Functional analysis of long noncoding RNAs in development and disease

Advances in Experimental Medicine and Biology

Volumn 825, Issue , 2014, Pages 129-158

  Chen, Ling Ling ^a   Zhao, Jing Crystal ^b  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b BURNHAM INSTITUTE   (United States)

Author keywords

Cancer; Chart; ChIRP; CLIP seq; Epigenetics; Long noncoding RNA; RIP seq; sno lncRNA; Xist

Indexed keywords

CIRCULAR RNA; LONG UNTRANSLATED RNA; NATURAL ANTISENSE TRANSCRIPT; POLYCOMB GROUP PROTEIN; PROMOTER ASSOCIATED LONG RNA; RING FINGER PROTEIN; SNORNA RELATED LONG RNA; UNCLASSIFIED DRUG; X INACTIVATION SPECIFIC TRANSCRIPT LNCRNA; DNA; RNA; RNA BINDING PROTEIN; TRANSCRIPTOME;

ARTICLE; BINDING SITE; CARCINOGENESIS; CELL DIFFERENTIATION; COMPLEX FORMATION; CROSS LINKING; DEVELOPMENT; DISEASE COURSE; EPIGENETICS; FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY; GENE DELETION; GENE SILENCING; GENETIC DISORDER; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOPRECIPITATION; INDIVIDUAL NUCLEOTIDE RESOLUTION CLIP SEQ; INVESTIGATIVE PROCEDURES; NONHUMAN; PHOTOACTIVATABLE RIBONUCLEOSIDE ENHANCED CLIP SEQ; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN RNA BINDING; REGULATORY MECHANISM; RNA ANALYSIS; TUMOR SUPPRESSOR GENE; X CHROMOSOME INACTIVATION; ANIMAL; GENETICS; METABOLISM; NEOPLASM;

MAMMALIA;

ANIMALS; DNA; DNA, NEOPLASM; HUMANS; NEOPLASMS; RNA, LONG NONCODING; RNA, NEOPLASM; RNA-BINDING PROTEINS; TRANSCRIPTOME;

EID: 84921980968     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1221-6_4     Document Type: Article

References (176)

1. Alkema MJ, van der Lugt NM, Bobeldijk RC, Berns A, van Lohuizen M (1995) Transformation of axial skeleton due to overexpression of bmi-1 in transgenic mice. Nature 374(6524):724-727
2. Anguera MC, Ma W, Clift D, Namekawa S, Kelleher RJ III, Lee JT (2011) Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain. PLoS Genet 7(9):e1002248
3. Anko ML, Muller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM (2012) The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol 13(3):R17
4. Barsyte-Lovejoy D, Lau SK, Boutros PC, Khosravi F, Jurisica I, Andrulis IL, Tsao MS, Penn LZ (2006) The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res 66(10):5330-5337
5. Beletskii A, Hong YK, Pehrson J, Egholm M, Strauss WM (2001) PNA interference mapping demonstrates functional domains in the noncoding RNA Xist. Proc Natl Acad Sci U S A 98(16):9215-9220
6. Borsani G, Tonlorenzi R, Simmler MC, Dandolo L, Arnaud D, Capra V, Grompe M, Pizzuti A, Muzny D, Lawrence C et al (1991) Characterization of a murine gene expressed from the inactive X chromosome. Nature 351(6324):325-329
7. Brockdorff N, Ashworth A, Kay GF, Cooper P, Smith S, McCabe VM, Norris DP, Penny GD, Patel D, Rastan S (1991) Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature 351(6324):329-331
8. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF (1991a) A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349(6304):38-44
9. Brown CJ, Lafreniere RG, Powers VE, Sebastio G, Ballabio A, Pettigrew AL, Ledbetter DH, Levy E, Craig IW, Willard HF (1991b) Localization of the X inactivation centre on the human X chromosome in Xq13. Nature 349(6304):82-84
10. Brown CJ, Willard HF (1994) The human X-inactivation centre is not required for maintenance of X-chromosome inactivation. Nature 368(6467):154-156
11. Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA (2012) Formation of triple-helical structures by the 3′-end sequences of MALAT1 and MENbeta noncoding RNAs. Proc Natl Acad Sci U S A 109(47):19202-19207
12. Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE (2010) Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 6(12):e1001233
13. Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149(4):819-831
14. Cabianca DS, Gabellini D (2010) The cell biology of disease: FSHD: copy number variations on the theme of muscular dystrophy. J Cell Biol 191(6):1049-1060
15. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915-1927
16. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298(5595): 1039-1043
17. Cassidy SB, Schwartz S, Miller JL, Driscoll DJ (2012) Prader-Willi syndrome. Genet Med 14(1):10-26
18. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM et al (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149(6):1393-1406
19. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2):358-369
20. Chen LL, Carmichael GG (2010) Long noncoding RNAs in mammalian cells: what, where, and why? Wiley Interdiscip Rev RNA 1(1):2-21
21. Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479-486
22. Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, Attreed M, Avner P, Wutz A, Barillot E et al (2010) LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141(6):956-969
23. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44(4):667-678
24. Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C (2011) Ftx is a noncoding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet 20(4):705-718
25. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322(5909):1845-1848
26. Csankovszki G, Panning B, Bates B, Pehrson JR, Jaenisch R (1999) Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation. Nat Genet 22(4):323-324
27. Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, Pirrotta V (2002) Drosophila enhancer of Zeste/ ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111(2):185-196
28. de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh M, Appanah R, Nesterova TB, Silva J, Otte AP, Vidal M et al (2004) Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev Cell 7(5):663-676
29. de Smith AJ, Purmann C, Walters RG, Ellis RJ, Holder SE, Van Haelst MM, Brady AF, Fairbrother UL, Dattani M, Keogh JM et al (2009) A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism. Hum Mol Genet 18(17):3257-3265
30. Dejardin J, Kingston RE (2009) Purification of proteins associated with specific genomic Loci. Cell 136(1):175-186
31. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775-1789
32. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al (2012) Landscape of transcription in human cells. Nature 489(7414): 101-108
33. Donohoe ME, Silva SS, Pinter SF, Xu N, Lee JT (2009) The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 460(7251):128-132
34. Duker AL, Ballif BC, Bawle EV, Person RE, Mahadevan S, Alliman S, Thompson R, Traylor R, Bejjani BA, Shaffer LG et al (2010) Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome. Eur J Hum Genet 18(11):1196-1201
35. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R et al (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74
36. Duszczyk MM, Sattler M (2012) (1)H, (1)(3)C, (1)(5)N and (3)(1)P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation. Biomol NMR Assign 6(1):75-77
37. Duszczyk MM, Wutz A, Rybin V, Sattler M (2011) The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. RNA 17(11):1973-1982
38. Duszczyk MM, Zanier K, Sattler M (2008) A NMR strategy to unambiguously distinguish nucleic acid hairpin and duplex conformations applied to a Xist RNA A-repeat. Nucleic Acids Res 36(22):7068-7077
39. Fang J, Chen T, Chadwick B, Li E, Zhang Y (2004) Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem 279(51):52812-52815
40. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17(15):1870-1881
41. Francis NJ, Kingston RE, Woodcock CL (2004) Chromatin compaction by a polycomb group protein complex. Science 306(5701):1574-1577
42. Gardner EJ, Nizami ZF, Talbot CC Jr, Gall JG (2012) Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev 26(22):2550-2559
43. Gelbart ME, Kuroda MI (2009) Drosophila dosage compensation: a complex voyage to the X chromosome. Development 136(9):1399-1410
44. Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K (2013) The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 152(4):743-754
45. Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470(7333):284-288
46. Graveley BR, Maniatis T (1998) Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing. Mol Cell 1(5):765-771
47. Guil S, Caceres JF (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 14(7):591-596
48. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071-1076
49. Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482(7385):339-346
50. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M et al (2010) Transcriptome-wide identification of RNAbinding protein and microRNA target sites by PAR-CLIP. Cell 141(1):129-141
51. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384-388
52. Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL, Clark SJ, Kjems J (2011) miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J 30(21):4414-4422
53. Harding KW, Gellon G, McGinnis N, McGinnis W (1995) A screen for modifiers of deformed function in Drosophila. Genetics 140(4):1339-1352
54. Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S (2010) The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev Cell 19(3):469-476
55. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW (2008) The antisense transcriptomes of human cells. Science 322(5909):1855-1857
56. Hendrich BD, Brown CJ, Willard HF (1993) Evolutionary conservation of possible functional domains of the human and murine XIST genes. Hum Mol Genet 2(6):663-672
57. Hoki Y, Kimura N, Kanbayashi M, Amakawa Y, Ohhata T, Sasaki H, Sado T (2009) A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse. Development 136(1):139-146
58. Hong YK, Ontiveros SD, Strauss WM (2000) A revision of the human XIST gene organization and structural comparison with mouse Xist. Mamm Genome 11(3):220-224
59. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M et al (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142(3):409-419
60. Iioka H, Loiselle D, Haystead TA, Macara IG (2011) Efficient detection of RNA-protein interactions using tethered RNAs. Nucleic Acids Res 39(8):e53 Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV, Ried T, Shav-Tal Y, Bertrand E, Singer RH et al (2004) From silencing to gene expression: real-time analysis in single cells. Cell 116(5):683-698
61. Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF, Sharpless NE (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19(2): 141-157
62. Jeon Y, Lee JT (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell 146(1): 119-133
63. Jones BK, Levorse JM, Tilghman SM (1998) Igf2 imprinting does not require its own DNA methylation or H19 RNA. Genes Dev 12(14):2200-2207
64. Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, Rentmeester E, Grosveld F, Grootegoed JA, Gribnau J (2009) RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation. Cell 139(5):999-1011
65. Kalantry S, Mills KC, Yee D, Otte AP, Panning B, Magnuson T (2006) The Polycomb group protein Eed protects the inactive X-chromosome from differentiation-induced reactivation. Nat Cell Biol 8(2):195-202
66. Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg D (2010) Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 24(23):2615-2620
67. Kanhere A, Viiri K, Araujo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW et al (2010) Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell 38(5):675-688
68. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL et al (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830):1484-1488
69. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J et al (2005) Antisense transcription in the mammalian transcriptome. Science 309(5740):1564-1566
70. Keene JD, Komisarow JM, Friedersdorf MB (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1(1):302-307
71. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106(28):11667-11672
72. Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M (2011) A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods 8(7):559-564
73. Kiss T (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J 20(14):3617-3622
74. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S et al (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152(3):570-583
75. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S et al (2011) Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 71(20):6320-6326
76. Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17(7):909-915
77. Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS et al (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4(10):e1000242
78. Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D (2002) Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev 16(22):2893-2905
79. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, Shiekhattar R (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494(7438):497-501
80. Lebedeva S, Jens M, Theil K, Schwanhausser B, Selbach M, Landthaler M, Rajewsky N (2011) Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol Cell 43(3):340-352
81. Lee JT, Davidow LS, Warshawsky D (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21(4):400-404
82. Lee JT, Lu N (1999) Targeted mutagenesis of Tsix leads to nonrandom X inactivation. Cell 99(1):47-57
83. Leung AK, Young AG, Bhutkar A, Zheng GX, Bosson AD, Nielsen CB, Sharp PA (2011) Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol 18(2):237-244
84. Li Y, Altman S (2002) Partial reconstitution of human RNase P in HeLa cells between its RNA subunit with an affinity tag and the intact protein components. Nucleic Acids Res 30(17):3706-3711
85. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X et al (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456(7221):464-469
86. Lyon MF (1998) X-chromosome inactivation: a repeat hypothesis. Cytogenet Cell Genet 80(1-4): 133-137
87. Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J (2011) Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates. Nat Struct Mol Biol 18(2):120-127
88. Maenner S, Blaud M, Fouillen L, Savoye A, Marchand V, Dubois A, Sanglier-Cianferani S, Van Dorsselaer A, Clerc P, Avner P et al (2010a) 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol 8(1):e1000276
89. Maenner S, Blaud M, Fouillen L, Savoye A, Marchand V, Dubois A, Sanglier-Cianferani S, Van Dorsselaer A, Clerc P, Avner P et al (2010b) 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol 8(1):e1000276
90. Maherali N, Sridharan R, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R et al (2007) Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1(1):55-70
91. Mao YS, Sunwoo H, Zhang B, Spector DL (2011) Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol 13(1):95-101
92. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445(7128): 666-670
93. Matouk IJ, DeGroot N, Mezan S, Ayesh S, Abu-lail R, Hochberg A, Galun E (2007) The H19 noncoding RNA is essential for human tumor growth. PLoS One 2(9):e845
94. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333-338
95. Min J, Zhang Y, Xu RM (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17(15):1823-1828
96. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322(5908):1717-1720
97. Navarro P, Chambers I, Karwacki-Neisius V, Chureau C, Morey C, Rougeulle C, Avner P (2008) Molecular coupling of Xist regulation and pluripotency. Science 321(5896):1693-1695
98. Navarro P, Oldfield A, Legoupi J, Festuccia N, Dubois A, Attia M, Schoorlemmer J, Rougeulle C, Chambers I, Avner P (2010) Molecular coupling of Tsix regulation and pluripotency. Nature 468(7322):457-460
99. Navarro P, Pichard S, Ciaudo C, Avner P, Rougeulle C (2005) Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation. Genes Dev 19(12):1474-1484
100. Nesterova TB, Senner CE, Schneider J, Alcayna-Stevens T, Tattermusch A, Hemberger M, Brockdorff N (2011) Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells. Epigenetics Chromatin 4(1):17
101. O'Neill MJ (2005) The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum Mol Genet 14(Spec No 1):R113-R120
102. Ogawa Y, Lee JT (2003) Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol Cell 11(3):731-743
103. Ogawa Y, Sun BK, Lee JT (2008) Intersection of the RNA interference and X-inactivation pathways. Science 320(5881):1336-1341
104. Okamoto I, Otte AP, Allis CD, Reinberg D, Heard E (2004) Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303(5658):644-649
105. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H et al (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420(6915):563-573
106. Okutsu T, Kuroiwa Y, Kagitani F, Kai M, Aisaka K, Tsutsumi O, Kaneko Y, Yokomori K, Surani MA, Kohda T et al (2000) Expression and imprinting status of human PEG8/IGF2AS, a paternally expressed antisense transcript from the IGF2 locus, in Wilms' tumors. J Biochem 127(3):475-483
107. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143(1):46-58
108. Pageau GJ, Hall LL, Ganesan S, Livingston DM, Lawrence JB (2007) The disappearing Barr body in breast and ovarian cancers. Nat Rev Cancer 7(8):628-633
109. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32(2):232-246
110. Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N (1996) Requirement for Xist in X chromosome inactivation. Nature 379(6561):131-137
111. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300(5616):131-135
112. Popova BC, Tada T, Takagi N, Brockdorff N, Nesterova TB (2006) Attenuated spread of X-inactivation in an X;autosome translocation. Proc Natl Acad Sci U S A 103(20):7706-7711
113. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH (2008) RNA exosome depletion reveals transcription upstream of active human promoters. Science 322(5909):1851-1854
114. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5(10):877-879
115. Rastan S (1983) Non-random X-chromosome inactivation in mouse X-autosome translocation embryos-location of the inactivation centre. J Embryol Exp Morphol 78:1-22
116. Rastan S, Robertson EJ (1985) X-chromosome deletions in embryo-derived (EK) cell lines associated with lack of X-chromosome inactivation. J Embryol Exp Morphol 90:379-388
117. Riley KJ, Steitz JA (2013) The "Observer Effect" in genome-wide surveys of protein-RNA interactions. Mol Cell 49(4):601-604
118. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145-166
119. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311-1323
120. Royce-Tolland ME, Andersen AA, Koyfman HR, Talbot DJ, Wutz A, Tonks ID, Kay GF, Panning B (2010) The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation. Nat Struct Mol Biol 17(8):948-954
121. Sado T, Hoki Y, Sasaki H (2005) Tsix silences Xist through modification of chromatin structure. Dev Cell 9(1):159-165
122. Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, Person RE, Garnica A, Cheung SW, Beaud AL, et al (2008) Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet 40(6):719-721
123. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146(3):353-358
124. Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7(2):e30733
125. Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y (2009) Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res 19(3):381-394
126. Sarma K, Levasseur P, Aristarkhov A, Lee JT (2010) Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. Proc Natl Acad Sci U S A 107(51):22196-22201
127. Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24(20):2264-2269
128. Schoeftner S, Sengupta AK, Kubicek S, Mechtler K, Spahn L, Koseki H, Jenuwein T, Wutz A (2006) Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J 25(13):3110-3122
129. Schor IE, Lleres D, Risso GJ, Pawellek A, Ule J, Lamond AI, Kornblihtt AR (2012) Perturbation of chromatin structure globally affects localization and recruitment of splicing factors. PLoS One 7(11):e48084
130. Shamovsky I, Ivannikov M, Kandel ES, Gershon D, Nudler E (2006) RNA-mediated response to heat shock in mammalian cells. Nature 440(7083):556-560
131. Shibata S, Lee JT (2003) Characterization and quantitation of differential Tsix transcripts: implications for Tsix function. Hum Mol Genet 12(2):125-136
132. Shin J, Bossenz M, Chung Y, Ma H, Byron M, Taniguchi-Ishigaki N, Zhu X, Jiao B, Hall LL, Green MR et al (2010) Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice. Nature 467(7318):977-981
133. Silva J, Mak W, Zvetkova I, Appanah R, Nesterova TB, Webster Z, Peters AH, Jenuwein T, Otte AP, Brockdorff N (2003) Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev Cell 4(4):481-495
134. Simon JA, Kingston RE (2013) Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell 49(5):808-824
135. Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE (2011) The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci U S A 108(51):20497-20502
136. Srisawat C, Engelke DR (2001) Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA 7(4):632-641
137. Srisawat C, Goldstein IJ, Engelke DR (2001) Sephadex-binding RNA ligands: rapid affinity purifi cation of RNA from complex RNA mixtures. Nucleic Acids Res 29(2):E4
138. Sun BK, Deaton AM, Lee JT (2006) A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell 21(5):617-628
139. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19(3):347-359
140. Surralles J, Natarajan AT (1998) Position effect of translocations involving the inactive X chromosome: physical linkage to XIC/XIST does not lead to long-range de novo inactivation in human differentiated cells. Cytogenet Cell Genet 82(1-2):58-66
141. Tian D, Sun S, Lee JT (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143(3):390-403
142. Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, Konig J, Hortobagyi T, Nishimura AL, Zupunski V et al (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci 14(4):452-458
143. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39(6):925-938
144. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992):689-693
145. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302(5648):1212-1215
146. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147(7):1537-1550
147. Urlaub H, Hartmuth K, Luhrmann R (2002) A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles. Methods 26(2):170-181
148. Vasudevan S, Steitz JA (2007) AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128(6):1105-1118
149. Walker SC, Scott FH, Srisawat C, Engelke DR (2008) RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. Methods Mol Biol 488:23-40
150. Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, Zhang Y (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431(7010):873-878
151. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120-124
152. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454(7200):126-130
153. Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J (2010) iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biol 8(10):e1000530
154. Wilusz JE, Freier SM, Spector DL (2008) 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135(5):919-932
155. Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA (2012) A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26(21): 2392-2407
156. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23:1494-1504
157. Wutz A, Rasmussen TP, Jaenisch R (2002) Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 30(2):167-174
158. Xu M, Medvedev S, Yang J, Hecht NB (2009) MIWI-independent small RNAs (MSY-RNAs) bind to the RNA-binding protein, MSY2, in male germ cells. Proc Natl Acad Sci U S A 106(30):12371-12376
159. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL (2011a) Genomewide characterization of non-polyadenylated RNAs. Genome Biol 12(2):R16
160. Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, Dorrestein PC, Rosenfeld MG (2011b) ncRNA-and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147(4):773-788
161. Yao H, Brick K, Evrard Y, Xiao T, Camerini-Otero RD, Felsenfeld G (2010) Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 24(22):2543-2555
162. Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38(5):662-674
163. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH (2009) An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16(2):130-137
164. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT (2013) Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 152(4):727-742
165. Yin QF, Yang L, Zhang Y, Xiang JF, Wu YW, Carmichael GG, Chen LL (2012) Long noncoding RNAs with snoRNA ends. Mol Cell 48(2):219-230
166. Yu BD, Hess JL, Horning SE, Brown GA, Korsmeyer SJ (1995) Altered Hox expression and segmental identity in Mll-mutant mice. Nature 378(6556):505-508
167. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451(7175):202-206
168. Zarnack K, Konig J, Tajnik M, Martincorena I, Eustermann S, Stevant I, Reyes A, Anders S, Luscombe NM, Ule J (2013) Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152(3):453-466
169. Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB (2010) Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science 329(5990):439-443
170. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40(6):939-953
171. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322(5902):750-756
172. Zhou W, Zhu P, Wang J, Pascual G, Ohgi KA, Lozach J, Glass CK, Rosenfeld MG (2008) Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol Cell 29(1):69-80
173. Zhou Z, Licklider LJ, Gygi SP, Reed R (2002) Comprehensive proteomic analysis of the human spliceosome. Nature 419(6903):182-185
174. Zhu S, Zhang X-O, Yang L (2013) Panning for Long Noncoding RNAs. Biomolecules 3(1):226-241
175. Zuo T, Wang L, Morrison C, Chang X, Zhang H, Li W, Liu Y, Wang Y, Liu X, Chan MW et al (2007) FOXP3 is an X-linked breast cancer suppressor gene and an important repressor of the HER-2/ErbB2 oncogene. Cell 129(7):1275-1286
176. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW (2010) Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol 17(2):173-179