[1] | Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu XW, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science, 2004, 306(5705): 2242-2246. | [2] | Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res, 2015, 43: D168-D173. | [3] | Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science, 2002, 295(5558): 1306-1311. | [4] | Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao YR, Liang J, Zhao HM, Lobanenkov VV, Ecker JR, Thomson JA, Ren B. Chromatin architecture reorganization during stem cell differentiation. Nature, 2015, 518(7539): 331-336. | [5] | Gloss BS, Dinger ME. The specificity of long noncoding RNA expression. Biochim Biophys Acta, 2016, 1859(1): 16-22. | [6] | Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem, 2012, 81: 145-166. | [7] | Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell, 2009, 136(4): 629-641. | [8] | Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet, 2016, 17(1): 47-62. | [9] | Flynn RA, Chang HY. Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell, 2014, 14(6): 752-761. | [10] | Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell, 2013, 152(6): 1298-1307. | [11] | Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res, 2011, 39(S1): D146-D151. | [12] | Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan XA, Ruan YJ, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res, 2012, 22(9): 1775-1789. | [13] | Huang S, Deerinck TJ, Ellisman MH, Spector DL. In vivo analysis of the stability and transport of nuclear poly(A)+ RNA. J Cell Biol, 1994, 126(4): 877-899. | [14] | Nickerson JA, Krochmalnic G, Wan KM, Penman S. Chromatin architecture and nuclear RNA. Proc Natl Acad Sci USA, 1989, 86(1): 177-181. | [15] | Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature, 2012, 482(7385): 339-346. | [16] | Kahn TG, Dorafshan E, Schultheis D, Zare A, Stenberg P, Reim I, Pirrotta V, Schwartz YB. Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements. Nucleic Acids Res, 2016, 44(21): 10132-10149. | [17] | Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science, 2010, 329(5992): 689-693. | [18] | Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang XP, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 2011, 477(7364): 295-300. | [19] | Sunwoo H, Wu JY, Lee JT. The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells. Proc Natl Acad Sci USA, 2015, 112(31): E4216-E4225. | [20] | Pombo A, Dillon N. Three-dimensional genome architecture: players and mechanisms. Nat Rev Mol Cell Biol, 2015, 16(4): 245-257. | [21] | Bhattacharya D, Talwar S, Mazumder A, Shivashankar GV. Spatio-temporal plasticity in chromatin organization in mouse cell differentiation and during Drosophila embryogenesis. Biophys J, 2009, 96(9): 3832-3839. | [22] | Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet, 2009, 41(2): 246-250. | [23] | Savi? N, B?r D, Leone S, Frommel SC, Weber FA, Vollenweider E, Ferrari E, Ziegler U, Kaech A, Shakhova O, Cinelli P, Santoro R. lncRNA maturation to initiate heterochromatin formation in the nucleolus is required for exit from pluripotency in ESCs. Cell Stem Cell, 2014, 15(6): 720-734. | [24] | Santoro R, Schmitz KM, Sandoval J, Grummt I. Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans. EMBO Rep, 2010, 11(1): 52-58. | [25] | Guetg C, Scheifele F, Rosenthal F, Hottiger MO, Santoro R. Inheritance of silent rDNA chromatin is mediated by PARP1 via noncoding RNA. Mol Cell, 2012, 45(6): 790-800. | [26] | B?hmdorfer G, Sethuraman S, Rowley MJ, Krzyszton M, Rothi MH, Bouzit L, Wierzbicki AT. Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin. eLife, 2016, 5: e19092. | [27] | Chen LL, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell, 2009, 35(4): 467-478. | [28] | Kawaguchi T, Hirose T. Chromatin remodeling complexes in the assembly of long noncoding RNA-dependent nuclear bodies. Nucleus, 2015, 6(6): 462-467. | [29] | Fox AH, Bond CS, Lamond AI. P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA- dependent manner. Mol Biol Cell, 2005, 16(11): 5304-5315. | [30] | Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, Boeckx B, Wijnhoven PWG, Radaelli E, Vermi W, Leucci E, Lapouge G, Beck B, van den Oord J, Nakagawa S, Hirose T, Sablina AA, Lambrechts D, Aerts S, Blanpain C, Marine JC. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat Med, 2016, 22(8): 861-868. | [31] | Shen W, Liang XH, Crooke ST. Phosphorothioate oligonucleotides can displace NEAT1 RNA and form nuclear paraspeckle-like structures. Nucleic Acids Res, 2014, 42(13): 8648-8662. | [32] | Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell, 2010, 39(6): 925-938. | [33] | Ji Q, Zhang L, Liu X, Zhou L, Wang W, Han Z, Sui H, Tang Y, Wang Y, Liu N, Ren J, Hou F, Li Q. Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex. Br J Cancer, 2014, 111(4): 736-748. | [34] | Hubner MR, Eckersley-Maslin MA, Spector DL. Chromatin organization and transcriptional regulation. Curr Opin Genet Dev, 2013, 23(2): 89-95. | [35] | Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol, 2015, 22(1): 29-35. | [36] | Melé M, Rinn JL. "Cat's cradling" the 3D genome by the Act of LncRNA transcription. Mol Cell, 2016, 62(5): 657-664. | [37] | Chen CK, Blanco M, Jackson C, Aznauryan E, Ollikainen N, Surka C, Chow A, Cerase A, McDonel P, Guttman M. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science, 2016, 354(6311): 468-472. | [38] | Naughton C, Sproul D, Hamilton C, Gilbert N. Analysis of active and inactive X chromosome architecture reveals the independent organization of 30 nm and large-scale chromatin structures. Mol Cell, 2010, 40(3): 397-409. | [39] | Kay GF, Penny GD, Patel D, Ashworth A, Brockdorff N, Rastan S. Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation. Cell, 1993, 72(2): 171-182. | [40] | Wutz A, Jaenisch R. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol Cell, 2000, 5(4): 695-705. | [41] | Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science, 2013, 341(6147): 1237973. | [42] | Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY. Systematic discovery of Xist RNA binding proteins. Cell, 2015, 161(2): 404-416. | [43] | McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su JL, Lander ES, Hess S, Plath K, Guttman M. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature, 2015, 521(7551): 232-236. | [44] | Minajigi A, Froberg JE, Wei C, Sunwoo H, Kesner B, Colognori D, Lessing D, Payer B, Boukhali M, Haas W, Lee JT. Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science, 2015, 349(6245), doi: 10.1126/science.aab2276. | [45] | Gruenbaum Y, Margalit A, Goldman RD, Shumaker DK, Wilson KL. The nuclear lamina comes of age. Nat Rev Mol Cell Biol, 2005, 6(1): 21-31. | [46] | Zhu Y, Chen Z, Zhang K, Wang MC, Medovoy D, Whitaker JW, Ding B, Li N, Zheng LN, Wang W. Constructing 3D interaction maps from 1D epigenomes. Nat Commun, 2016, 7: 10812. | [47] | Kubiak M, Lewandowska MA. Can chromatin conformation technologies bring light into human molecular pathology?. Acta Biochim Pol, 2015, 62(3): 483-489. | [48] | Wang Y, Xu ZY, Jiang JF, Xu C, Kang JH, Xiao L, Wu MJ, Xiong J, Guo XC, Liu HQ. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell, 2013, 25(1): 69-80. | [49] | Mora A, Sandve GK, Gabrielsen OS, Eskeland R. In the loop: promoter-enhancer interactions and bioinformatics. Brief Bioinform, 2015, 17(6): 980-995. | [50] | Tuan D, Kong SM, Hu K. Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc Natl Acad Sci USA, 1992, 89(23): 11219-11223. | [51] | Ling JH, Ainol L, Zhang L, Yu XP, Pi WH, Tuan D. HS2 enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter. J Biol Chem, 2004, 279(49): 51704-51713. | [52] | Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature, 2013, 494(7438): 497-501. | [53] | Li WB, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song XY, Oh S, Kim HS, Glass CK, Rosenfeld MG. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature, 2013, 498(7455): 516-520. | [54] | Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L, Schmitt N, Dold A, Ginsberg D, Grummt I. LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell, 2015, 60(4): 626-636. | [55] | Cusanelli E, Romero CAP, Chartrand P. Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres. Mol Cell, 2013, 51(6): 780-791. | [56] | Azzalin CM, Lingner J. Telomere functions grounding on TERRA firma. Trends Cell Biol, 2015, 25(1): 29-36. | [57] | Rippe K, Luke B. TERRA and the state of the telomere. Nat Struct Mol Biol, 2015, 22(11): 853-858. | [58] | Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet, 2001, 2(4): 292-301. | [59] | Williams A, Spilianakis CG, Flavell RA. Interchromosomal association and gene regulation in trans. Trends Genet, 2010, 26: 188-197. | [60] | Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan BB, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci USA, 2013, 110: 3387-3392. | [61] | Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol, 2014, 21(2): 198-206. | [62] | Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 2007, 129(7): 1311-1323. | [63] | Zhang KL, Sun XT, Zhou X, Han L, Chen LY, Shi ZD, Zhang AL, Ye MH, Wang QX, Liu CY, Wei JW, Ren Y, Yang JX, Zhang JN, Pu PY, Li M, Kang CS. Long non-coding RNA HOTAIR promotes glioblastoma cell cycle progression in an EZH2 dependent manner. Oncotarget, 2015, 6(1): 537-546. | [64] | Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang YL, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 2010, 464(7291): 1071-1076. | [65] | Zhang ZZ, Shen ZY, Shen YY, Zhao EH, Wang M, Wang CJ, Cao H, Xu J. HOTAIR long noncoding RNA promotes gastric cancer metastasis through suppression of poly r(C)-binding protein (PCBP) 1. Mol Cancer Ther, 2015, 14(5): 1162-1170. | [66] | Liu XH, Liu ZL, Sun M, Liu J, Wang ZX, De W. The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer. BMC Cancer, 2013, 13: 464. | [67] | Alves CP, Fonseca AS, Muys BR, de Barros ELBR, Bürger MC, de Souza JES, Valente V, Zago MA, Silva WA, Jr. Brief report: the lincRNA Hotair is required for epithelial-to-mesenchymal transition and stemness maintenance of cancer cell lines. Stem Cells, 2013, 31(12): 2827-2832. | [68] | Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res, 2011, 71(20): 6320-6326. | [69] | Angrand PO, Vennin C, Le Bourhis X, Adriaenssens E. The role of long non-coding RNAs in genome formatting and expression. Front Genet, 2015, 6: 165. | [70] | Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Morales DR, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA, 2009, 106(28): 11667-11672. | [71] | Leucci E, Vendramin R, Spinazzi M, Laurette P, Fiers M, Wouters J, Radaelli E, Eyckerman S, Leonelli C, Vanderheyden K, Rogiers A, Hermans E, Baatsen P, Aerts S, Amant F, Van Aelst S, van den Oord J, de Strooper B, Davidson I, Lafontaine DLJ, Gevaert K, Vandesompele J, Mestdagh P, Marine JC. Melanoma addiction to the long non-coding RNA SAMMSON. Nature, 2016, 531(7595): 518-522. | [72] | Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, Poliakov A, Cao XH, Dhanasekaran SM, Wu YM, Robinson DR, Beer DG, Feng FY, Iyer HK, Chinnaiyan AM. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet, 2015, 47(3): 199-208. | [73] | Zhou XY, Yin CQ, Dang YN, Ye F, Zhang GX. Identification of the long non-coding RNA H19 in plasma as a novel biomarker for diagnosis of gastric cancer. Sci Rep, 2015, 5: 11516. | [74] | Merola R, Tomao L, Antenucci A, Sperduti I, Sentinelli S, Masi S, Mandoj C, Orlandi G, Papalia R, Guaglianone S, Costantini M, Cusumano G, Cigliana G, Ascenzi P, Gallucci M, Conti L. PCA3 in prostate cancer and tumor aggressiveness detection on 407 high-risk patients: a National Cancer Institute experience. J Exp Clin Cancer Res, 2015, 34(1): 15. | [75] | Hu B, Yang HM, Yang HW. Diagnostic value of urine prostate cancer antigen 3 test using a cutoff value of 35 μg/L in patients with prostate cancer. Tumour Biol, 2014, 35(9): 8573-8580. | [76] | Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wu Z, Zhang SF, Wang HB, Ge JH, Lu XH, Yang L, Chen LL. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res, 2014, 24(5): 513-531. | [77] | McCleland ML, Mesh K, Lorenzana E, Chopra VS, Segal E, Watanabe C, Haley B, Mayba O, Yaylaoglu M, Gnad F, Firestein R. CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer. J Clin Invest, 2016, 126(2): 639-652. | [78] | Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 2013, 502(7469): 59-64. |
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