Interrogation of MicroRNAs involved in gastric cancer using 5p-arm and 3p-arm annotated MicroRNAs

Anticancer Research

Volumn 35, Issue 3, 2015, Pages 1345-1352

  Kuo, Wei Ting ^a,b   Ho, Meng Ru ^c   Wu, Chew Wun ^b   Fang, Wen Liang ^b   Huang, Kuo Hung ^b   Lin, Wen Chang ^a,b  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

^c BIODIVERSITY RESEARCH CENTER   (Taiwan)

Author keywords

3p arm; 5p arm; Bioinformatics; Gastric cancer; MicroRNA

Indexed keywords

MICRORNA; MICRORNA 105 5P; MICRORNA 106A 3P; MICRORNA 1199 3P; MICRORNA 1199 5P; MICRORNA 1231 5P; MICRORNA 1291 5P; MICRORNA 1912 3P; MICRORNA 20B 3P; MICRORNA 300 3P; MICRORNA 329 3P; MICRORNA 345 5P; MICRORNA 3620 5P; MICRORNA 376B 3P; MICRORNA 449C 3P; MICRORNA 449C 5P; MICRORNA 450A 2 3P; MICRORNA 489 3P; MICRORNA 503 3P; MICRORNA 509 5P; MICRORNA 511 5P; MICRORNA 541 5P; MICRORNA 654 5P; MICRORNA 676 3P; MICRORNA 6769B 3P; MICRORNA 875 3P; MICRORNA 92A 1 5P; MICRORNA 92A 2 5P; NUCLEOTIDE; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ARTICLE; CANCER TISSUE; DOWN REGULATION; HUMAN; HUMAN TISSUE; MOUSE; NONHUMAN; PRIORITY JOURNAL; STOMACH CANCER; UPREGULATION; ANIMAL; GENE EXPRESSION REGULATION; GENETICS; PHYSIOLOGY; STOMACH TUMOR;

ANIMALS; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICE; MICRORNAS; STOMACH NEOPLASMS;

EID: 84924955683     PISSN: 02507005     EISSN: 17917530     Source Type: Journal    
DOI: None     Document Type: Article

References (33)

1. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297, 2004.
2. Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233, 2009.
3. Li SC, Chan WC, Hu LY, Lai CH, Hsu CN and Lin WC: Identification of homologous microRNAs in 56 animal genomes. Genomics 96: 1-9, 2010.
4. Li SC, Shiau CK and Lin WC: Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic acids research 36: D184-189, 2008.
5. Lin WC, Li SC, Lin W-c, Shin JW, Hu SN, Yu XM, Huang TY, Chen SC, Chen HC, Chen SJ, Huang PJ, Gan RR, Chiu CH and Tang P: Identification of microRNA in the protist Trichomonas vaginalis. Genomics 93: 487-493, 2009.
6. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP and Schier AF: MicroRNAs regulate brain morphogenesis in zebrafish. Science 308: 833-838, 2005.
7. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP and Burge CB: Prediction of mammalian microRNA targets. Cell 115: 787-798, 2003.
8. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT and Kim VN: Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887-901, 2006.
9. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S and Kim VN: The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419, 2003.
10. Gregory RI, Chendrimada TP, Cooch N and Shiekhattar R: Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123: 631-640, 2005.
11. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T and Zamore PD: A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838, 2001.
12. Khvorova A, Reynolds A and Jayasena SD: Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216, 2003.
13. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N and Zamore PD: Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208, 2003.
14. Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC and Lai EC: Widespread regulatory activity of vertebrate microRNA∗ species. RNA 17: 312-326, 2011.
15. Kozomara A and Griffiths-Jones S: miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42: D68-73, 2014.
16. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A and Enright AJ: miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-144, 2006.
17. Griffiths-Jones S, Saini HK, van Dongen S and Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158, 2008.
18. Li SC, Liao YL, Ho MR, Tsai KW, Lai CH and Lin WC: miRNA arm selection and isomiR distribution in gastric cancer. BMC Genomics 13(Suppl 1): S13, 2012.
19. Zhou H, Arcila ML, Li Z, Lee EJ, Henzler C, Liu J, Rana TM and Kosik KS: Deep annotation of mouse iso-miR and iso-moR variation. Nucleic Acids Res 40: 5864-5875, 2012.
20. Langmead B and Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359, 2012.
21. Lin WC, Li AF, Chi CW, Chung WW, Huang CL, Lui WY, Kung HJ and Wu CW: tie-1 protein tyrosine kinase: a novel independent prognostic marker for gastric cancer. Clinical cancer research: an official journal of the American Association for Cancer Research 5: 1745-1751, 1999.
22. Tsai KW, Hu LY, Wu CW, Li SC, Lai CH, Kao HW, Fang WL and Lin WC: Epigenetic regulation of miR-196b expression in gastric cancer. Genes, chromosomes & cancer 49: 969-980, 2010.
23. Wu CW, Li AF, Chi CW, Huang CL, Shen KH, Liu WY and Lin W: Human gastric cancer kinase profile and prognostic significance of MKK4 kinase. Am J Pathol 156: 2007-2015, 2000.
24. Hansen TB, Kjems J and Bramsen JB: Enhancing miRNA annotation confidence in miRBase by continuous cross dataset analysis. RNA Biology 8: 378-383, 2011.
25. Neilsen CT, Goodall GJ and Bracken CP: IsomiRs-the overlooked repertoire in the dynamic microRNAome. Trends Genet 28: 544-549, 2012.
26. Chan SH, Wu CW, Li AF, Chi CW and Lin WC: miR-21 microRNA expression in human gastric carcinomas and its clinical association. Anticancer Res 28: 907-911, 2008.
27. Liao YL, Hu LY, Tsai KW, Wu CW, Chan WC, Li SC, Lai CH, Ho MR, Fang WL, Huang KH and Lin WC: Transcriptional regulation of miR-196b by ETS2 in gastric cancer cells. Carcinogenesis 33: 760-769, 2012.
28. Tsai KW, Liao YL, Wu CW, Hu LY, Li SC, Chan WC, Ho MR, Lai CH, Kao HW, Fang WL, Huang KH and Lin WC: Aberrant expression of miR-196a in gastric cancers and correlation with recurrence. Genes Chromosomes Cancer 51: 394-401, 2012.
29. Auyeung VC, Ulitsky I, McGeary SE and Bartel DP: Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152: 844-858, 2013.
30. Wu HH, Lin WC and Tsai KW: Advances in molecular biomarkers for gastric cancer: miRNAs as emerging novel cancer markers. Expert Rev Mol Med 16: e1, 2014.
31. Bang C, Batkai S, Dangwal S, Gupta SK, Foinquinos A, Holzmann A, Just A, Remke J, Zimmer K, Zeug A, Ponimaskin E, Schmiedl A, Yin X, Mayr M, Halder R, Fischer A, Engelhardt S, Wei Y, Schober A, Fiedler J and Thum T: Cardiac fibroblast-derived microRNA passenger strand-enriched exosomes mediate cardiomyocyte hypertrophy. J Clin Invest 124: 2136-2146, 2014.
32. Indolfi C and Curcio A: Stargazing microRNA maps a new miR-21 star for cardiac hypertrophy. J Clin Invest 124: 1896-1898, 2014.
33. Lo TF, Tsai WC and Chen ST: MicroRNA-21-3p, a berberine-induced miRNA, directly down-regulates human methionine adenosyltransferases 2A and 2B and inhibits hepatoma cell growth. PLoS One 8: e75628, 2013.