Antisense transcription in the mammalian transcriptome[J]. Science, 2005, 309(5740): 1564-1566.
[35] Berx G, Van Roy F. Involvement of members of the cadherin superfamily in cancer [J]. Cold Spring Harbor Perspectives in Biology, 2009, 1(6): a003129.
[36] Beltran M, Puig I, Pena C, et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition[J]. Genes & Development, 2008, 22(6): 756-769.
[37] Sch¨oler N, Langer C, D¨ohner H, et al. Serum microRNAs as a novel class of biomarkers: A comprehensive review of the literature [J]. Experimental Hematology,2010, 38(12): 1126-1130.
[38] Kosaka N, Iguchi H, Ochiya T. Circulating microRNA in body fluid: A new potential biomarker for cancer diagnosis and prognosis [J]. Cancer Science,2010, 101(10): 2087-2092.
[39] Lin R, Maeda S, Liu C, et al. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas [J]. Oncogene, 2007,26(6): 851-858.
[40] Lai M C, Yang Z, Zhou L, et al. Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation[J]. Medical Oncology, 2012, 29(3): 1810-1816.
[41] Yang Z, Zhou L, Wu L M, et al. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation [J]. Annals of Surgical Oncology,2011, 18(5): 1243-1250.
[42] Tinzl M, Marberger M, Horvath S, et al.DD3PCA3 RNA analysis in urine: A new perspective for detecting prostate cancer [J]. European Urology,2004, 46(2): 182-186.
[43] Lee G L, Dobi A, Srivastava S. Prostate cancer:Diagnostic performance of the PCA3 urine test [J]. Nature Reviews Urology, 2011, 8(3): 123-124.
[44] Costa F F. Non-coding RNAs and new opportunities for the private sector [J]. Drug Discovery Today, 2009,14(9-10): 446-452.
[45] Castanotto D, Rossi J J. The promises and pitfalls of RNA-interference-based therapeutics [J]. Nature,2009, 457(7228): 426-433.
