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BioMed Research International
Volume 2013 (2013), Article ID 902467, 10 pages
http://dx.doi.org/10.1155/2013/902467
Research Article

miR-1279, miR-548j, miR-548m, and miR-548d-5p Binding Sites in CDSs of Paralogous and Orthologous PTPN12, MSH6, and ZEB1 Genes

National Nanotechnology Laboratory, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan

Received 27 February 2013; Revised 14 May 2013; Accepted 28 May 2013

Academic Editor: Vassily Lyubetsky

Copyright © 2013 Anatoliy T. Ivashchenko et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. C. Lee, R. L. Feinbaum, and V. Ambros, “The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-4,” Cell, vol. 75, no. 5, pp. 843–854, 1993. View at Publisher · View at Google Scholar · View at Scopus
  2. P. Xu, S. Y. Vernooy, M. Guo, and B. A. Hay, “The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism,” Current Biology, vol. 13, no. 9, pp. 790–795, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. J. Brennecke, D. R. Hipfner, A. Stark, R. B. Russell, and S. M. Cohen, “bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila,” Cell, vol. 113, no. 1, pp. 25–36, 2003. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Liu and H. Chen, “The role of microRNAs in colorectal cancer,” Journal of Genetics and Genomics, vol. 37, no. 6, pp. 347–358, 2010. View at Publisher · View at Google Scholar · View at Scopus
  5. J. Krol, I. Loedige, and W. Filipowicz, “The widespread regulation of microRNA biogenesis, function and decay,” Nature Reviews Genetics, vol. 11, no. 9, pp. 597–610, 2010. View at Publisher · View at Google Scholar · View at Scopus
  6. T. M. Witkos, E. Koscianska, and W. J. Krzyzosiak, “Practical aspects of microRNA target prediction,” Current Molecular Medicine, vol. 11, no. 2, pp. 93–109, 2011. View at Scopus
  7. N. Rajewsky, “microRNA target predictions in animals,” Nature Genetics, vol. 38, supplement 1, pp. S8–S13, 2006. View at Publisher · View at Google Scholar · View at Scopus
  8. C. Zhao, C. Huang, T. Weng, X. Xiao, H. Ma, and L. Liu, “Computational prediction of MicroRNAs targeting GABA receptors and experimental verification of miR-181, miR-216 and miR-203 targets in GABA-A receptor,” BMC Research Notes, vol. 5, no. 91, pp. 1–8, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. P. Lekprasert, M. Mayhew, and U. Ohler, “Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements,” PLoS ONE, vol. 6, no. 6, Article ID e20622, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. A. J. Enright, B. John, U. Gaul, T. Tuschl, C. Sander, and D. S. Marks, “MicroRNA targets in Drosophila,” Genome Biology, vol. 5, no. 1, p. R1, 2003. View at Scopus
  11. B. P. Lewis, C. B. Burge, and D. P. Bartel, “Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets,” Cell, vol. 120, no. 1, pp. 15–20, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. D. Grün, Y. Wang, D. Langenberger, K. C. Gunsalus, and N. Rajewsky, “MicroRNA target predictions across seven drosophilo species and comparison to mammalian targets,” PLoS Computational Biology, vol. 1, no. 1, Article ID e13, 2005. View at Scopus
  13. M. Kiriakidou, P. T. Nelson, A. Kouranov et al., “A combined computational-experimental approach predicts human microRNA targets,” Genes and Development, vol. 18, no. 10, pp. 1165–1178, 2004. View at Publisher · View at Google Scholar · View at Scopus
  14. A. Stark, J. Brennecke, R. B. Russell, and S. M. Cohen, “Identification of Drosophila microRNA targets,” PLoS Biology, vol. 1, no. 3, Article ID E60, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. M. Rehmsmeier, P. Steffen, M. Höchsmann, and R. Giegerich, “Fast and effective prediction of microRNA/target duplexes,” RNA, vol. 10, no. 10, pp. 1507–1517, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. M. Schnall-Levin, O. S. Rissland, W. K. Johnston, N. Perrimon, D. P. Bartel, and B. Berger, “Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs,” Genome Research, vol. 21, no. 9, pp. 1395–1403, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. L. D. Hurst, “Preliminary assessment of the impact of microrna-mediated regulation on coding sequence evolution in mammals,” Journal of Molecular Evolution, vol. 63, no. 2, pp. 174–182, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. X. Zhou, X. Duan, J. Qian, and F. Li, “Abundant conserved microRNA target sites in the 5′-untranslated region and coding sequence,” Genetica, vol. 137, no. 2, pp. 159–164, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. A. S. Issabekova, O. A. Berillo, M. Regnier, and A. T. Ivashchenko, “Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis,” Bioinformation, vol. 8, no. 11, pp. 513–518, 2012. View at Publisher · View at Google Scholar
  20. S. Volinia, M. Galasso, M. E. Sana et al., “Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 8, pp. 3024–3029, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. G. Kaur, A. Masoud, N. Raihan, M. Radzi, W. Khamizar, and L. S. Kam, “Mismatch repair genes expression defects and association with clinicopathological characteristics in colorectal carcinoma,” Indian Journal of Medical Research, vol. 134, no. 2, pp. 186–192, 2011. View at Scopus
  22. T. Ripperger, C. Beger, N. Rahner et al., “Constitutional mismatch repair deficiency and childhood leukemia/lymphoma-report on a novel biallelic ?MSH6 mutation,” Haematologica, vol. 95, no. 5, pp. 841–844, 2010. View at Publisher · View at Google Scholar · View at Scopus
  23. A. Feber, L. Xi, J. D. Luketich et al., “MicroRNA expression profiles of esophageal cancer,” Journal of Thoracic and Cardiovascular Surgery, vol. 135, no. 2, pp. 255–260, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. T. Sun, N. Aceto, K. L. Meerbrey et al., “Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphatase,” Cell, vol. 144, no. 5, pp. 703–718, 2011. View at Publisher · View at Google Scholar · View at Scopus
  25. A. K. Win, J. P. Young, N. M. Lindor et al., “Colorectal and other cancer risks for carriers and noncarriers from families with a DNA mismatch repair gene mutation: a prospective cohort study,” Journal of Clinical Oncology, vol. 30, no. 9, pp. 958–964, 2012. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Ollikainen, W. M. Abdel-Rahman, A. Moisio et al., “Molecular analysis of familial endometrial carcinoma: a manifestation of hereditary nonpolyposis colorectal cancer or a separate syndrome?” Journal of Clinical Oncology, vol. 23, no. 21, pp. 4609–4616, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. Y. Arima, H. Hayashi, M. Sasaki et al., “Induction of ZEB proteins by inactivation of RB protein is key determinant of mesenchymal phenotype of breast cancer,” Journal of Biological Chemistry, vol. 287, no. 11, pp. 7896–7906, 2012. View at Publisher · View at Google Scholar · View at Scopus
  28. I. Lee, S. S. Ajay, I. Y. Jong et al., “New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites,” Genome Research, vol. 19, no. 7, pp. 1175–1183, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. A. S. Issabekova, O. A. Berillo, V. A. Khailenko, S. A. Atambayeva, M. Regnier, and A. T. Ivachshenko, “Characteristics of intronic and intergenic human miRNAs and features of their interaction with mRNA,” World Academy of Science, Engineering and Technology, no. 59, pp. 63–66, 2011.
  30. S. Miura, M. Nozawa, and M. Nei, “Evolutionary changes of the target sites of two MicroRNAs encoded in the Hox gene cluster of Drosophila and other insect species,” Genome Biology and Evolution, vol. 3, no. 1, pp. 129–139, 2011. View at Publisher · View at Google Scholar · View at Scopus
  31. M. Nozawa, S. Miura, and M. Nei, “Origins and evolution of microRNA genes in Drosophila species,” Genome Biology and Evolution, vol. 2, no. 1, pp. 180–189, 2010. View at Publisher · View at Google Scholar · View at Scopus