Regulatory non-coding RNAs: Revolutionizing the RNA world

Molecular Biology Reports

Volumn 41, Issue 6, 2014, Pages 3915-3923

  Huang, Biao ^a   Zhang, Rongxin ^a  

^a TIANJIN MEDICAL UNIVERSITY   (China)

Author keywords

Modes of action; Regulatory non coding RNAs; RNA world

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA; SMALL UNTRANSLATED RNA; UNTRANSLATED RNA;

DNA SEQUENCE; EMBRYO DEVELOPMENT; GENE EXPRESSION REGULATION; GENE SILENCING; HUMAN; NONHUMAN; POLYADENYLATION; PROMOTER REGION; REGULATORY MECHANISM; REVIEW; RNA EDITING; TRANSPOSON; ANIMAL; CLASSIFICATION; CYTOPLASM; GENETICS; REGULATOR GENE;

MAMMALIA;

ANIMALS; CYTOPLASM; GENES, REGULATOR; MICRORNAS; RNA, LONG NONCODING; RNA, SMALL UNTRANSLATED;

EID: 84902375620     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-014-3259-6     Document Type: Review

References (64)

1. Gilbert W (1986) Origin of life: The RNA world. Nature 319:6055
2. Chitwood DH, Timmermans MCP (2010) Small RNAs are on the move. Nature 467(7314):415-419
3. Lee Y, Kim M, Han J, Yeom K-H, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051-4060 (Pubitemid 39472426)
4. Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler EL, Zapp ML, Weng Z (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320(5879):1077-1081 (Pubitemid 351929549)
5. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442(7099):199-202 (Pubitemid 44086566)
6. Esteller M (2011) Non-coding RNAs in human disease. Nat Rev Genet 12(12):861-874
7. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10(2):126-139
8. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10(2):94-108
9. Humphreys DT, Westman BJ, Martin DIK, Preiss T (2005) MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly (A) tail function. Proc Natl Acad Sci USA 102(47):16961-16966 (Pubitemid 41692666)
10. Petersen CP, Bordeleau ME, Pelletier J, Sharp PA (2006) Short RNAs repress translation after initiation in mammalian cells. Mol Cell 21(4):533-542 (Pubitemid 43228008)
11. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9(2):102-114
12. Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466(7308):835-840
13. Houseley J, Tollervey D (2009) The many pathways of RNA degradation. Cell 136(4):763-776
14. Djuranovic S, Nahvi A, Green R (2012) miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336(6078):237-240
15. Bazzini AA, Lee MT, Giraldez AJ (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336(6078):233-237
16. Moazed D (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457(7228):413-420
17. Bühler M, Moazed D (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14(11):1041-1048 (Pubitemid 350060336)
18. Kim DH, Sætrom P, Snøve O, Rossi JJ (2008) MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci 105(42):16230-16235
19. Mitchell Guttman IA, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235):223-227
20. Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482(7385):339-346
21. Paralkar VR, Weiss MJ (2011) A new 'Linc'between noncoding RNAs and blood development. Genes Dev 25(24):2555-2558
22. Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GXY, Chow J, Kim GE (2012) Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev 26(4):338-343
23. 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
24. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477(7364):295-300
25. Mattick JS (2009) The genetic signatures of noncoding RNAs. PLoS Genet 5(4):e1000459
26. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071-1076
27. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29(8):742-749
28. 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
29. Yuan SX, Yang F, Yang Y, Tao QF, Zhang J, Huang G, Yang Y, Wang RY, Yang S, Huo XS (2012) Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients' poor recurrence-free survival after hepatectomy. Hepatology 56(6):2231-2241
30. Wu W, Bhagat TD, Yang X, Song JH, Cheng Y, Agarwal R, Abraham JM, Ibrahim S, Hussain Z, Suzuki M (2013) Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1 in Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterology 144(5):956-966
31. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009) MEN e/b nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19(3):347-359
32. Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S, Etkin LD (2005) 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 (Pubitemid 41246119)
33. Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429(6991):571-574 (Pubitemid 38737662)
34. Uhler JP, Hertel C, Svejstrup JQ (2007) A role for noncoding transcription in activation of the yeast PHO5 gene. Proc Natl Acad Sci 104(19):8011-8016 (Pubitemid 47185867)
35. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23(13):1494-1504
36. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Morales DR, Thomas K, Presser A, Bernstein BE, Van Oudenaarden A (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci 106(28):11667-11672
37. Margueron R, Reinberg D (2011) The Polycomb complex PRC2 and its mark in life. Nature 469(7330):343-349
38. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119(7):941-953 (Pubitemid 40037608)
39. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough H, Helms JA, Farnham PJ, Segal E (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by non-coding RNAs. Cell 129(7):1311
40. Hess JL (2004) MLL: a histone methyltransferase disrupted in leukemia. Trends Mol Med 10(10):500-507
41. Trievel RC, Shilatifard A (2009) WDR5, a complexed protein. Nat Struct Mol Biol 16(7):678-680
42. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120-124
43. Mohammad F, Pandey GK, Mondal T, Enroth S, Redrup L, Gyllensten U, Kanduri C (2012) Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development 139(15):2792-2803
44. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Non-coding RNA gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3(107):8
45. 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
46. Martianov I, Ramadass A, Barros AS, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445(7128):666-670 (Pubitemid 46232888)
47. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Sci Signal 20(11):1470
48. Ørom UA, Shiekhattar R (2011) Long non-coding RNAs and enhancers. Curr Opin Genet Dev 21(2):194-198
49. 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
50. Kugel JF, Goodrich JA (2012) Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci 37:144-151
51. Wilusz JE, Freier SM, Spector DL (2008) 30 end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135(5):919-932
52. Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10(3):155-159
53. Ogawa Y, Sun BK, Lee JT (2008) Intersection of the RNA interference and X-inactivation pathways. Science 320(5881):1336-1341 (Pubitemid 351929469)
54. Keniry A, Oxley D, Monnier P, Kyba M, Dandolo L, Smits G, Reik W (2012) The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat Cell Biol 14(7):659-665
55. Beltran M, Puig I, Peña C, García JM, Álvarez AB, Peña R, Bonilla F, de Herreros AG (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 22(6):756-769 (Pubitemid 351439107)
56. 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
57. Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3 [prime] UTRs via Alu elements. Nature 470(7333):284-288
58. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J (2012) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493(7431):231-235
59. Sharma S, Findlay GM, Bandukwala HS, Oberdoerffer S, Baust B, Li Z, Schmidt V, Hogan PG, Sacks DB, Rao A (2011) Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex. Proc Natl Acad Sci 108(28):11381-11386
60. Inui M, Montagner M, Piccolo S (2011) miRNAs and morphogen gradients. Current Opinion Cell Biol 24(2):194-201
61. Yoon WH, Meinhardt H, Montell DJ (2011) miRNA-Mediated feedback inhibition of JAK/STAT morphogen signalling establishes a cell fate threshold. Nat Cell Biol 13(9):1062-1069
62. 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
63. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465(7301):1033-1038
64. Wang GK, Zhu JQ, Zhang JT, Li Q, Li Y, He J, Qin YW, Jing Q (2010) Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans. Eur Heart J 31(6):659-666