Scholarly Research Excellence

Digital Open Science Index

Commenced in January 2007 Frequency: Monthly Edition: International Publications Count: 29054


Select areas to restrict search in scientific publication database:
14212
Intragenic MicroRNAs Binding Sites in MRNAs of Genes Involved in Carcinogenesis
Abstract:
MiRNAs participate in gene regulation of translation. Some studies have investigated the interactions between genes and intragenic miRNAs. It is important to study the miRNA binding sites of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid programmes were used to compute the hybridization free energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%, and 39.7% of miRNA binding sites were present in the 5'UTRs, CDSs, and 3'UTRs, respectively. The density of the binding sites for miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to 8.0 times greater than in the CDS and 3'UTR, respectively. Three types of miRNA interactions with mRNAs have been revealed: 5'- dominant canonical, 3'-compensatory, and complementary binding sites. MiRNAs regulate gene expression, and information on the interactions between miRNAs and mRNAs could be useful in molecular medicine. We recommend that newly described sites undergo validation by experimental investigation.
Keywords:
Digital Object Identifier (DOI):

References:

[1] V. Ambros, "microRNAs: tiny regulators with great potential", Cell, vol. 7, no. 107, pp. 823-6. 2001.
[2] V. N. Kim, J. Han, M.C. Siomi, "Biogenesis of small RNAs in animals", Nat Rev Mol Cell Biol, no. 10, pp. 126-139. 2009.
[3] Y. K. Kim, V. N. Kim "Processing of intronic microRNAs", Embo J, no. 26, pp. 775-783. 2007.
[4] A. Rodriguez, S. Griffiths-Jones, J. L. Ashurst, A. Bradley, "Identification of mammalian microRNA host genes and transcription units" Genome Res, no. 14, pp. 1902-1910. 2004.
[5] V. Maselli, D. Di Bernardo, S. Banfi, "CoGemiR: A comparative genomics microRNA database", BMC Genomics, no. 9, pp. 457. 2008.
[6] B. N. Davis, A. Hata, "Regulation of MicroRNA Biogenesis: A miRiad of mechanisms", Cell Commun. Signal, no. 10, pp. 7:18. 2009.
[7] M. Selbach, B. Schwanhausser, N. Thierfelder, Z. Fang, R. Khanin, N. Rajewsky, "Widespread changes in protein synthesis induced by microRNAs", Nature, no. 455, pp. 58-63. 2008.
[8] B. Zhang, X. Pan, G. P. Cobb, T.A. Anderson, "microRNAs as oncogenes and tumor suppressors", Dev Biol, no. 302, pp. 1-12. 2007.
[9] L. Zhang, J. Huang, N. Yang, "microRNAs exhibit high frequency genomic alterations in human cancer", Proc Natl Acad Sci USA, no. 103, pp. 9136-41. 2006.
[10] X. Zhou, C. Marian, K. H. Makambi, O. Kosti, B. V. Kallakury, C. A. Loffredo, Y. L. Zheng, "MicroRNA-9 as Potential Biomarker for Breast Cancer Local Recurrence and Tumor Estrogen Receptor Status", PLoS One,; vol. 6, no. 7, pp. E39011. 2012.
[11] C. Wang, X. Zheng, C. Shen, Y. Shi, "MicroRNA-203 suppresses cell proliferation and migration by targeting BIRC5 and LASP1 in human triple-negative breast cancer cells", J Exp Clin Cancer Res, vol. 1, no. 31, pp. 58. 2012.
[12] M. Raychaudhuri, T. Schuster, T. Buchner, K. Malinowsky, H. Bronger, U. Schwarz-Boeger, H. Höfler, S. Avril, "Intratumoral Heterogeneity of MicroRNA Expression in Breast Cancer", J Mol Diagn, vol. 4, no. 14, pp. 376-84. 2012.
[13] R. Liu, J. Liao , M. Yang , J. Sheng , H. Yang, Y. Wang, E. Pan, W. Guo, Y. Pu, S. J. Kim, L. Yin, "The cluster of miR-143 and miR-145 affects the risk for esophageal squamous cell carcinoma through coregulating fascin homolog 1", PLoS One, vol. 3, no. 7, pp. e33987. 2012.
[14] S. C. Li, Y. L. Liao, M. R. Ho, K. W. Tsai, C. H. Lai, W. C. Lin, "miRNA arm selection and isomiR distribution in gastric cancer", BMC Genomics, vol 13, pp. S13. 2012.
[15] J. Zhang, Z. Xiao, D. Lai, J. Sun, C. He, Z. Chu, H. Ye, S. Chen, J. Wang, "miR-21, miR-17 and miR-19a induced by phosphatase of regenerating liver-3 promote the proliferation and metastasis of colon cancer", Br J Cancer, vol. 2, no. 107, pp. 352-9. 2012.
[16] A. J. Schetter, H. Okayama, C. C. Harris, "The Role of MicroRNAs in Colorectal Cancer", Cancer J, vol. 3, no. 18, pp. 244-52. 2012.
[17] L. H. Yang, Z. Dong, Z. H. Gong, "Extracellular miRNA: a novel molecular biomarker for lung cancer", Yi Chuan, vol. 6, no. 34, pp. 651- 8. 2012.
[18] R. Kumarswamy, I. Volkmann, T. Thum, "Regulation and function of miRNA-21 in health and disease", RNA Biology, vol. 5, no. 8, pp. 706- 13. 2011.
[19] E. Meiri, W. C. Mueller, S. Rosenwald, M. Zepeniuk, E. Klinke, T.B. Edmonston, "A Second-Generation MicroRNA-Based Assay for Diagnosing Tumor Tissue Origin", Oncologist, vol. 6, no. 17, pp. 801- 12. 2012.
[20] M. G. Schrauder, R. Strick, R. Schulz-Wendtland, P. L. Strissel, L. Kahmann, C. R. Loehberg, "Circulating micro-RNAs as potential bloodbased markers for early stage breast cancer detection", PLoS One, vol. 1, no. 7, pp. e29770. 2012.
[21] S. Barik, "An intronic microRNA silences genes that are functionally antagonistic to its host gene", Nucleic Acids Res, no. 36, pp. 5232-5241. 2008.
[22] C. Delay, F. Calon, P. Matthews, S. Hébert, "Alzheimer-specific variants in the 3'UTR of amyloid precursor protein affect microRNA function", Molecular neurodegeneration, no. 6, pp. 70. 2011.
[23] M. V. Iorio, C. M. Croce, "MicroRNAs in cancer: small molecules with a huge impact", J. Clin. Oncol., no. 27, pp. 5848-5856. 2009.
[24] M. Isik, H. Korswagen, E. Berezikov, "Expression patterns of intronic microRNAs in Caenorhabditis elegans", Silence, no. 1, pp. 1758-907X. 2010.
[25] J. Kruger, M. Rehmsmeier, "RNAhybrid: microRNA target prediction easy, fast and flexible", Nucleic Acids Res, no. 34, pp. W451-454. 2006.
[26] J. Satoh, H. Tabunoki, "Comprehensive analysis of human microRNA target networks", BioData Mining, no. 4, pp. 17. 2011.
[27] A. Duursma, M. Kedde, M. Schrier, C. Sage, R. Agami, "miR-148 targets human DNMT3b protein coding region", RNA, no. 14, pp. 872- 877. 2008.
[28] I. Elcheva, F. Goswami, K. Noubissi, V. Spiegelman, "CRD-BP protects the coding region of βTrCP1 mRNA from miR-183-mediated degradation", Mol. Cell, no. 35, pp. 240-246. 2009.
[29] S. Kulkarni, R. Savan, Y. Qi, "Differential microRNA regulation of HLA-C expression and its association with HIV control", Nature, no. 472, pp. 495-499. 2011.
[30] F. Moretti, R. Thermann, M. Hentze, "Mechanism of translational regulation by miR-2 from sites in the 5' untranslated region or the open reading frame", RNA, no. 16, pp. 2493-2502. 2010.
[31] N. P. Tsai, Y. L. Lin, L. N. Wei, "MicroRNA mir-346 targets the 5'UTR of RIP140 mRNA and up-regulates its protein expression", Biochem. J., no. 424, pp. 411-418. 2009.
[32] I. Lee, S. S. Ajay, J. I. Yook, H. S. Kim, S. H. Hong, N. H. Kim, S. M. Dhanasekaran, A. M. Chinnaiyan, B. D. Athey, "New class of microRNA targets containing simultaneous 5ÔÇ▓-UTR and 3 ÔÇ▓-UTR interaction sites", Genome Res, vol. 7, no. 19, pp. 1175-1183. 2009.
[33] A. Issabekova, O. Berillo, M. Regnier, A. T. Ivashchenko, "Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis", Biomedical Informatics, vol. 11, no. 8, pp. 513-518. 2012.
[34] D. Betel, A. Koppal, P. Agius, C. Sander, C. L. Betel, "Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites", Genome Biology, no. 11, pp. R90. 2010.
[35] S. Ji, G. Ye, J. Zhang, L. Wang, T. Wang, Z. Wang, T. Zhang, G. Wang, Z. Guo, Y. Luo, J. Cai, J.Y. Yang, "miR-574-5p negatively regulates Qki6/7 to impact β-catenin/Wnt signalling and the development of colorectal cancer", Gut. 10.1136/gutjnl-2011-301083. 2012
[36] K. M. Foss, C. Sima, D. Ugolini, M. Neri, K. E. Allen, G. J. Weiss, "miR-1254 and miR-574-5p: serum-based microRNA biomarkers for early-stage non-small cell lung cancer", J Thorac Oncol, vol. 3, no. 6, pp. 482-8. 2011.
[37] W. Wang, L. J. Zhao, Y. X. Tan, H. Ren, Z. T. Qi, "MiR-138 induces cell cycle arrest by targeting cyclin D3", Carcinogenesis, vol. 5, no. 33, pp. 1113-20. 2012.
[38] T. H. Kim, Y. K. Kim, Y. Kwon, J. H. Heo, H. Kang, G. Kim, H. J. An, "Deregulation of miR-519a, 153, and 485-5p and its clinicopathological relevance in ovarian epithelial tumours", Histopathology, vol. 5, no. 57, pp. 734-43. 2010.
[39] A. Torres, K. Torres, A. Pesci, M. Ceccaroni, T. Paszkowski, P. Cassandrini, G. Zamboni, R. Maciejewski, "Deregulation of miR-100, miR-99a and miR-199b in tissues and plasma coexists with increased expression of mTOR kinase in endometrioid endometrial carcinoma", BMC Cancer, vol. 1, no. 12, pp. 369. 2012.
Vol:12 No:11 2018Vol:12 No:10 2018Vol:12 No:09 2018Vol:12 No:08 2018Vol:12 No:07 2018Vol:12 No:06 2018Vol:12 No:05 2018Vol:12 No:04 2018Vol:12 No:03 2018Vol:12 No:02 2018Vol:12 No:01 2018
Vol:11 No:12 2017Vol:11 No:11 2017Vol:11 No:10 2017Vol:11 No:09 2017Vol:11 No:08 2017Vol:11 No:07 2017Vol:11 No:06 2017Vol:11 No:05 2017Vol:11 No:04 2017Vol:11 No:03 2017Vol:11 No:02 2017Vol:11 No:01 2017
Vol:10 No:12 2016Vol:10 No:11 2016Vol:10 No:10 2016Vol:10 No:09 2016Vol:10 No:08 2016Vol:10 No:07 2016Vol:10 No:06 2016Vol:10 No:05 2016Vol:10 No:04 2016Vol:10 No:03 2016Vol:10 No:02 2016Vol:10 No:01 2016
Vol:9 No:12 2015Vol:9 No:11 2015Vol:9 No:10 2015Vol:9 No:09 2015Vol:9 No:08 2015Vol:9 No:07 2015Vol:9 No:06 2015Vol:9 No:05 2015Vol:9 No:04 2015Vol:9 No:03 2015Vol:9 No:02 2015Vol:9 No:01 2015
Vol:8 No:12 2014Vol:8 No:11 2014Vol:8 No:10 2014Vol:8 No:09 2014Vol:8 No:08 2014Vol:8 No:07 2014Vol:8 No:06 2014Vol:8 No:05 2014Vol:8 No:04 2014Vol:8 No:03 2014Vol:8 No:02 2014Vol:8 No:01 2014
Vol:7 No:12 2013Vol:7 No:11 2013Vol:7 No:10 2013Vol:7 No:09 2013Vol:7 No:08 2013Vol:7 No:07 2013Vol:7 No:06 2013Vol:7 No:05 2013Vol:7 No:04 2013Vol:7 No:03 2013Vol:7 No:02 2013Vol:7 No:01 2013
Vol:6 No:12 2012Vol:6 No:11 2012Vol:6 No:10 2012Vol:6 No:09 2012Vol:6 No:08 2012Vol:6 No:07 2012Vol:6 No:06 2012Vol:6 No:05 2012Vol:6 No:04 2012Vol:6 No:03 2012Vol:6 No:02 2012Vol:6 No:01 2012
Vol:5 No:12 2011Vol:5 No:11 2011Vol:5 No:10 2011Vol:5 No:09 2011Vol:5 No:08 2011Vol:5 No:07 2011Vol:5 No:06 2011Vol:5 No:05 2011Vol:5 No:04 2011Vol:5 No:03 2011Vol:5 No:02 2011Vol:5 No:01 2011
Vol:4 No:12 2010Vol:4 No:11 2010Vol:4 No:10 2010Vol:4 No:09 2010Vol:4 No:08 2010Vol:4 No:07 2010Vol:4 No:06 2010Vol:4 No:05 2010Vol:4 No:04 2010Vol:4 No:03 2010Vol:4 No:02 2010Vol:4 No:01 2010
Vol:3 No:12 2009Vol:3 No:11 2009Vol:3 No:10 2009Vol:3 No:09 2009Vol:3 No:08 2009Vol:3 No:07 2009Vol:3 No:06 2009Vol:3 No:05 2009Vol:3 No:04 2009Vol:3 No:03 2009Vol:3 No:02 2009Vol:3 No:01 2009
Vol:2 No:12 2008Vol:2 No:11 2008Vol:2 No:10 2008Vol:2 No:09 2008Vol:2 No:08 2008Vol:2 No:07 2008Vol:2 No:06 2008Vol:2 No:05 2008Vol:2 No:04 2008Vol:2 No:03 2008Vol:2 No:02 2008Vol:2 No:01 2008
Vol:1 No:12 2007Vol:1 No:11 2007Vol:1 No:10 2007Vol:1 No:09 2007Vol:1 No:08 2007Vol:1 No:07 2007Vol:1 No:06 2007Vol:1 No:05 2007Vol:1 No:04 2007Vol:1 No:03 2007Vol:1 No:02 2007Vol:1 No:01 2007