Diverse functions of nuclear non-coding RNAs in eukaryotic gene expression

Frontiers in Bioscience

Volumn 17, Issue 4, 2012, Pages 1402-1417

  Chinen, Madoka ^a   Tani, Tokio ^a  

^a KUMAMOTO UNIVERSITY   (Japan)

Author keywords

Fission yeast; Gene silencing; Heterochromatin; Non coding RNA; Nucleus; Pre mRNA splicing; Review; RNAi; Transcription

Indexed keywords

EUKARYOTA; SCHIZOSACCHAROMYCETACEAE;

UNTRANSLATED RNA;

ARTICLE; GENE EXPRESSION; GENE SILENCING; GENETIC EPIGENESIS; HETEROCHROMATIN; METABOLISM; PHYSIOLOGY; RNA INTERFERENCE; RNA PROCESSING;

EPIGENESIS, GENETIC; GENE EXPRESSION; GENE SILENCING; HETEROCHROMATIN; RNA INTERFERENCE; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, UNTRANSLATED;

EID: 84859256772     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3994     Document Type: Review

References (100)

1. P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi- Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed : The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559-1563 (2005).
2. P. Kapranov, J. Cheng, S. Dike, D. A. Nix, R. Duttagupta, A. T. Willingham, P. F. Stadler, J. Hertel, J. Hackermuller, I. L. Hofacker, I. Bell, E. Cheung, J. Drenkow, E. Dumais, S. Patel, G. Helt, M. Ganesh, S. Ghosh, A. Piccolboni, V. Sementchenko, H. Tammana and T. R. Gingeras: RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316(5830), 1484-1488 (2007). (Pubitemid 46906616)
3. P. Kapranov, J. Drenkow, J. Cheng, J. Long, G. Helt, S. Dike and T. R. Gingeras: Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res, 15(7), 987-997 (2005). (Pubitemid 40994219)
4. Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, H. Bono, S. Kondo, I. Nikaido, N. Osato, R. Saito, H. Suzuki, I. Yamanaka, H. Kiyosawa, K. Yagi, Y. Tomaru, Y. Hasegawa, A. Nogami, C. Schonbach, T. Gojobori, R. Baldarelli, D. P. Hill, C. Bult, D. A. Hume, J. Quackenbush, L. M. Schriml, A. Kanapin, H. Matsuda, S. Batalov, K. W. Beisel, J. A. Blake, D. Bradt, V. Brusic, C. Chothia, L. E. Corbani, S. Cousins, E. Dalla, T. A. Dragani, C. F. Fletcher, A. Forrest, K. S. Frazer, T. Gaasterland, M. Gariboldi, C. Gissi, A. Godzik, J. Gough, S. Grimmond, S. Gustincich, N. Hirokawa, I. J. Jackson, E. D. Jarvis, A. Kanai, H. Kawaji, Y. Kawasawa, R. M. Kedzierski, B. L. King, A. Konagaya, I. V. Kurochkin, Y. Lee, B. Lenhard, P. A. Lyons, D. R. Maglott, L. Maltais, L. Marchionni, L. McKenzie, H. Miki, T. Nagashima, K. Numata, T. Okido, W. J. Pavan, G. Pertea, G. Pesole, N. Petrovsky, R. Pillai, J. U. Pontius, D. Qi, S. Ramachandran, T. Ravasi, J. C. Reed, D. J. Reed, J. Reid, B. Z. Ring, M. Ringwald, A. Sandelin, C. Schneider, C. A. Semple, M. Setou, K. Shimada, R. Sultana, Y. Takenaka, M. S. Taylor, R. D. Teasdale, M. Tomita, R. Verardo, L. Wagner, C. Wahlestedt, Y. Wang, Y. Watanabe, C. Wells, L. G. Wilming, A. Wynshaw-Boris, M. Yanagisawa, I. Yang, L. Yang, Z. Yuan, M. Zavolan, Y. Zhu, A. Zimmer, P. Carninci, N. Hayatsu, T. Hirozane-Kishikawa, H. Konno, M. Nakamura, N. Sakazume, K. Sato, T. Shiraki, K. Waki, J. Kawai : Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature, 420(6915), 563-573 (2002). (Pubitemid 35477049)
5. E. Birney, et al: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816 (2007). (Pubitemid 46920138)
6. C. P. Ponting, P. L. Oliver and W. Reik: Evolution and functions of long noncoding RNAs. Cell, 136(4), 629-641 (2009).
7. J. Ponjavic, C. P. Ponting and G. Lunter: Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res, 17(5), 556-565 (2007). (Pubitemid 46715505)
8. K. Struhl: Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol, 14(2), 103-105 (2007).
9. K. Hirota, T. Miyoshi, K. Kugou, C. S. Hoffman, T. Shibata and K. Ohta: Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature, 456(7218), 130-134 (2008).
10. T. R. Mercer, M. E. Dinger and J. S. Mattick: Long non-coding RNAs: insights into functions. Nat Rev Genet, 10(3), 155-159 (2009).
11. M. E. Dinger, P. P. Amaral, T. R. Mercer, K. C. Pang, S. J. Bruce, B. B. Gardiner, M. E. Askarian-Amiri, K. Ru, G. Solda, C. Simons, S. M. Sunkin, M. L. Crowe, S. M. Grimmond, A. C. Perkins and J. S. Mattick: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res, 18(9), 1433-1445 (2008).
12. T. R. Mercer, M. E. Dinger, S. M. Sunkin, M. F. Mehler and J. S. Mattick: Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A, 105(2), 716-721 (2008). (Pubitemid 351171774)
13. Y. T. Sasaki, M. Sano, T. Ideue, T. Kin, K. Asai and T. Hirose: Identification and characterization of human noncoding RNAs with tissue-specific expression. Biochem Biophys Res Commun, 357(4), 991-996 (2007). (Pubitemid 46693670)
14. C. B. Burge, T. Tuschl and P. A. Sharp: Splicing of precursors to mRNA by the spliceosome. In: The RNA word. Ed R. F. Gesteland, T. R. Cech&J. F. Atkins. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1999).
15. J. Feng, C. Bi, B. S. Clark, R. Mady, P. Shah and J. D. Kohtz: The Evf-2 noncoding RNA is transcribed from the Dlx- 5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev, 20(11), 1470-1484 (2006). (Pubitemid 43830654)
16. X. Wang, S. Arai, X. Song, D. Reichart, K. Du, G. Pascual, P. Tempst, M. G. Rosenfeld, C. K. Glass and R. Kurokawa: Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature, 454(7200), 126-130 (2008). (Pubitemid 351934270)
17. I. Martianov, A. Ramadass, A. Serra Barros, N. Chow and A. Akoulitchev: Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature, 445(7128), 666-670 (2007). (Pubitemid 46232888)
18. A. R. Morgan and R. D. Wells: Specificity of the threestranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J Mol Biol, 37(1), 63-80 (1968).
19. D. Umlauf, P. Fraser and T. Nagano: The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme. J Biol Chem, 389(4), 323-331 (2008). (Pubitemid 351773916)
20. F. De Lucia and C. Dean: Long non-coding RNAs and chromatin regulation. Curr Opin Plant Biol, 14, 1-6 (2010).
21. J. L. Rinn, M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, J. A. Helms, P. J. Farnham, E. Segal and H. Y. Chang: Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129(7), 1311- 1323 (2007). (Pubitemid 46962090)
22. M. J. Koziol and J. L. Rinn: RNA traffic control of chromatin complexes. Curr Opin Genet Dev, 20(2), 142- 148 (2010).
23. C. Kanduri: Kcnq1ot1: A chromatin regulatory RNA. Semin Cell Dev Biol, in press (2011).
24. N. J. Smilinich, C. D. Day, G. V. Fitzpatrick, G. M. Caldwell, A. C. Lossie, P. R. Cooper, A. C. Smallwood, J. A. Joyce, P. N. Schofield, W. Reik, R. D. Nicholls, R. Weksberg, D. J. Driscoll, E. R. Maher, T. B. Shows and M. J. Higgins: A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc Natl Acad Sci U S A, 96(14), 8064-8069 (1999). (Pubitemid 29328408)
25. F. Mohammad, T. Mondal, N. Guseva, G. K. Pandey and C. Kanduri: Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development, 137(15), 2493-2499 (2010).
26. L. Redrup, M. R. Branco, E. R. Perdeaux, C. Krueger, A. Lewis, F. Santos, T. Nagano, B. S. Cobb, P. Fraser and W. Reik: The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development, 136(4), 525-530 (2009).
27. R. R. Pandey, T. Mondal, F. Mohammad, S. Enroth, L. Redrup, J. Komorowski, T. Nagano, D. Mancini-Dinardo and C. Kanduri: Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell, 32(2), 232-246 (2008).
28. R. Terranova, S. Yokobayashi, M. B. Stadler, A. P. Otte, M. van Lohuizen, S. H. Orkin and A. H. Peters: Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell, 15(5), 668-679 (2008).
29. T. Nagano, J. A. Mitchell, L. A. Sanz, F. M. Pauler, A. C. Ferguson-Smith, R. Feil and P. Fraser: The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science, 322(5908), 1717-1720 (2008).
30. G. D. Penny, G. F. Kay, S. A. Sheardown, S. Rastan and N. Brockdorff: Requirement for Xist in X chromosome inactivation. Nature, 379(6561), 131-137 (1996). (Pubitemid 26020194)
31. M. Leeb, P. A. Steffen and A. Wutz: X chromosome inactivation sparked by non-coding RNAs. RNA Biol, 6(2), 94-99 (2009).
32. J. T. Lee and N. Lu: Targeted mutagenesis of Tsix leads to nonrandom X inactivation. Cell, 99(1), 47-57 (1999). (Pubitemid 29468629)
33. J. Zhao, B. K. Sun, J. A. Erwin, J. J. Song and J. T. Lee: Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science, 322(5902), 750-756 (2008).
34. Y. Ogawa, B. K. Sun and J. T. Lee: Intersection of the RNA interference and X-inactivation pathways. Science, 320(5881), 1336-1341 (2008). (Pubitemid 351929469)
35. C. Kanellopoulou, S. A. Muljo, S. D. Dimitrov, X. Chen, C. Colin, K. Plath and D. M. Livingston: X chromosome inactivation in the absence of Dicer. Proc Natl Acad Sci U S A, 106(4), 1122-1127 (2009).
36. R. Reddy and H. Busch: Small nuclear RNAs: RNA sequences, structure, and modification. In: Structure and function of major and minor small nuclear ribonucleoprotein particles. Ed M. L. Birnstiel. Springer- Verlag, Berlin (1988).
37. C. L. Will and R. Luhrmann: Splicing of a rare class of introns by the U12-dependent spliceosome. J Biol Chem, 386(8), 713-724 (2005). (Pubitemid 41448152)
38. T. Tani, Y. Takahashi and Y. Ohshima: Activity of chimeric RNAs of U6 snRNA and (-)sTRSV in the cleavage of a substrate RNA. Nucleic Acids Res, 20(12), 2991-2996 (1992).
39. S. Valadkhan, A. Mohammadi, Y. Jaladat and S. Geisler: Protein-free small nuclear RNAs catalyze a twostep splicing reaction. Proc Natl Acad Sci U S A, 106(29), 11901-11906 (2009).
40. Y. He, B. Vogelstein, V. E. Velculescu, N. Papadopoulos and K. W. Kinzler: The antisense transcriptomes of human cells. Science, 322(5909), 1855- 1857 (2008).
41. M. Beltran, I. Puig, C. Pena, J. M. Garcia, A. B. Alvarez, R. Pena, F. Bonilla and A. G. de Herreros: A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev, 22(6), 756-769 (2008). (Pubitemid 351439107)
42. V. Tripathi, J. D. Ellis, Z. Shen, D. Y. Song, Q. Pan, A. T. Watt, S. M. Freier, C. F. Bennett, A. Sharma, P. A. Bubulya, B. J. Blencowe, S. G. Prasanth and K. V. Prasanth: The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell, 39(6), 925-938 (2010).
43. B. R. Graveley: Alternative splicing: increasing diversity in the proteomic world. Trends Genet, 17(2), 100-107 (2001). (Pubitemid 32140790)
44. M. L. Anko and K. M. Neugebauer: Long noncoding RNAs add another layer to pre-mRNA splicing regulation. Mol Cell, 39(6), 833-834 (2010).
45. A. T. Willingham, A. P. Orth, S. Batalov, E. C. Peters, B. G. Wen, P. Aza-Blanc, J. B. Hogenesch and P. G. Schultz: A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science, 309(5740), 1570-1573 (2005). (Pubitemid 41266484)
46. M. Dundr and T. Misteli: Functional architecture in the cell nucleus. Biochem J, 356(Pt 2), 297-310 (2001). (Pubitemid 32532339)
47. C. S. Bond and A. H. Fox: Paraspeckles: nuclear bodies built on long noncoding RNA. J Cell Biol, 186(5), 637-644 (2009).
48. L. L. Chen and G. G. Carmichael: Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell, 35(4), 467-478 (2009).
49. K. V. Prasanth, S. G. Prasanth, Z. Xuan, S. Hearn, S. M. Freier, C. F. Bennett, M. Q. Zhang and D. L. Spector: Regulating gene expression through RNA nuclear retention. Cell, 123(2), 249-263 (2005). (Pubitemid 41457215)
50. Y. T. Sasaki, T. Ideue, M. Sano, T. Mituyama and T. Hirose: MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A, 106(8), 2525-2530 (2009).
51. Y. S. Mao, H. Sunwoo, B. Zhang and D. L. Spector: Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol, 13(1), 95- 101 (2011).
52. S. P. Shevtsov and M. Dundr: Nucleation of nuclear bodies by RNA. Nat Cell Biol, 13(2), 167-173 (2011).
53. M. D. Blower, M. Nachury, R. Heald and K. Weis: A Rae1-containing ribonucleoprotein complex is required for mitotic spindle assembly. Cell, 121(2), 223-234 (2005). (Pubitemid 40546390)
54. M. Kloc, K. Wilk, D. Vargas, Y. Shirato, S. Bilinski and L. D. Etkin: Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes. Development, 132(15), 3445-3457 (2005). (Pubitemid 41246119)
55. M. Kloc, S. Bilinski and M. T. Dougherty: Organization of cytokeratin cytoskeleton and germ plasm in the vegetal cortex of Xenopus laevis oocytes depends on coding and non-coding RNAs: three-dimensional and ultrastructural analysis. Exp Cell Res, 313(8), 1639-1651 (2007). (Pubitemid 46589440)
56. S. I. Grewal and S. Jia: Heterochromatin revisited. Nat Rev Genet, 8(1), 35-46 (2007). (Pubitemid 46006048)
57. M. Buhler and D. Moazed: Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol, 14(11), 1041-1048 (2007). (Pubitemid 350060336)
58. D. W. Cleveland, Y. Mao and K. F. Sullivan: Centromeres and kinetochores: from epigenetics to mitotic checkpoint signaling. Cell, 112(4), 407-421 (2003). (Pubitemid 36263076)
59. T. Jenuwein and C. D. Allis: Translating the histone code. Science, 293(5532), 1074-1080 (2001). (Pubitemid 32758077)
60. J. Nakayama, J. C. Rice, B. D. Strahl, C. D. Allis and S. I. Grewal: Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science, 292(5514), 110-113 (2001). (Pubitemid 32289138)
61. M. Lachner, D. O'Carroll, S. Rea, K. Mechtler and T. Jenuwein: Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature, 410(6824), 116-120 (2001). (Pubitemid 32225847)
62. A. J. Bannister, P. Zegerman, J. F. Partridge, E. A. Miska, J. O. Thomas, R. C. Allshire and T. Kouzarides: Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature, 410(6824), 120-124 (2001). (Pubitemid 32225848)
63. P. J. Horn, J. N. Bastie and C. L. Peterson: A Rik1- associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev, 19(14), 1705- 1714 (2005). (Pubitemid 41058366)
64. S. Jia, R. Kobayashi and S. I. Grewal: Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol, 7(10), 1007-1013 (2005). (Pubitemid 41486275)
65. G. Thon, K. R. Hansen, S. P. Altes, D. Sidhu, G. Singh, J. Verhein-Hansen, M. J. Bonaduce and A. J. Klar: The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate heterochromatin formation in the fission yeast Schizosaccharomyces pombe. Genetics, 171(4), 1583-1595 (2005).
66. I. M. Hall, G. D. Shankaranarayana, K. Noma, N. Ayoub, A. Cohen and S. I. Grewal: Establishment and maintenance of a heterochromatin domain. Science, 297(5590), 2232-2237 (2002).
67. M. Grunstein: Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell, 93(3), 325-328 (1998). (Pubitemid 28232076)
68. H. P. Cam, T. Sugiyama, E. S. Chen, X. Chen, P. C. FitzGerald and S. I. Grewal: Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet, 37(8), 809-819 (2005). (Pubitemid 41077106)
69. T. A. Volpe, C. Kidner, I. M. Hall, G. Teng, S. I. Grewal and R. A. Martienssen: Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297(5588), 1833-1837 (2002). (Pubitemid 35024336)
70. M. R. Motamedi, A. Verdel, S. U. Colmenares, S. A. Gerber, S. P. Gygi and D. Moazed: Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell, 119(6), 789-802 (2004). (Pubitemid 40017686)
71. A. Verdel, S. Jia, S. Gerber, T. Sugiyama, S. Gygi, S. I. Grewal and D. Moazed: RNAi-mediated targeting of heterochromatin by the RITS complex. Science, 303(5658), 672-676 (2004). (Pubitemid 38141633)
72. M. Sadaie, T. Iida, T. Urano and J. Nakayama: A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J, 23(19), 3825- 3835 (2004). (Pubitemid 39389713)
73. A. Kloc and R. Martienssen: RNAi, heterochromatin and the cell cycle. Trends Genet, 24(10), 511-517 (2008).
74. S. I. Grewal: RNAi-dependent formation of heterochromatin and its diverse functions. Curr Opin Genet Dev, 20(2), 134-141 (2010).
75. M. Buhler, A. Verdel and D. Moazed: Tethering RITS to a nascent transcript initiates RNAi- and heterochromatindependent gene silencing. Cell, 125(5), 873-886 (2006). (Pubitemid 43795192)
76. K. Noma, T. Sugiyama, H. Cam, A. Verdel, M. Zofall, S. Jia, D. Moazed and S. I. Grewal: RITS acts in cis to promote RNA interference-mediated transcriptional and posttranscriptional silencing. Nat Genet, 36(11), 1174-1180 (2004). (Pubitemid 41288966)
77. V. J. Petrie, J. D. Wuitschick, C. D. Givens, A. M. Kosinski and J. F. Partridge: RNA interference (RNAi)- dependent and RNAi-independent association of the Chp1 chromodomain protein with distinct heterochromatic loci in fission yeast. Mol Cell Biol, 25(6), 2331-2346 (2005). (Pubitemid 40354629)
78. T. Schalch, G. Job, V. J. Noffsinger, S. Shanker, C. Kuscu, L. Joshua-Tor and J. F. Partridge: High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin. Mol Cell, 34(1), 36-46 (2009).
79. E. H. Bayne, S. A. White, A. Kagansky, D. A. Bijos, L. Sanchez-Pulido, K. L. Hoe, D. U. Kim, H. O. Park, C. P. Ponting, J. Rappsilber and R. C. Allshire: Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell, 140(5), 666-677 (2010).
80. T. Sugiyama, H. Cam, A. Verdel, D. Moazed and S. I. Grewal: RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc Natl Acad Sci U S A, 102(1), 152-157 (2005). (Pubitemid 40094444)
81. H. Kato, D. B. Goto, R. A. Martienssen, T. Urano, K. Furukawa and Y. Murakami: RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science, 309(5733), 467-469 (2005). (Pubitemid 40994685)
82. I. Djupedal, M. Portoso, H. Spahr, C. Bonilla, C. M. Gustafsson, R. C. Allshire and K. Ekwall: RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev, 19(19), 2301-2306 (2005). (Pubitemid 41396907)
83. E. S. Chen, K. Zhang, E. Nicolas, H. P. Cam, M. Zofall and S. I. Grewal: Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature, 451(7179), 734-737 (2008). (Pubitemid 351220568)
84. E. H. Bayne, M. Portoso, A. Kagansky, I. C. Kos- Braun, T. Urano, K. Ekwall, F. Alves, J. Rappsilber and R. C. Allshire: Splicing factors facilitate RNAi-directed silencing in fission yeast. Science, 322(5901), 602-606 (2008).
85. M. Chinen, M. Morita, K. Fukumura and T. Tani: Involvement of the spliceosomal U4 small nuclear RNA in heterochromatic gene silencing at fission yeast centromeres. J Biol Chem, 285(8), 5630-5638 (2010).
86. J. Potashkin, R. Li and D. Frendewey: Pre-mRNA splicing mutants of Schizosaccharomyces pombe. EMBO J, 8(2), 551-559 (1989). (Pubitemid 19274975)
87. S. Urushiyama, T. Tani and Y. Ohshima: Isolation of novel pre-mRNA splicing mutants of Schizosaccharomyces pombe. Mol Gen Genet, 253(1-2), 118-127 (1996). (Pubitemid 26419996)
88. W. H. McDonald, R. Ohi, N. Smelkova, D. Frendewey and K. L. Gould: Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. Mol Cell Biol, 19(8), 5352-5362 (1999). (Pubitemid 29339894)
89. N. F. Kaüfer and J. Potashkin: Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals. Nucleic Acids Res, 28(16), 3003-3010 (2000). (Pubitemid 30624088)
90. J. A. Box, J. T. Bunch, W. Tang and P. Baumann: Spliceosomal cleavage generates the 3' end of telomerase RNA. Nature, 456(7224), 910-914 (2008).
91. N. Hug and J. Lingner: Telomere length homeostasis. Chromosoma, 115(6), 413-425 (2006). (Pubitemid 44642634)
92. G. L. Yu, J. D. Bradley, L. D. Attardi and E. H. Blackburn: In vivo alteration of telomere sequences and senescence caused by mutated Tetrahymena telomerase RNAs. Nature, 344(6262), 126-132 (1990).
93. J. Lingner, T. R. Hughes, A. Shevchenko, M. Mann, V. Lundblad and T. R. Cech: Reverse transcriptase motifs in the catalytic subunit of telomerase. Science, 276(5312), 561-567 (1997). (Pubitemid 27193675)
94. K. Okamura, J. W. Hagen, H. Duan, D. M. Tyler and E. C. Lai: The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell, 130(1), 89-100 (2007). (Pubitemid 47031325)
95. E. Berezikov, W. J. Chung, J. Willis, E. Cuppen and E. C. Lai: Mammalian mirtron genes. Mol Cell, 28(2), 328- 336 (2007). (Pubitemid 47600007)
96. J. Krol, I. Loedige and W. Filipowicz: The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet, 11(9), 597-610 (2010).
97. C. Tufarelli, J. A. Stanley, D. Garrick, J. A. Sharpe, H. Ayyub, W. G. Wood and D. R. Higgs: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet, 34(2), 157-165 (2003). (Pubitemid 36666926)
98. H. Kaneko, S. Dridi, V. Tarallo, B. D. Gelfand, B. J. Fowler, W. G. Cho, M. E. Kleinman, S. L. Ponicsan, W. W. Hauswirth, V. A. Chiodo, K. Kariko, J. W. Yoo, D. K. Lee, M. Hadziahmetovic, Y. Song, S. Misra, G. Chaudhuri, F. W. Buaas, R. E. Braun, D. R. Hinton, Q. Zhang, H. E. Grossniklaus, J. M. Provis, M. C. Madigan, A. H. Milam, N. L. Justice, R. J. Albuquerque, A. D. Blandford, S. Bogdanovich, Y. Hirano, J. Witta, E. Fuchs, D. R. Littman, B. K. Ambati, C. M. Rudin, M. M. Chong, P. Provost, J. F. Kugel, J. A. Goodrich, J. L. Dunaief, J. Z. Baffi and J. Ambati: DICER1 deficit induces Alu RNA toxicity in agerelated macular degeneration. Nature, 471(7338), 325-330 (2011).
99. M. Garofalo and C. M. Croce: microRNAs: Master regulators as potential therapeutics in cancer. Annu Rev Pharmacol Toxicol, 51, 25-43 (2011).
100. K. Tano, R. Mizuno, T. Okada, R. Rakwal, J. Shibato, Y. Masuo, K. Ijiri and N. Akimitsu: MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes. FEBS Lett, 584(22), 4575-4580 (2010).