Regulation of mammalian transcription and splicing by Nuclear RNAi

Nucleic Acids Research

Volumn 44, Issue 2, 2016, Pages 524-537

  Kalantari, Roya ^a   Chiang, Cheng Ming ^a,b   Corey, David R ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE PROTEIN; HISTONE; NUCLEAR RNA; RIBONUCLEOPROTEIN; TRANSCRIPTION FACTOR; AUTOANTIGEN; AUTOANTIGEN GW182, HUMAN; DEAD BOX PROTEIN; DICER1 PROTEIN, HUMAN; EIF2C1 PROTEIN, HUMAN; INITIATION FACTOR; MICRORNA; NCOA6 PROTEIN, HUMAN; NUCLEAR RECEPTOR COACTIVATOR; PROTEIN BINDING; RIBONUCLEASE III; RNA BINDING PROTEIN; SMALL INTERFERING RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CELL NUCLEUS; COMPLEX FORMATION; GENE EXPRESSION REGULATION; HUMAN; MAMMAL; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; RNA BINDING; RNA INTERFERENCE; RNA SPLICING; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; ANIMAL; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; PLANT; SCHIZOSACCHAROMYCES;

ANIMALS; ARGONAUTE PROTEINS; AUTOANTIGENS; CELL NUCLEUS; DEAD-BOX RNA HELICASES; EUKARYOTIC INITIATION FACTORS; HUMANS; MICRORNAS; NUCLEAR RECEPTOR COACTIVATORS; PLANTS; PROTEIN BINDING; RIBONUCLEASE III; RNA INTERFERENCE; RNA SPLICING; RNA, SMALL INTERFERING; RNA-BINDING PROTEINS; SCHIZOSACCHAROMYCES; TRANSCRIPTION, GENETIC;

EID: 84966335519     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1305     Document Type: Article

References (198)

1. Zhou,H.L., Luo,G., Wise,J.A. and Lou,H. (2014) Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms. Nucleic Acids Res., 42, 701-713.
2. Braunschweig,U., Gueroussov,S., Plocik,A.M., Graveley,B.R. and Blencowe,B.J. (2013) Dynamic integration of splicing within gene regulatory pathways. Cell, 152, 1252-1269.
3. Kornblihtt,A.R., Schor,I.E., Allo,M., Dujardin,G., Petrillo,E. and Munoz,M.J. (2013) Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell. Biol., 14, 153-165.
4. Ipsaro,J.J. and Joshua-Tor,L. (2015) From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat. Struct. Mol. Biol., 22, 20-28.
5. Wilson,R.C. and Doudna,J.A. (2013) Molecular mechanisms of RNA interference. Annu. Rev. Biophys., 42, 217-239.
6. Stark,A., Brennecke,J., Bushati,N., Russell,R.B. and Cohen,S.M. (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′ UTR evolution. Cell, 123, 1133-1146.
7. Elbashir,S.M., Harborth,J., Lendeckel,W., Yalcin,A., Weber,K. and Tuschl,T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
8. Meister,G., Landthaler,M., Patkaniowska,A., Dorsett,Y., Teng,G. and Tuschl,T. (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell, 15, 185-197.
9. Rand,T.A., Ginalski,K., Grishin,N.V. and Wang,X. (2004) Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc. Natl. Acad. Sci. U.S.A., 101, 14385-14389.
10. Liu,J., Carmell,M.A., Rivas,F.V., Marsden,C.G., Thomson,J.M., Song,J.J., Hammond,S.M., Joshua-Tor,L. and Hannon,G.J. (2004)Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305, 1437-1441.
11. Jakymiw,A., Lian,S., Eystathioy,T., Li,S., Satoh,M., Hamel,J.C., Fritzler,M.J. and Chan,E.K. (2005) Disruption of GW bodies impairs mammalian RNA interference. Nat. Cell Biol., 7, 1267-1274.
12. Eulalio,A., Huntzinger,E. and Izaurralde,E. (2008) GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nat. Struct. Mol. Biol., 15, 346-353.
13. Lima,W.F., Prakash,T.P., Murray,H.M., Kinberger,G.A., Li,W., Chappell,A.E., Li,C.S., Murray,S.F., Gaus,H., Seth,P.P. et al. (2012) Single-stranded siRNAs activate RNAi in animals. Cell, 150, 883-894.
14. Ha,M. and Kim,V.N. (2014) Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol., 15, 509-524.
15. Hammond,S.M. (2015) An overview of microRNAs. Adv. Drug Deliv. Rev., 87, 3-14.
16. Jonas,S. and Izaurralde,E. (2015) Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet., 16, 421-433.
17. Meister,G. (2013) Argonaute proteins: functional insights and emerging roles. Nat. Rev. Genet., 14, 447-459.
18. Ruda,V.M., Chandwani,R., Sehgal,A., Bogorad,R.L., Akinc,A., Charisse,K., Tarakhovsky,A., Novobrantseva,T.I. and Koteliansky,V. (2014) The roles of individual mammalian argonautes in RNA interference in vivo. PLoS One, 9, e101749.
19. Liu,J., Rivas,F.V., Wohlschlegel,J., Yates,J.R. 3rd, Parker,R. and Hannon,G.J. (2005) A role for the P-body component GW182 in microRNA function. Nat. Cell Biol., 7, 1261-1266.
20. Meister,G., Landthaler,M., Peters,L., Chen,P.Y., Urlaub,H., Luhrmann,R. and Tuschl,T. (2005) Identification of novel argonaute-associated proteins. Curr. Biol., 15, 2149-2155.
21. Pfaff,J. and Meister,G. (2013) Argonaute and GW182 proteins: an effective alliance in gene silencing. Biochem. Soc. Trans., 41, 855-860.
22. Ui-Tei,K., Nishi,K., Takahashi,T. and Nagasawa,T. (2012) Thermodynamic Control of Small RNA-Mediated Gene Silencing. Front. Genet., 3, 101.
23. Martinez,J., Patkaniowska,A., Urlaub,H., Luhrmann,R. and Tuschl,T. (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563-574.
24. Schirle,N.T. and MacRae,I.J. (2012) The crystal structure of human Argonaute2. Science, 336, 1037-1040.
25. Elkayam,E., Kuhn,C.D., Tocilj,A., Haase,A.D., Greene,E.M., Hannon,G.J. and Joshua-Tor,L. (2012) The structure of human argonaute-2 in complex with miR-20a. Cell, 150, 100-110.
26. Salomon,W.E., Jolly,S.M., Moore,M.J., Zamore,P.D. and Serebrov,V. (2015) Single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides. Cell, 162, 84-95.
27. Holoch,D. and Moazed,D. (2015) RNA-mediated epigenetic regulation of gene expression. Nat. Rev. Genet., 16, 71-84.
28. Creamer,K.M. and Partridge,J.F. (2011) RITS-connecting transcription, RNA interference, and heterochromatin assembly in fission yeast. Wiley Interdiscip. Rev. RNA, 2, 632-646.
29. Rogers,K. and Chen,X. (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell, 25, 2383-2399.
30. Castel,S.E. and Martienssen,R.A. (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Genet., 14, 100-112.
31. Cecere,G. and Grishok,A. (2014) A nuclear perspective on RNAi pathways in metazoans. Biochim. Biophys. Acta, 1839, 223-233.
32. Wassenegger,M., Heimes,S., Riedel,L. and Sanger,H.L. (1994) RNA-directed de novo methylation of genomic sequences in plants. Cell, 76, 567-576.
33. Mette,M.F., Aufsatz,W., van der Winden,J., Matzke,M.A. and Matzke,A.J. (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J., 19, 5194-5201.
34. Zilberman,D., Cao,X. and Jacobsen,S.E. (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299, 716-719.
35. McCue,A.D., Panda,K., Nuthikattu,S., Choudury,S.G., Thomas,E.N. and Slotkin,R.K. (2015) ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. EMBO J., 34, 20-35.
36. Underwood,C.J. and Martienssen,R.A. (2015) Argonautes team up to silence transposable elements in Arabidopsis. EMBO J., 34, 579-580.
37. Duan,C.G., Zhang,H., Tang,K., Zhu,X., Qian,W., Hou,Y.J., Wang,B., Lang,Z., Zhao,Y., Wang,X. et al. (2015) Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation. EMBO J., 34, 581-592.
38. Haag,J.R. and Pikaard,C.S. (2011) Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell. Biol., 12, 483-492.
39. 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.
40. Zhao,Y. and Chen,X. (2014) Noncoding RNAs and DNA methylation in plants. Natl. Sci. Rev., 1, 219-229.
41. Zhu,Y., Rowley,M.J., Bohmdorfer,G. and Wierzbicki,A.T. (2013) A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol. Cell, 49, 298-309.
42. Verdel,A., Jia,S., Gerber,S., Sugiyama,T., Gygi,S., Grewal,S.I. and Moazed,D. (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science, 303, 672-676.
43. Martienssen,R. and Moazed,D. (2015) RNAi and heterochromatin assembly. Cold Spring. Harb. Perspect. Biol., 7, a019323.
44. Wu,L., Mao,L. and Qi,Y. (2012) Roles of dicer-like and argonaute proteins in TAS-derived small interfering RNA-triggered DNA methylation. Plant Physiol., 160, 990-999.
45. Halic,M. and Moazed,D. (2010) Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell, 140, 504-516.
46. Reinhart,B.J. and Bartel,D.P. (2002) Small RNAs correspond to centromere heterochromatic repeats. Science, 297, 1831.
47. Volpe,T.A., Kidner,C., Hall,I.M., Teng,G., Grewal,S.I. and Martienssen,R.A. (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297, 1833-1837.
48. Jia,S., Kobayashi,R. and Grewal,S.I. (2005) Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat. Cell Biol., 7, 1007-1013.
49. Horn,P.J., Bastie,J.N. and Peterson,C.L. (2005) A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev., 19, 1705-1714.
50. Hong,E.J., Villen,J., Gerace,E.L., Gygi,S.P. and Moazed,D. (2005) A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol., 2, 106-111.
51. Kowalik,K.M., Shimada,Y., Flury,V., Stadler,M.B., Batki,J. and Buhler,M. (2015) The Paf1 complex represses small-RNA-mediated epigenetic gene silencing. Nature, 520, 248-252.
52. Guerin,T.M., Palladino,F. and Robert,V.J. (2014) Transgenerational functions of small RNA pathways in controlling gene expression in C. elegans. Epigenetics, 9, 37-44.
53. Knight,S.W. and Bass,B.L. (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science, 293, 2269-2271.
54. Grishok,A., Pasquinelli,A.E., Conte,D., Li,N., Parrish,S., Ha,I., Baillie,D.L., Fire,A., Ruvkun,G. and Mello,C.C. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23-34.
55. Ketting,R.F., Fischer,S.E., Bernstein,E., Sijen,T., Hannon,G.J. and Plasterk,R.H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev., 15, 2654-2659.
56. Gu,W., Shirayama,M., Conte,D. Jr, Vasale,J., Batista,P.J., Claycomb,J.M., Moresco,J.J., Youngman,E.M., Keys,J., Stoltz,M.J. et al. (2009) Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol. Cell, 36, 231-244.
57. Guang,S., Bochner,A.F., Pavelec,D.M., Burkhart,K.B., Harding,S., Lachowiec,J. and Kennedy,S. (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science, 321, 537-541.
58. Guang,S., Bochner,A.F., Burkhart,K.B., Burton,N., Pavelec,D.M. and Kennedy,S. (2010) Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature, 465, 1097-1101.
59. Gu,S.G., Pak,J., Guang,S., Maniar,J.M., Kennedy,S. and Fire,A. (2012) Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint. Nat. Genet., 44, 157-164.
60. Burkhart,K.B., Guang,S., Buckley,B.A., Wong,L., Bochner,A.F. and Kennedy,S. (2011) A pre-mRNA-associating factor links endogenous siRNAs to chromatin regulation. PLoS Genet., 7, e1002249.
61. Burton,N.O., Burkhart,K.B. and Kennedy,S. (2011) Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A., 108, 19683-19688.
62. Zeng,Y. and Cullen,B.R. (2002) RNA interference in human cells is restricted to the cytoplasm. RNA, 8, 855-860.
63. Vickers,T.A., Koo,S., Bennett,C.F., Crooke,S.T., Dean,N.M. and Baker,B.F. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem., 278, 7108-7118.
64. Stalder,L., Heusermann,W., Sokol,L., Trojer,D., Wirz,J., Hean,J., Fritzsche,A., Aeschimann,F., Pfanzagl,V., Basselet,P. et al. (2013) The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing. EMBO J., 32, 1115-1127.
65. Ikeda,K., Satoh,M., Pauley,K.M., Fritzler,M.J., Reeves,W.H. and Chan,E.K. (2006) Detection of the argonaute protein Ago2 and microRNAs in the RNA induced silencing complex (RISC) using a monoclonal antibody. J. Immunol. Methods, 317, 38-44.
66. Sen,G.L. and Blau,H.M. (2005) Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat. Cell Biol., 7, 633-636.
67. Morris,K.V., Chan,S.W., Jacobsen,S.E. and Looney,D.J. (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science, 305, 1289-1292.
68. Kawasaki,H. and Taira,K. (2004) Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 431, 211-217.
69. Ting,A.H., Schuebel,K.E., Herman,J.G. and Baylin,S.B. (2005) Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat. Genet., 37, 906-910.
70. Taira,K. (2006) Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature, 441, 1176.
71. Robb,G.B., Brown,K.M., Khurana,J. and Rana,T.M. (2005) Specific and potent RNAi in the nucleus of human cells. Nat. Struct. Mol. Biol., 12, 133-137.
72. Ohrt,T., Mutze,J., Staroske,W., Weinmann,L., Hock,J., Crell,K., Meister,G. and Schwille,P. (2008) Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Res., 36, 6439-6449.
73. Rudel,S., Flatley,A., Weinmann,L., Kremmer,E. and Meister,G. (2008) A multifunctional human Argonaute2-specific monoclonal antibody. RNA, 14, 1244-1253.
74. Wei,Y., Li,L., Wang,D., Zhang,C.Y. and Zen,K. (2014) Importin 8 regulates the transport of mature microRNAs into the cell nucleus. J. Biol. Chem., 289, 10270-10275.
75. Weinmann,L., Hock,J., Ivacevic,T., Ohrt,T., Mutze,J., Schwille,P., Kremmer,E., Benes,V., Urlaub,H. and Meister,G. (2009) Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell, 136, 496-507.
76. Till,S., Lejeune,E., Thermann,R., Bortfeld,M., Hothorn,M., Enderle,D., Heinrich,C., Hentze,M.W. and Ladurner,A.G. (2007) A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain. Nat. Struct. Mol. Biol., 14, 897-903.
77. Nishi,K., Nishi,A., Nagasawa,T. and Ui-Tei,K. (2013) Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus. RNA, 19, 17-35.
78. Schraivogel,D., Schindler,S.G., Danner,J., Kremmer,E., Pfaff,J., Hannus,S., Depping,R. and Meister,G. (2015) Importin-beta facilitates nuclear import of human GW proteins and balances cytoplasmic gene silencing protein levels. Nucleic Acids Res., 43, 7447-7461.
79. Pfaff,J., Hennig,J., Herzog,F., Aebersold,R., Sattler,M., Niessing,D. and Meister,G. (2013) Structural features of Argonaute-GW182 protein interactions. Proc. Natl. Acad. Sci. U.S.A., 110, E3770-E3779.
80. White,E., Schlackow,M., Kamieniarz-Gdula,K., Proudfoot,N.J. and Gullerova,M. (2014) Human nuclear Dicer restricts the deleterious accumulation of endogenous double-stranded RNA. Nat. Struct. Mol. Biol., 21, 552-559.
81. Hirsch,M. and Helm,M. (2015) Live cell imaging of duplex siRNA intracellular trafficking. Nucleic Acids Res., 43, 4650-4660.
82. Gagnon,K.T., Li,L., Chu,Y., Janowski,B.A. and Corey,D.R. (2014) RNAi factors are present and active in human cell nuclei. Cell Rep., 6, 211-221.
83. Gagnon,K.T., Li,L., Janowski,B.A. and Corey,D.R. (2014) Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat. Protoc., 9, 2045-2060.
84. Matsui,M., Li,L., Janowski,B.A. and Corey,D.R. (2015) Reduced expression of argonaute 1, argonaute 2, and TRBP changes levels and intracellular distribution of RNAi factors. Sci. Rep., 5, 12855.
85. Hauptmann,J., Schraivogel,D., Bruckmann,A., Manickavel,S., Jakob,L., Eichner,N., Pfaff,J., Urban,M., Sprunck,S., Hafner,M. et al. (2015) Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc. Natl. Acad. Sci. U.S.A., 112, 11841-11845.
86. Behlke,K.A.L.M.A. (2015) Cellular localization affects knockdown efficiency of long non-coding RNAs. Nucleic Acids Res., doi:10.1093/nar/gkv1206.
87. Gao,M., Wei,W., Li,M.M., Wu,Y.S., Ba,Z., Jin,K.X., Liao,Y.Q., Adhikari,S., Chong,Z., Zhang,T. et al. (2014) Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination. Cell Res., 24, 532-541.
88. d'Adda di Fagagna,F. (2014) A direct role for small non-coding RNAs in DNA damage response. Trends Cell Biol., 24, 171-178.
89. Michalik,K.M., Bottcher,R. and Forstemann,K. (2012) A small RNA response at DNA ends in Drosophila. Nucleic Acids Res., 40, 9596-9603.
90. Francia,S., Michelini,F., Saxena,A., Tang,D., de Hoon,M., Anelli,V., Mione,M., Carninci,P. and d'Adda di Fagagna,F. (2012) Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature, 488, 231-235.
91. Castanotto,D., Tommasi,S., Li,M., Li,H., Yanow,S., Pfeifer,G.P. and Rossi,J.J. (2005) Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol. Ther., 12, 179-183.
92. Janowski,B.A., Kaihatsu,K., Huffman,K.E., Schwartz,J.C., Ram,R., Hardy,D., Mendelson,C.R. and Corey,D.R. (2005) Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nat. Chem. Biol., 1, 210-215.
93. Janowski,B.A., Huffman,K.E., Schwartz,J.C., Ram,R., Hardy,D., Shames,D.S., Minna,J.D. and Corey,D.R. (2005) Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat. Chem. Biol., 1, 216-222.
94. Cho,S., Park,J.S. and Kang,Y.K. (2014) AGO2 and SETDB1 cooperate in promoter-targeted transcriptional silencing of the androgen receptor gene. Nucleic Acids Res., 42, 13545-13556.
95. Roberts,T.C., Hart,J.R., Kaikkonen,M.U., Weinberg,M.S., Vogt,P.K. and Morris,K.V. (2015) Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nat. Protoc., 10, 1198-1211.
96. Napoli,S., Pastori,C., Magistri,M., Carbone,G.M. and Catapano,C.V. (2009) Promoter-specific transcriptional interference and c-myc gene silencing by siRNAs in human cells. EMBO J., 28, 1708-1719.
97. Zhang,M.X., Ou,H., Shen,Y.H., Wang,J., Coselli,J. and Wang,X.L. (2005) Regulation of endothelial nitric oxide synthase by small RNA. Proc. Natl. Acad. Sci. U.S.A., 102, 16967-16972.
98. Hawkins,P.G., Santoso,S., Adams,C., Anest,V. and Morris,K.V. (2009) Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res., 37, 2984-2995.
99. Roberts,T.C., Andaloussi,S.E., Morris,K.V., McClorey,G. and Wood,M.J. (2012) Small RNA-mediated epigenetic myostatin silencing. Mol. Ther. Nucleic Acids, 1, e23.
100. Weinberg,M.S., Villeneuve,L.M., Ehsani,A., Amarzguioui,M., Aagaard,L., Chen,Z.X., Riggs,A.D., Rossi,J.J. and Morris,K.V. (2006) The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA, 12, 256-262.
101. Suzuki,K., Shijuuku,T., Fukamachi,T., Zaunders,J., Guillemin,G., Cooper,D. and Kelleher,A. (2005) Prolonged transcriptional silencing and CpG methylation induced by siRNAs targeted to the HIV-1 promoter region. J. RNAi Gene Silencing, 1, 66-78.
102. Mendez,C., Ahlenstiel,C.L. and Kelleher,A.D. (2015) Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J. Virol., 4, 219-244.
103. Lim,J.W., Snider,L., Yao,Z., Tawil,R., Van Der Maarel,S.M., Rigo,F., Bennett,C.F., Filippova,G.N. and Tapscott,S.J. (2015) DICER/AGO-dependent epigenetic silencing of D4Z4 repeats enhanced by exogenous siRNA suggests mechanisms and therapies for FSHD. Hum. Mol. Genet., 24, 4817-4828.
104. Turunen,M.P., Husso,T., Musthafa,H., Laidinen,S., Dragneva,G., Laham-Karam,N., Honkanen,S., Paakinaho,A., Laakkonen,J.P., Gao,E. et al. (2014) Epigenetic upregulation of endogenous VEGF-A reduces myocardial infarct size in mice. PLoS One, 9, e89979.
105. Reebye,V., Saetrom,P., Mintz,P.J., Huang,K.W., Swiderski,P., Peng,L., Liu,C., Liu,X., Lindkaer-Jensen,S., Zacharoulis,D. et al. (2014) Novel RNA oligonucleotide improves liver function and inhibits liver carcinogenesis in vivo. Hepatology, 59, 216-227.
106. Lee,A.Y. and Chiang,C.M. (2009) Chromatin adaptor Brd4 modulates E2 transcription activity and protein stability. J. Biol. Chem., 284, 2778-2786.
107. Mao,C.D. and Byers,S.W. (2011) Cell-context dependent TCF/LEF expression and function: alternative tales of repression, de-repression and activation potentials. Crit. Rev. Eukaryot. Gene Expr., 21, 207-236.
108. Schlereth,K., Heyl,C., Krampitz,A.M., Mernberger,M., Finkernagel,F., Scharfe,M., Jarek,M., Leich,E., Rosenwald,A. and Stiewe,T. (2013) Characterization of the p53 cistrome-DNA binding cooperativity dissects p53's tumor suppressor functions. PLoS Genet., 9, e1003726.
109. Kamachi,Y. and Kondoh,H. (2013) Sox proteins: regulators of cell fate specification and differentiation. Development, 140, 4129-4144.
110. Gow,C.H., Guo,C., Wang,D., Hu,Q. and Zhang,J. (2014) Differential involvement of E2A-corepressor interactions in distinct leukemogenic pathways. Nucleic Acids Res., 42, 137-152.
111. Yoshida,H., Hirano,K., Sato,T., Mitsuda,N., Nomoto,M., Maeo,K., Koketsu,E., Mitani,R., Kawamura,M., Ishiguro,S. et al. (2014) DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins. Proc. Natl. Acad. Sci. U.S.A., 111, 7861-7866.
112. Stonestrom,A.J., Hsu,S.C., Jahn,K.S., Huang,P., Keller,C.A., Giardine,B.M., Kadauke,S., Campbell,A.E., Evans,P., Hardison,R.C. et al. (2015) Functions of BET proteins in erythroid gene expression. Blood, 125, 2825-2834.
113. Shi,Y., Lee,J.S. and Galvin,K.M. (1997) Everything you have ever wanted to know about Yin Yang 1. Biochim. Biophys. Acta, 1332, F49-F66.
114. Weth,O. and Renkawitz,R. (2011) CTCF function is modulated by neighboring DNA binding factors. Biochem. Cell Biol., 89, 459-468.
115. Li,L.C., Okino,S.T., Zhao,H., Pookot,D., Place,R.F., Urakami,S., Enokida,H. and Dahiya,R. (2006) Small dsRNAs induce transcriptional activation in human cells. Proc. Natl. Acad. Sci. U.S.A., 103, 17337-17342.
116. Weinberg,M.S. and Morris,K.V. (2013) Long non-coding RNA targeting and transcriptional de-repression. Nucleic Acid Ther., 23, 9-14.
117. Huang,V., Qin,Y., Wang,J., Wang,X., Place,R.F., Lin,G., Lue,T.F. and Li,L.C. (2010) RNAa is conserved in mammalian cells. PLoS One, 5, e8848.
118. Wang,C., Chen,Z., Ge,Q., Hu,J., Li,F., Xu,H., Ye,Z. and Li,L.C. (2014)Up-regulation of p21(WAF1/CIP1) by miRNAs and its implications in bladder cancer cells. FEBS Lett., 588, 4654-4664.
119. Wang,J., Huang,V., Ye,L., Barcena,A., Lin,G., Lue,T.F. and Li,L.C. (2015) Identification of small activating RNAs that enhance endogenous OCT4 expression in human mesenchymal stem cells. Stem Cells Dev., 24, 345-353.
120. Chen,Z., Place,R.F., Jia,Z.J., Pookot,D., Dahiya,R. and Li,L.C. (2008) Antitumor effect of dsRNA-induced p21(WAF1/CIP1) gene activation in human bladder cancer cells. Mol. Cancer Ther., 7, 698-703.
121. Wang,J., Place,R.F., Huang,V., Wang,X., Noonan,E.J., Magyar,C.E., Huang,J. and Li,L.C. (2010) Prognostic value and function of KLF4 in prostate cancer: RNAa and vector-mediated overexpression identify KLF4 as an inhibitor of tumor cell growth and migration. Cancer Res., 70, 10182-10191.
122. Janowski,B.A., Younger,S.T., Hardy,D.B., Ram,R., Huffman,K.E. and Corey,D.R. (2007) Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat. Chem. Biol., 3, 166-173.
123. Watts,J.K., Yu,D., Charisse,K., Montaillier,C., Potier,P., Manoharan,M. and Corey,D.R. (2010) Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters. Nucleic Acids Res., 38, 5242-5259.
124. Matsui,M., Chu,Y., Zhang,H., Gagnon,K.T., Shaikh,S., Kuchimanchi,S., Manoharan,M., Corey,D.R. and Janowski,B.A. (2013) Promoter RNA links transcriptional regulation of inflammatory pathway genes. Nucleic Acids Res., 41, 10086-10109.
125. Matsui,M., Sakurai,F., Elbashir,S., Foster,D.J., Manoharan,M. and Corey,D.R. (2010) Activation of LDL receptor expression by small RNAs complementary to a noncoding transcript that overlaps the LDLR promoter. Chem. Biol., 17, 1344-1355.
126. (2003) Whither RNAi? Nat. Cell Biol., 5, 489-490.
127. Weinberg,M.S., Barichievy,S., Schaffer,L., Han,J. and Morris,K.V. (2007) An RNA targeted to the HIV-1 LTR promoter modulates indiscriminate off-target gene activation. Nucleic Acids Res., 35, 7303-7312.
128. Moses,J., Goodchild,A. and Rivory,L.P. (2010) Intended transcriptional silencing with siRNA results in gene repression through sequence-specific off-targeting. RNA, 16, 430-441.
129. Janowski,B.A., Huffman,K.E., Schwartz,J.C., Ram,R., Nordsell,R., Shames,D.S., Minna,J.D. and Corey,D.R. (2006) Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat. Struct. Mol. Biol., 13, 787-792.
130. Chu,Y., Yue,X., Younger,S.T., Janowski,B.A. and Corey,D.R. (2010) Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter. Nucleic Acids Res., 38, 7736-7748.
131. Zhang,X., Li,H., Burnett,J.C. and Rossi,J.J. (2014) The role of antisense long noncoding RNA in small RNA-triggered gene activation. RNA, 20, 1916-1928.
132. Kim,D.H., Villeneuve,L.M., Morris,K.V. and Rossi,J.J. (2006) Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol., 13, 793-797.
133. Morris,K.V., Santoso,S., Turner,A.M., Pastori,C. and Hawkins,P.G. (2008) Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet., 4, e1000258.
134. Huang,V., Zheng,J., Qi,Z., Wang,J., Place,R.F., Yu,J., Li,H. and Li,L.C. (2013) Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet., 9, e1003821.
135. Toscano-Garibay,J.D. and Aquino-Jarquin,G. (2014) Transcriptional regulation mechanism mediated by miRNA-DNA∗DNA triplex structure stabilized by Argonaute. Biochim. Biophys. Acta, 1839, 1079-1083.
136. Nakama,M., Kawakami,K., Kajitani,T., Urano,T. and Murakami,Y. (2012) DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation. Genes Cells, 17, 218-233.
137. Zhang,Y., Fan,M., Zhang,X., Huang,F., Wu,K., Zhang,J., Liu,J., Huang,Z., Luo,H., Tao,L. et al. (2014) Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs. RNA, 20, 1878-1889.
138. Carninci,P., Kasukawa,T., Katayama,S., Gough,J., Frith,M.C., Maeda,N., Oyama,R., Ravasi,T., Lenhard,B., Wells,C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
139. Kapranov,P., Cheng,J., Dike,S., Nix,D.A., Duttagupta,R., Willingham,A.T., Stadler,P.F., Hertel,J., Hackermuller,J., Hofacker,I.L. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316, 1484-1488.
140. Yelin,R., Dahary,D., Sorek,R., Levanon,E.Y., Goldstein,O., Shoshan,A., Diber,A., Biton,S., Tamir,Y., Khosravi,R. et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol., 21, 379-386.
141. Katayama,S., Tomaru,Y., Kasukawa,T., Waki,K., Nakanishi,M., Nakamura,M., Nishida,H., Yap,C.C., Suzuki,M., Kawai,J. et al. (2005) Antisense transcription in the mammalian transcriptome. Science, 309, 1564-1566.
142. Morris,K.V. and Mattick,J.S. (2014) The rise of regulatory RNA. Nat. Rev. Genet., 15, 423-437.
143. Schwartz,J.C., Younger,S.T., Nguyen,N.B., Hardy,D.B., Monia,B.P., Corey,D.R. and Janowski,B.A. (2008) Antisense transcripts are targets for activating small RNAs. Nat. Struct. Mol. Biol., 15, 842-848.
144. Sanyal,A., Lajoie,B.R., Jain,G. and Dekker,J. (2012) The long-range interaction landscape of gene promoters. Nature, 489, 109-113.
145. Zong,X., Huang,L., Tripathi,V., Peralta,R., Freier,S.M., Guo,S. and Prasanth,K.V. (2015) Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides. Methods Mol. Biol., 1262, 321-331.
146. Wang,Y., Juranek,S., Li,H., Sheng,G., Tuschl,T. and Patel,D.J. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature, 456, 921-926.
147. Bassett,A.R., Akhtar,A., Barlow,D.P., Bird,A.P., Brockdorff,N., Duboule,D., Ephrussi,A., Ferguson-Smith,A.C., Gingeras,T.R., Haerty,W. et al. (2014) Considerations when investigating lncRNA function in vivo. Elife, 3, e03058.
148. Dodd,D.W., Gagnon,K.T. and Corey,D.R. (2013) Digital quantitation of potential therapeutic target RNAs. Nucleic Acids Ther., 23, 188-194.
149. Woolnough,J.L., Atwood,B.L. and Giles,K.E. (2015) Argonaute 2 binds directly to tRNA genes and promotes gene repression in cis. Mol. Cell. Biol., 35, 2278-2294.
150. Grewal,S.I. and Moazed,D. (2003) Heterochromatin and epigenetic control of gene expression. Science, 301, 798-802.
151. Thomas,M.C. and Chiang,C.M. (2006) The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol., 41, 105-178.
152. Venters,B.J. and Pugh,B.F. (2009) How eukaryotic genes are transcribed. Crit. Rev. Biochem. Mol. Biol., 44, 117-141.
153. Core,L.J., Martins,A.L., Danko,C.G., Waters,C.T., Siepel,A. and Lis,J.T. (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet., 46, 1311-1320.
154. Thomas,M.C. and Chiang,C.M. (2005) E6 oncoprotein represses p53-dependent gene activation via inhibition of protein acetylation independently of inducing p53 degradation. Mol. Cell, 17, 251-264.
155. Mulligan,P., Westbrook,T.F., Ottinger,M., Pavlova,N., Chang,B., Macia,E., Shi,Y.J., Barretina,J., Liu,J., Howley,P.M. et al. (2008) CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation. Mol. Cell, 32, 718-726.
156. Jeon,Y. and Lee,J.T. (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell, 146, 119-133.
157. Jain,A.K., Allton,K., Iacovino,M., Mahen,E., Milczarek,R.J., Zwaka,T.P., Kyba,M. and Barton,M.C. (2012) p53 regulates cell cycle and microRNAs to promote differentiation of human embryonic stem cells. PLoS Biol., 10, e1001268.
158. Wen,H., Li,Y., Xi,Y., Jiang,S., Stratton,S., Peng,D., Tanaka,K., Ren,Y., Xia,Z., Wu,J. et al. (2014) ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature, 508, 263-268.
159. Rauwel,B., Jang,S.M., Cassano,M., Kapopoulou,A., Barde,I. and Trono,D. (2015) Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch. Elife, 4, doi:10.7554/eLife.06068.
160. Hou,S.Y., Wu,S.Y., Zhou,T., Thomas,M.C. and Chiang,C.M. (2000) Alleviation of human papillomavirus E2-mediated transcriptional repression via formation of a TATA binding protein (or TFIID)-TFIIB-RNA polymerase II-TFIIF preinitiation complex. Mol. Cell. Biol., 20, 113-125.
161. Bourdon,J.C., Fernandes,K., Murray-Zmijewski,F., Liu,G., Diot,A., Xirodimas,D.P., Saville,M.K. and Lane,D.P. (2005) p53 isoforms can regulate p53 transcriptional activity. Genes Dev., 19, 2122-2137.
162. Wang,W.M., Wu,S.Y., Lee,A.Y. and Chiang,C.M. (2011) Binding site specificity and factor redundancy in activator protein-1-driven human papillomavirus chromatin-dependent transcription. J. Biol. Chem., 286, 40974-40986.
163. Wu,S.Y. and Chiang,C.M. (2007) The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J. Biol. Chem., 282, 13141-13145.
164. Agalioti,T., Lomvardas,S., Parekh,B., Yie,J., Maniatis,T. and Thanos,D. (2000) Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell, 103, 667-678.
165. Roe,J.S., Mercan,F., Rivera,K., Pappin,D.J. and Vakoc,C.R. (2015) BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell, 58, 1028-1039.
166. Shi,J., Wang,Y., Zeng,L., Wu,Y., Deng,J., Zhang,Q., Lin,Y., Li,J., Kang,T., Tao,M. et al. (2014) Disrupting the interaction of BRD4 with diacetylated Twist suppresses tumorigenesis in basal-like breast cancer. Cancer Cell, 25, 210-225.
167. Li,W., Hu,Y., Oh,S., Ma,Q., Merkurjev,D., Song,X., Zhou,X., Liu,Z., Tanasa,B., He,X. et al. (2015) Condensin I and II complexes license full estrogen receptor alpha-dependent enhancer Activation. Mol. Cell, 59, 188-202.
168. Sahu,G., Wang,D., Chen,C.B., Zhurkin,V.B., Harrington,R.E., Appella,E., Hager,G.L. and Nagaich,A.K. (2010) p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element. J. Biol. Chem., 285, 1321-1332.
169. Kaneko,S., Son,J., Bonasio,R., Shen,S.S. and Reinberg,D. (2014) Nascent RNA interaction keeps PRC2 activity poised and in check. Genes Dev., 28, 1983-1988.
170. Hojfeldt,J.W., Van Dyke,A.R. and Mapp,A.K. (2011) Transforming ligands into transcriptional regulators: building blocks for bifunctional molecules. Chem. Soc. Rev., 40, 4286-4294.
171. Jiao,A.L. and Slack,F.J. (2014) RNA-mediated gene activation. Epigenetics, 9, 27-36.
172. Liao,J.Y., Ma,L.M., Guo,Y.H., Zhang,Y.C., Zhou,H., Shao,P., Chen,Y.Q. and Qu,L.H. (2010) Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3′ trailers. PLoS One, 5, e10563.
173. Jeffries,C.D., Fried,H.M. and Perkins,D.O. (2011) Nuclear and cytoplasmic localization of neural stem cell microRNAs. RNA, 17, 675-686.
174. Roberts,T.C. (2014) The MicroRNA biology of the mammalian nucleus. Mol. Ther. Nucleic Acids, 3, e188.
175. Hwang,H.W., Wentzel,E.A. and Mendell,J.T. (2007) A hexanucleotide element directs microRNA nuclear import. Science, 315, 97-100.
176. Chu,Y., Wang,T., Dodd,D., Xie,Y., Janowski,B.A. and Corey,D.R. (2015) Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells. Nucleic Acids Res., 43, e75.
177. Portnoy,V., Huang,V., Place,R.F. and Li,L.C. (2011) Small RNA and transcriptional upregulation. Wiley Interdiscip. Rev. RNA, 2, 748-760.
178. Salmanidis,M., Pillman,K., Goodall,G. and Bracken,C. (2014) Direct transcriptional regulation by nuclear microRNAs. Int. J. Biochem. Cell Biol., 54, 304-311.
179. Place,R.F., Li,L.C., Pookot,D., Noonan,E.J. and Dahiya,R. (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl. Acad. Sci. U.S.A., 105, 1608-1613.
180. Kim,D.H., Saetrom,P., Snove,O. Jr and Rossi,J.J. (2008) MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl. Acad. Sci. U.S.A., 105, 16230-16235.
181. Huang,V., Place,R.F., Portnoy,V., Wang,J., Qi,Z., Jia,Z., Yu,A., Shuman,M., Yu,J. and Li,L.C. (2012)Upregulation of Cyclin B1 by miRNA and its implications in cancer. Nucleic Acids Res., 40, 1695-1707.
182. Younger,S.T. and Corey,D.R. (2011) Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters. Nucleic Acids Res., 39, 5682-5691.
183. Naftelberg,S., Schor,I.E., Ast,G. and Kornblihtt,A.R. (2015) Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu. Rev. Biochem., 84, 165-198.
184. Allo,M., Buggiano,V., Fededa,J.P., Petrillo,E., Schor,I., de la Mata,M., Agirre,E., Plass,M., Eyras,E., Elela,S.A. et al. (2009) Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol., 16, 717-724.
185. Allo,M., Agirre,E., Bessonov,S., Bertucci,P., Gomez Acuna,L., Buggiano,V., Bellora,N., Singh,B., Petrillo,E., Blaustein,M. et al. (2014) Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. Proc. Natl. Acad. Sci. U.S.A., 111, 15622-15629.
186. Ameyar-Zazoua,M., Rachez,C., Souidi,M., Robin,P., Fritsch,L., Young,R., Morozova,N., Fenouil,R., Descostes,N., Andrau,J.C. et al. (2012) Argonaute proteins couple chromatin silencing to alternative splicing. Nat. Struct. Mol. Biol., 19, 998-1004.
187. Batsche,E. and Ameyar-Zazoua,M. (2015)The influence of Argonaute proteins on alternative RNA splicing. Wiley Interdiscip. Rev. RNA, 6, 141-156.
188. Agirre,E., Bellora,N., Allo,M., Pages,A., Bertucci,P., Kornblihtt,A.R. and Eyras,E. (2015) A chromatin code for alternative splicing involving a putative association between CTCF and HP1alpha proteins. BMC Biol., 13, 31.
189. Arechavala-Gomeza,V., Graham,I.R., Popplewell,L.J., Adams,A.M., Aartsma-Rus,A., Kinali,M., Morgan,J.E., van Deutekom,J.C., Wilton,S.D., Dickson,G. et al. (2007) Comparative analysis of antisense oligonucleotide sequences for targeted skipping of exon 51 during dystrophin pre-mRNA splicing in human muscle. Hum. Gene Ther., 18, 798-810.
190. Aartsma-Rus,A., Janson,A.A., Kaman,W.E., Bremmer-Bout,M., den Dunnen,J.T., Baas,F., van Ommen,G.J. and van Deutekom,J.C. (2003) Therapeutic antisense-induced exon skipping in cultured muscle cells from six different DMD patients. Hum. Mol. Genet., 12, 907-914.
191. van Deutekom,J.C., Janson,A.A., Ginjaar,I.B., Frankhuizen,W.S., Aartsma-Rus,A., Bremmer-Bout,M., den Dunnen,J.T., Koop,K., van der Kooi,A.J., Goemans,N.M. et al. (2007) Local dystrophin restoration with antisense oligonucleotide PRO051. N. Engl. J. Med., 357, 2677-2686.
192. Voit,T., Topaloglu,H., Straub,V., Muntoni,F., Deconinck,N., Campion,G., De Kimpe,S.J., Eagle,M., Guglieri,M., Hood,S. et al. (2014) Safety and efficacy of drisapersen for the treatment of Duchenne muscular dystrophy (DEMAND II): an exploratory, randomised, placebo-controlled phase 2 study. Lancet Neuro.l, 13, 987-996.
193. Jarver,P., O'Donovan,L. and Gait,M.J. (2014) A chemical view of oligonucleotides for exon skipping and related drug applications. Nucleic Acids Ther., 24, 37-47.
194. Kang,S.H., Cho,M.J. and Kole,R. (1998) Up-regulation of luciferase gene expression with antisense oligonucleotides: implications and applications in functional assay development. Biochemistry, 37, 6235-6239.
195. Liu,J., Hu,J. and Corey,D.R. (2012) Expanding the action of duplex RNAs into the nucleus: redirecting alternative splicing. Nucleic Acids Res., 40, 1240-1250.
196. Yu,D., Sakurai,F. and Corey,D.R. (2011) Clonal Rett Syndrome cell lines to test compounds for activation of wild-type MeCP2 expression. Bioorg. Med. Chem. Lett., 21, 5202-5205.
197. Liu,J., Hu,J., Hicks,J.A., Prakash,T.P. and Corey,D.R. (2015) Modulation of splicing by single-stranded silencing RNAs. Nucleic Acids Ther., 25, 113-120.
198. Taliaferro,J.M., Aspden,J.L., Bradley,T., Marwha,D., Blanchette,M. and Rio,D.C. (2013) Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. Genes Dev., 27, 378-389.