Screening for possible miRNA-mRNA associations in a colon cancer cell line

Gene

Volumn 533, Issue 2, 2014, Pages 520-531

  Kanematsu, Sotaro ^a   Tanimoto, Kousuke ^b   Suzuki, Yutaka ^a   Sugano, Sumio ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

Author keywords

Cancer; Hypoxia; MicroRNA; Next generation sequencing; RNA immunoprecipitation assay; RNA induced silencing complex

Indexed keywords

ARGONAUTE 1 PROTEIN; ARGONAUTE 2 PROTEIN; MESSENGER RNA; MICRORNA; MICRORNA 103; MICRORNA 164; MICRORNA 34; MICRORNA 391; MICRORNA 45; MICRORNA 81; RNA; SMALL UNTRANSLATED RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; BINDING SITE; CANCER CELL; CANCER CELL CULTURE; CELL FUNCTION; CELL HYPOXIA; CHROMATIN IMMUNOPRECIPITATION; COLON CANCER; COMPUTER MODEL; CONTROLLED STUDY; GENE EXPRESSION; GENE TARGETING; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; SCREENING TEST; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; TRANSLATION REGULATION;

AGO; ALPHA THALASSEMIA/MENTAL RETARDATION SYNDROME X-LINKED; ARGONAUTE; ATRX; B-CELL CLL/LYMPHOMA 2; BCL2; BCL2-INTERACTING MEDIATOR OF CELL DEATH; BIM; CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE KINASE 2; CAMKK2; CANCER; DACT1; DAPPER, ANTAGONIST OF BETA-CATENIN HOMOLOG 1; HIC2; HIF1A; HIGH MOBILITY GROUP AT-HOOK 2; HMGA2; HYPERMETHYLATED IN CANCER 2; HYPOXIA; HYPOXIA INDUCIBLE FACTOR 1 ALPHA SUBUNIT; MECHANISTIC TARGET OF RAPAMYCIN; MICRORNA; MIRNA-SILENCING EFFECTOR PROTEIN COMPLEXES; MIRNPS; MTOR; NEXT GENERATION SEQUENCING; RIBOSOMAL PROTEIN LARGE P2; RNA IMMUNOPRECIPITATION ASSAY; RNA-INDUCED SILENCING COMPLEX; RPLP2; TSC; TUBEROUS SCLEROSIS; VASCULAR ENDOTHELIAL GROWTH FACTOR; VEGF;

ANOXIA; ARGONAUTE PROTEINS; BINDING SITES; CELL LINE, TUMOR; COLONIC NEOPLASMS; EPISTASIS, GENETIC; EUKARYOTIC INITIATION FACTORS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; IMMUNOPRECIPITATION; MICRORNAS; PROTEIN BINDING; RNA, MESSENGER;

EID: 84887609017     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.08.005     Document Type: Article

References (69)

1. Adams G.E. Hypoxia-mediated drugs for radiation and chemotherapy. Cancer 1981, 48:696-707.
2. Azuma-Mukai A., et al. Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:7964-7969.
3. Bagga S., et al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 2005, 122:553-563.
4. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 408:363-366.
5. Bonauer A., et al. MicroRNA-92a controls angiogenesis and functional recovery of ischemic tissues in mice. Science 2009, 324:1710-1713.
6. Bonnet E., et al. Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLoS One 2010, 5:e10162.
7. Broderick J.A., Salomon W.E., Ryder S.P., Aronin N., Zamore P.D. Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA 2011, 17:1858-1869.
8. Buechner J., et al. Tumour-suppressor microRNAs let-7 and miR-101 target the proto-oncogene MYCN and inhibit cell proliferation in MYCN-amplified neuroblastoma. Br. J. Cancer 2011, 105:296-303.
9. Burroughs A.M., et al. Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol. 2011, 8:158-177.
10. Calin G.A., Croce C.M. Genomics of chronic lymphocytic leukemia microRNAs as new players with clinical significance. Semin. Oncol. 2006, 33:167-173.
11. Cernilogar F.M., et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 2011, 480:391-395.
12. Chen C.Z., Li L., Lodish H.F., Bartel D.P. MicroRNAs modulate hematopoietic lineage differentiation. Science 2004, 303:83-86.
13. Chi S.W., Zang J.B., Mele A., Darnell R.B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-480.
14. Cimmino A., et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:13944-13949.
15. Dachs G.U., et al. Targeting gene expression to hypoxic tumor cells. Nat. Med. 1997, 3:515-520.
16. Deltour S., Pinte S., Guerardel C., Leprince D. Characterization of HRG22, a human homologue of the putative tumor suppressor gene HIC1. Biochem. Biophys. Res. Commun. 2001, 287:427-434.
17. Dobashi Y., Suzuki S., Sato E., Hamada Y., Yanagawa T., Ooi A. EGFR-dependent and independent activation of Akt/mTOR cascade in bone and soft tissue tumors. Mod. Pathol. 2009, 22:1328-1340.
18. Easton J.B., Houghton P.J. mTOR and cancer therapy. Oncogene 2006, 25:6436-6446.
19. Ender C., et al. A human snoRNA with microRNA-like functions. Mol. Cell. 2008, 32:519-528.
20. Enerly E., et al. miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS One 2011, 6:e16915.
21. Forbes S.A., et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011, 39:d945-d950.
22. Forsythe J.A., et al. Activation of vascular endothelial growth factor gene transcription by hypoxia-inducible factor 1. Mol. Cell. Biol. 1996, 16:4604-4613.
23. Friedman R.C., Farh K.K., Burge C.B., Bartel D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009, 19:92-105.
24. Friend K., Campbell Z.T., Cooke A., Kroll-Conner P., Wickens M.P., Kimble J. A conserved PUF-Ago-eEF1A complex attenuates translation elongation. Nat. Struct. Mol. Biol. 2012, 19:176-183.
25. Gao X., et al. Tsc tumor suppressor proteins antagonize amino-acid-TOR signalling. Nat. Cell Biol. 2002, 4:699-704.
26. Hammond S.M., Boettcher S., Caudy A.A., Kobayashi R., Hannon G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 2001, 293:1146-1150.
27. Hayashita Y., et al. A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res. 2005, 65:9628-9632.
28. Heaphy C.M., et al. Altered telomeres in tumors with ATRX and DAXX mutations. Science 2011, 333:425.
29. Hendrickson D.G., Hogan D.J., Herschlag D., Ferrell J.E., Brown P.O. Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One 2008, 3:e2126.
30. Inomata M., Tagawa H., Guo Y.M., Kameoka Y., Takahashi N., Sawada K. MicroRNA-17-92 down-regulates expression of distinct targets in different B-cell lymphoma subtypes. Blood 2009, 8:396-402.
31. Jiao Y., et al. DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 2011, 331:1199-1203.
32. Johnson S.M., et al. RAS is regulated by the let-7 microRNA family. Cell 2005, 120:635-647.
33. Karginov F.V., et al. A biochemical approach to identifying microRNA targets. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:19291-19296.
34. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003, 115:209-216.
35. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39:d152-d157.
36. Kuhn A.R., Schlauch K., Lao R., Halayko A.J., Gerthoffer W.T., Singer C.A. MicroRNA expression in human airway smooth muscle cells: role of miR-25 in regulation of airway smooth muscle phenotype. Am. J. Respir. Cell Mol. Biol. 2010, 42:506-513.
37. Kulshreshtha R., et al. A microRNA signature of hypoxia. Mol. Cell. Biol. 2007, 27:1859-1867.
38. Kwiatkowski D.J., et al. A mouse model of TSC1 reveals sex-dependent lethality from liver hemangiomas, and up-regulation of p70S6 kinase activity in Tsc1 null cells. Hum. Mol. Genet. 2002, 11:525-534.
39. Landthaler M., et al. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA 2008, 14:2580-2596.
40. Lee Y., et al. The nuclear RNase III DROSHA initiates microRNA processing. Nature 2003, 425:415-419.
41. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
42. Li Y., et al. Role of the miR-106b-25 microRNA cluster in hepatocellular carcinoma. Cancer Sci. 2009, 100:1234-1242.
43. Li X., Gill R., Cooper N.G., Yoo J.K., Datta S. Modeling microRNA-mRNA interactions using PLS regression in human colon cancer. BMC Med. Genomics 2011, 4:44.
44. Liu J., et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 2004, 305:1437-1441.
45. Mayr C., Hemann M.T., Bartel D.P. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 2007, 315:1576-1579.
46. Meister G., Landthaler M., Patkaniowska A., Dorsett Y., Teng G., Tuschl T. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 2004, 15:185-197.
47. O'Donnell K.A., Wentzel E.A., Zeller K.I., Dang C.V., Mendell J.T. C-Myc-regulated microRNAs modulate E2F1 expression. Nature 2005, 435:839-843.
48. Parisi C., et al. Ago1 and Ago2 differentially affect cell proliferation, motility and apoptosis when overexpressed in SH-SY5Y neuroblastoma cells. FEBS Lett. 2011, 585:2965-2971.
49. Petersen C.P., Bordeleau M.E., Pelletier J., Sharp P.A. Short RNAs repress translation after initiation in mammalian cells. Mol. Cell 2006, 21:533-542.
50. Pillai R.S., et al. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 2005, 309:1573-1576.
51. Pouyssegur J., Dayan F., Mazure N.M. Hypoxia signalling in cancer and approaches to enforce tumour regression. Nature 2006, 441:437-443.
52. Rehwinkel J., Behm-Ansmant I., Gatfield D., Izaurralde E. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 2005, 11:1640-1647.
53. Righi L., et al. Mammalian target of rapamycin signaling activation patterns in neuroendocrine tumors of the lung. Endocr. Relat. Cancer 2010, 17:977-987.
54. Schwartzentruber J., et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012, 482:226-231.
55. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
56. Sephton C.F., et al. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. J. Biol. Chem. 2011, 286:1204-1215.
57. Taft R.J., Glazov E.A., Lassmann T., Hayashizaki Y., Carninci P., Mattick J.S. Small RNAs derived from snoRNAs. RNA 2009, 15:1233-1240.
58. Tamburrino A., et al. Activation of the mTOR pathway in primary medullary thyroid carcinoma and lymph node metastases. Clin. Cancer Res. 2012, 18:3532-3540.
59. Tomari Y., Du T., Zamore P.D. Sorting of Drosophila small silencing RNAs. Cell 2007, 130:299-308.
60. Tsuchida A., et al. miR-92 is a key oncogenic component of the miR-17-92 cluster in colon cancer. Cancer Sci. 2011, 102:2264-2271.
61. Wang D., et al. Quantitative functions of Argonaute proteins in mammalian development. Genes Dev. 2012, 26:693-704.
62. Wong H.C., et al. Direct binding of the PDZ domain of Dishevelled to a conserved internal sequence in the C-terminal region of Frizzled. Mol. Cell 2003, 12:1251-1260.
63. Wu L., Fan J., Belasco J.G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:4034-4039.
64. Xiao C., et al. Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat. Immunol. 2008, 9:405-414.
65. Yamashita R., et al. Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res. 2011, 21:775-789.
66. Yang Z.Q., et al. Downregulation of HDPR1 is associated with poor prognosis and affects expression levels of p120-catenin and beta-catenin in nonsmall cell lung cancer. Mol. Carcinog. 2010, 49:508-519.
67. Yau T.O., et al. HDPR1, a novel inhibitor of the WNT/beta-catenin signaling, is frequently downregulated in hepatocellular carcinoma: involvement of methylation-mediated gene silencing. Oncogene 2005, 24:1607-1614.
68. Zhang C., Darnell R.B. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 2011, 29:607-614.
69. Zhao J., et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 2010, 40:939-953.