The emerging role of pseudogene expressed non-coding RNAs in cellular functions

International Journal of Biochemistry and Cell Biology

Volumn 54, Issue , 2014, Pages 350-355

  Groen, Jessica N ^a   Capraro, David ^a   Morris, Kevin V ^a,b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Epigenetic control; lncRNAs; Pseudogenes; Transcription

Indexed keywords

COMPLEMENTARY RNA; LONG UNTRANSLATED RNA; UNTRANSLATED RNA;

CELL FUNCTION; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; PSEUDOGENE; REGULATOR GENE; REVIEW; ANIMAL; GENE EXPRESSION REGULATION; GENETICS;

ANIMALS; EPIGENOMICS; GENE EXPRESSION REGULATION; HUMANS; PSEUDOGENES; RNA, ANTISENSE; RNA, LONG NONCODING; TRANSCRIPTION, GENETIC;

EID: 84925330067     PISSN: 13572725     EISSN: 18785875     Source Type: Journal    
DOI: 10.1016/j.biocel.2014.05.008     Document Type: Review

References (69)

1. N. Agrawal, and P.V. Dasaradhi RNA interference: biology, mechanism, and applications Microbiol Mol Biol Rev 67 4 2003 657 685
2. A. Di Ruscio, A.K. Ebralidze, T. Benoukraf, G. Amabile, L.A. Goff, and J. Terragni DNMT1-interacting RNAs block gene-specific DNA methylation Nature 503 2013 371 376
3. S.E. Artandi, and R.A. DePinho Telomeres and telomerase in cancer Carcinogenesis 31 1 2010 9 18
4. B. Banfai, and H. Jia Long noncoding RNAs are rarely translated in two human cell lines Genome Res 22 9 2012 1646 1657
5. B.E. Bernstein, and E. Birney An integrated encyclopedia of DNA elements in the human genome Nature 489 7414 2012 57 74
6. B. Capel, and A. Swain Circular transcripts of the testis-determining gene Sry in adult mouse testis Cell 73 5 1993 1019 1030
7. A. Care, and D. Catalucci MicroRNA-133 controls cardiac hypertrophy Nat Med 13 5 2007 613 618
8. P. Carninci, and T. Kasukawa The transcriptional landscape of the mammalian genome Science 309 5740 2005 1559 1563
9. T.C. Chang, and E.A. Wentzel Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis Mol Cell 26 5 2007 745 752
10. G.P. Chrousos, and T. Kino Intracellular glucocorticoid signaling: a formerly simple system turns stochastic Sci STKE 304 2005 pe48
11. C. Chu, and K. Qu Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions Mol Cell 44 4 2011 667 678
12. C. Chu, and J. Quinn Chromatin isolation by RNA purification (ChIRP) J Vis Exp 61 2012
13. K. Collins Physiological assembly and activity of human telomerase complexes Mech Ageing Dev 129 1-2 2008 91 98
14. S. Djebali, and C.A. Davis Landscape of transcription in human cells Nature 489 7414 2012 101 108
15. J.T. Do, and D.W. Han Enhanced reprogramming of Xist by induced upregulation of Tsix and Dnmt3a Stem Cells 26 11 2008 2821 2831
16. L. Duret, and C. Chureau The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene Science 312 5780 2006 1653 1655
17. M.S. Ebert, and J.R. Neilson MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells Nat Methods 4 9 2007 721 726
18. F. Fuks, and W.A. Burgers Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription EMBO J 20 10 2001 2536 2544
19. H. Ginisty, and H. Sicard Structure and functions of nucleolin J Cell Sci 112 Pt 6 1999 761 772
20. R.A. Gupta, and N. Shah Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis Nature 464 7291 2010 1071 1076
21. T.B. Hansen, and T.I. Jensen Natural RNA circles function as efficient microRNA sponges Nature 495 7441 2013 384 388
22. T.B. Hansen, and E.D. Wiklund miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA EMBO J 30 21 2011 4414 4422
23. P.G. Hawkins, and K.V. Morris RNA and transcriptional modulation of gene expression Cell Cycle 7 5 2008 602 607
24. P.G. Hawkins, and K.V. Morris Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5 Transcription 1 3 2010 165 175
25. C. Holz-Schietinger, and N.O. Reich RNA modulation of the human DNA methyltransferase 3A Nucleic Acids Res 40 17 2012 8550 8557
26. T. Hung, and H.Y. Chang Long noncoding RNA in genome regulation: prospects and mechanisms RNA Biol 7 5 2010 582 585
27. T. Hung, and Y.L. Wang Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters Nat Genet 43 7 2011 621 629
28. L. Jeffery, and S. Nakielny Components of the DNA methylation system of chromatin control are RNA-binding proteins J Biol Chem 279 47 2004 49479 49487
29. P. Johnsson, and A. Ackley A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells Nat Struct Mol Biol 20 4 2013 440 446
30. A.M. Khalil, and M. Guttman Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression Proc Natl Acad Sci U S A 106 28 2009 11667 11672
31. T. Kino, and D.E. Hurt Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor Sci. Signal. 3 107 2010 ra8
32. Q. Liu, and J. Huang LncRNA loc285194 is a p53-regulated tumor suppressor Nucleic Acids Res 41 9 2013 4976 4987
33. J. Lu, and J. Qian Differential expression of components of the microRNA machinery during mouse organogenesis Biochem Biophys Res Commun 334 2 2005 319 323
34. A.J. Lustig Telomerase RNA: a flexible RNA scaffold for telomerase biosynthesis Curr Biol 14 14 2004 R565 R567
35. J. Mazar, and S. Sinha Protein-coding and non-coding gene expression analysis in differentiating human keratinocytes using a three-dimensional epidermal equivalent Mol Genet Genomics 284 1 2010 1 9
36. G. Meister, and M. Landthaler Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs Mol Cell 15 2 2004 185 197
37. G. Mittler, and F. Butter A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements Genome Res 19 2 2009 284 293
38. F. Modarresi, and M.A. Faghihi Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation Nat Biotechnol 2012
39. K.V. Morris RNA-directed transcriptional gene silencing and activation in human cells Oligonucleotides 19 2009 299 306
40. K.V. Morris, and S. Santoso Bidirectional transcription directs both transcriptional gene activation and suppression in human cells PLoS Genet 4 11 2008 e1000258
41. L. Poliseno, and L. Salmena A coding-independent function of gene and pseudogene mRNAs regulates tumour biology Nature 465 7301 2010 1033 1038
42. C.P. Ponting, and P.L. Oliver Evolution and functions of long noncoding RNAs Cell 136 4 2009 629 641
43. P. Qi, and M.D. Xu Low expression of LOC285194 is associated with poor prognosis in colorectal cancer J Transl Med 11 1 2013 122
44. J.L. Rinn, and M. Kertesz Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs Cell 129 7 2007 1311 1323
45. J.P. Ross, and I. Suetake Recombinant mammalian DNA methyltransferase activity on model transcriptional gene silencing short RNA-DNA heteroduplex substrates Biochem J 432 2 2010 323 332
46. S. Saayman, A. Ackley, A.W. Turner, M. Famiglietti, A. Bosque, and M. Clemson An HIV-encoded antisense long non-coding RNA epigenetically regulates viral transcription Mol Ther 2014 Accession 24576854
47. L. Salmena, and L. Poliseno A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146 3 2011 353 358
48. M. Sauvageau, and L.A. Goff Multiple knockout mouse models reveal lincRNAs are required for life and brain development Elife 2 2013 e01749
49. C. Schneider, and R.M. King Genes specifically expressed at growth arrest of mammalian cells Cell 54 6 1988 787 793
50. C. Shiau, and M.J. Trnka Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase Chem Biol 20 4 2013 494 499
51. D.B. Spicer, and G.E. Sonenshein An antisense promoter of the murine c-myc gene is localized within intron 2 Mol Cell Biol 12 3 1992 1324 1329
52. P.A. Steck, and M.A. Pershouse Identification of a candidate tumour suppressor gene, MMAC1, at chromosome 10q23.3 that is mutated in multiple advanced cancers Nat Genet 15 4 1997 356 362
53. J. Stenvang, and A. Petri Inhibition of microRNA function by antimiR oligonucleotides Silence 3 1 2012 1
54. K. Suzuki, and T. Juelich Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region J Biol Chem 283 34 2008 23353 23363
55. S.-K. Tay, and J. Blythe Global discovery of primate-specific genes in the human genome Proc Natl Acad Sci U S A 106 29 2009 12019 12024
56. D.H. Teng, and R. Hu MMAC1/PTEN mutations in primary tumor specimens and tumor cell lines Cancer Res 57 23 1997 5221 5225
57. M.C. Tsai, and O. Manor Long noncoding RNA as modular scaffold of histone modification complexes Science 329 5992 2010 689 693
58. C. Tufarelli, and J.A. Stanley Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease Nat Genet 34 2 2003 157 165
59. E. Vire, and C. Brenner The Polycomb group protein EZH2 directly controls DNA methylation Nature 439 2005 871 874
60. J. Wang, and X. Liu CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer Nucleic Acids Res 38 16 2010 5366 5383
61. L. Wang, and Z.Y. Guo Pseudogene OCT4-pg4 functions as a natural micro RNA sponge to regulate OCT4 expression by competing for miR-145 in hepatocellular carcinoma Carcinogenesis 34 8 2013 1773 1781
62. Y. Wang, and Z. Xu Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal Dev Cell 25 1 2013 69 80
63. M.S. Weinberg, and K.V. Morris Long non-coding RNA targeting and transcriptional de-repression Nucleic Acid Ther 23 1 2013 9 14
64. M.S. Weinberg, and L.M. Villeneuve The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells RNA 12 2 2006 256 262
65. M.Z. Xing Genetic alterations in the phosphatidylinositol-3 kinase/Akt pathway in thyroid cancer Thyroid 20 7 2010 697 706
66. H. Yamaguchi, and G.M. Baerlocher Mutations of the human telomerase RNA gene (TERC) in aplastic anemia and myelodysplastic syndrome Blood 102 3 2003 916 918
67. K.L. Yap, and S. Li 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 2010 662 674
68. Y. Yin, and W.H. Shen PTEN: a new guardian of the genome Oncogene 27 41 2008 5443 5453
69. W. Yu, and D. Gius Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA Nature 451 7175 2008 202 206