An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA

RNA

Volumn 17, Issue 4, 2011, Pages 555-562

  Moore, Hayley C ^a   Johnston, Michael ^b   Nicol, Samantha M ^a   Bourdon, Jean Christophe ^a   Thompson, Alastair M ^a   Hutvagner, Gyorgy ^b,c   Fuller Pace, Frances V ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

^c UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

Author keywords

Alternatively spliced intron; miRNA; p68 DDX5; RNA helicase

Indexed keywords

DEAD BOX PROTEIN; DEAD BOX PROTEIN 5; MESSENGER RNA; MICRORNA; PROTEIN P68; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; ARTICLE; CANCER CELL; CONTROLLED STUDY; GENE EXPRESSION; GENE MUTATION; GENE TARGETING; HUMAN; HUMAN CELL; INTRON; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; RNA PROCESSING; RNA SEQUENCE;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CELL LINE, TUMOR; CONSERVED SEQUENCE; DEAD-BOX RNA HELICASES; DOGS; EVOLUTION, MOLECULAR; HUMANS; INTRONS; MICE; MICRORNAS; MOLECULAR SEQUENCE DATA;

EID: 79953016022     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2591611     Document Type: Article

References (43)

1. Barta I, Iggo R. 1995. Autoregulation of expression of the yeast Dbp2p 'DEAD-box' protein is mediated by sequences in the conserved DBP2 intron. EMBO J 14: 3800-3808.
2. Bates GJ, Nicol SM, Wilson BJ, Jacobs AM, Bourdon JC, Wardrop J, Gregory DJ, Lane DP, Perkins ND, Fuller-Pace FV. 2005. The DEAD box protein p68: a novel transcriptional coactivator of the p53 tumour suppressor. EMBO J 24: 543-553. (Pubitemid 40343256)
3. Bond AT, Mangus DA, He F, Jacobson A. 2001. Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing. Mol Cell Biol 21: 7366-7379. (Pubitemid 32953489)
4. Caretti G, Schiltz RL, Dilworth FJ, Di Padova M, Zhao P, Ogryzko V, Fuller-Pace FV, Hoffman EP, Tapscott SJ, Sartorelli V. 2006. The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell 11: 547-560.
5. Causevic M, Hislop RG, Kernohan NM, Carey FA, Kay RA, Steele RJ, Fuller-Pace FV. 2001. Overexpression and poly-ubiquitylation of the DEAD-box RNA helicase p68 in colorectal tumours. Oncogene 20: 7734-7743. (Pubitemid 33121946)
6. Clark EL, Coulson A, Dalgliesh C, Rajan P, Nicol SM, Fleming S, Heer R, Gaughan L, Leung HY, Elliott DJ, et al. 2008. The RNA helicase p68 is a novel androgen receptor coactivator involved in splicing and is overexpressed in prostate cancer. Cancer Res 68: 7938-7946.
7. Croce CM. 2009. Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet 10: 704-714.
8. Endoh H, Maruyama K, Masuhiro Y, Kobayashi Y, Goto M, Tai H, Yanagisawa J, Metzger D, Hashimoto S, Kato S. 1999. Purification and identification of p68 RNA helicase acting as a transcriptional coactivator specific for the activation function 1 of human estrogen receptor a. Mol Cell Biol 19: 5363-5372. (Pubitemid 29339895)
9. Ford MJ, Anton IA, Lane DP. 1988. Nuclear protein with sequence homology to translation initiation factor eIF-4A. Nature 332: 736-738.
10. Fukuda T, Yamagata K, Fujiyama S, Matsumoto T, Koshida I, Yoshimura K, Mihara M, Naitou M, Endoh H, Nakamura T, et al. 2007. DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol 9: 604-611. (Pubitemid 46696543)
11. Fuller-Pace FV. 2006. DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation. Nucleic Acids Res 34: 4206-4215. (Pubitemid 44542200)
12. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. 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. (Pubitemid 32709955)
13. Guil S, Gattoni R, Carrascal M, Abian J, Stevenin J, Bach-Elias M. 2003. Roles of hnRNP A1, SR proteins, and p68 helicase in c-H-ras alternative splicing regulation. Mol Cell Biol 23: 2927-2941. (Pubitemid 36403089)
14. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. 2004. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18: 3016-3027. (Pubitemid 39658171)
15. Hock J, Meister G. 2008. The Argonaute protein family. Genome Biol 9: 210. doi: 10.1186/gb-2008-9-2-210.
16. Hutvagner G, Simard MJ. 2008. Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9: 22-32.
17. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838. (Pubitemid 32743968)
18. Iggo RD, Jamieson DJ, MacNeill SA, Southgate J, McPheat J, Lane DP. 1991. p68 RNA helicase: Identification of a nucleolar form and cloning of related genes containing a conserved intron in yeasts. Mol Cell Biol 11: 1326-1333. (Pubitemid 21895488)
19. Ishizuka A, Siomi MC, Siomi H. 2002. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev 16: 2497-2508.
20. Jensen ED, Niu L, Caretti G, Nicol SM, Teplyuk N, Stein GS, Sartorelli V, van Wijnen AJ, Fuller-Pace FV, Westendorf JJ. 2008. p68 (Ddx5) interacts with Runx2 and regulates osteoblast differentiation. J Cell Biochem 103: 1438-1451. (Pubitemid 351490713)
21. Johnston M, Geoffroy MC, Sobala A, Hay R, Hutvagner G. 2010. HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells. Mol Biol Cell 21: 1462-1469.
22. Kahlina K, Goren I, Pfeilschifter J, Frank S. 2004. p68 DEAD box RNA helicase expression in keratinocytes. Regulation, nucleolar localization, and functional connection to proliferation and vascular endothelial growth factor gene expression. J Biol Chem 279: 44872-44882. (Pubitemid 39430899)
23. Kim YK, Kim VN. 2007. Processing of intronic microRNAs. EMBO J 26: 775-783.
24. Kim VN, Han J, Siomi MC. 2009. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10: 126-139.
25. Kitamura A, Nishizuka M, Tominaga K, Tsuchiya T, Nishihara T, Imagawa M. 2001. Expression of p68 RNA helicase is closely related to the early stage of adipocyte differentiation of mouse 3T3-L1 cells. Biochem Biophys Res Commun 287: 435-439. (Pubitemid 32917617)
26. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419. (Pubitemid 37187272)
27. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. 2003. Prediction of mammalian microRNA targets. Cell 115: 787-798. (Pubitemid 38058492)
28. Linder P. 2006. DEAD-box proteins: a family affair-active and passive players in RNP-remodeling. Nucleic Acids Res 34: 4168-4180. (Pubitemid 44542196)
29. Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, et al. 2009. Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 6: 474-476.
30. Liu ZR. 2002. p68 RNA helicase is an essential human splicing factor that acts at the U1 snRNA-5′ splice site duplex. Mol Cell Biol 22: 5443-5450.
31. Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD. 2005. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123: 607-620. (Pubitemid 41608464)
32. Niwa R, Slack FJ. 2007. The evolution of animal microRNA function. Curr Opin Genet Dev 17: 145-150. (Pubitemid 46566505)
33. Pall GS, Codony-Servat C, Byrne J, Ritchie L, Hamilton A. 2007. Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by Northern blot. Nucleic Acids Res 35: e60. doi: 10.1093/nar/gkm112.
34. Rearick D, Prakash A, McSweeny A, Shepard SS, Fedorova L, Fedorov A. 2010. Critical association of ncRNA with introns. Nucleic Acids Res doi: 10.1093/nar/gkq1080.
35. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res 14: 1902-1910. (Pubitemid 39386503)
36. Rossler OG, Hloch P, Schutz N, Weitzenegger T, Stahl H. 2000. Structure and expression of the human p68 RNA helicase gene. Nucleic Acids Res 28: 932-939. (Pubitemid 30085319)
37. Rudel S, Flatley A, Weinmann L, Kremmer E, Meister G. 2008. A multifunctional human Argonaute2-specific monoclonal antibody. RNA 14: 1244-1253. (Pubitemid 351717503)
38. Seufert DW, Kos R, Erickson CA, Swalla BJ. 2000. p68, a DEAD-box RNA helicase, is expressed in chordate embryo neural and mesodermal tissues. J Exp Zool 288: 193-204.
39. Shin S, Rossow KL, Grande JP, Janknecht R. 2007. Involvement of RNA helicases p68 and p72 in colon cancer. Cancer Res 67: 7572-7578. (Pubitemid 47281348)
40. Stevenson RJ, Hamilton SJ, MacCallum DE, Hall PA, Fuller-Pace FV. 1998. Expression of the 'DEAD box' RNA helicase p68 is developmentally and growth regulated and correlates with organ differentiation/maturation in the fetus. J Pathol 184: 351-359.
41. Wortham NC, Ahamed E, Nicol SM, Thomas RS, Periyasamy M, Jiang J, Ochocka AM, Shousha S, Huson L, Bray SE, et al. 2009. The DEAD-box protein p72 regulates ERa-/oestrogen-dependent transcription and cell growth, and is associated with improved survival in ERa-positive breast cancer. Oncogene 28: 4053-4064.
42. Yang L, Lin C, Liu ZR. 2005. Phosphorylations of DEAD box p68 RNA helicase are associated with cancer development and cell proliferation. Mol Cancer Res 3: 355-363. (Pubitemid 40905627)
43. Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, Showe LC, Showe MK. 2006. Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 22: 1325-1334. (Pubitemid 43985268)