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Comparative and Functional Genomics
Volume 2011 (2011), Article ID 910769, 9 pages
The Influence of 3′UTRs on MicroRNA Function Inferred from Human SNP Data
1Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, Departments of Ophthalmology, Biostatistics, and Medicine, State University of New York (SUNY), Buffalo, NY 14260, USA
2SUNY Eye Institute, Syracuse, NY 13202, USA
3Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York (SUNY), Buffalo, NY 14260, USA
Received 24 May 2011; Revised 14 August 2011; Accepted 22 August 2011
Academic Editor: E. Hovig
Copyright © 2011 Zihua Hu and Andrew E. Bruno. 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.
- W. P. Kloosterman and R. H. A. Plasterk, “The diverse functions of microRNAs in animal development and disease,” Developmental Cell, vol. 11, no. 4, pp. 441–450, 2006.
- O. Voinnet, “Origin, biogenesis, and activity of plant microRNAs,” Cell, vol. 136, no. 4, pp. 669–687, 2009.
- P. Sarnow, C. L. Jopling, K. L. Norman, S. Schütz, and K. A. Wehner, “MicroRNAs: expression, avoidance and subversion by vertebrate viruses,” Nature Reviews Microbiology, vol. 4, no. 9, pp. 651–659, 2006.
- A. Esquela-Kerscher and F. J. Slack, “Oncomirs—microRNAs with a role in cancer,” Nature Reviews Cancer, vol. 6, no. 4, pp. 259–269, 2006.
- T. C. Chang and J. T. Mendell, “MicroRNAs in vertebrate physiology and human disease,” Annual Review of Genomics and Human Genetics, vol. 8, pp. 215–239, 2007.
- J. Krützfeldt and M. Stoffel, “MicroRNAs: a new class of regulatory genes affecting metabolism,” Cell Metabolism, vol. 4, no. 1, pp. 9–12, 2006.
- J. G. Doench and P. A. Sharp, “Specificity of microRNA target selection in translational repression,” Genes and Development, vol. 18, no. 5, pp. 504–511, 2004.
- J. Brennecke, A. Stark, R. B. Russell, and S. M. Cohen, “Principles of microRNA-target recognition.,” PLoS Biology, vol. 3, no. 3, p. e85, 2005.
- 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.
- H. Robins and W. H. Press, “Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 43, pp. 15557–15562, 2005.
- A. Grimson, K. K. H. Farh, W. K. Johnston, P. Garrett-Engele, L. P. Lim, and D. P. Bartel, “MicroRNA targeting specificity in mammals: determinants beyond seed pairing,” Molecular Cell, vol. 27, no. 1, pp. 91–105, 2007.
- D. Gaidatzis, E. van Nimwegen, J. Hausser, and M. Zavolan, “Inference of miRNA targets using evolutionary conservation and pathway analysis,” BMC Bioinformatics, vol. 8, article 69, 2007.
- W. H. Majoros and U. Ohler, “Spatial preferences of microRNA targets in 3' untranslated regions,” BMC Genomics, vol. 8, article 152, 2007.
- D. Long, R. Lee, P. Williams, C. Y. Chan, V. Ambros, and Y. Ding, “Potent effect of target structure on microRNA function,” Nature Structural and Molecular Biology, vol. 14, no. 4, pp. 287–294, 2007.
- H. Tafer, S. L. Ameres, G. Obernosterer et al., “The impact of target site accessibility on the design of effective siRNAs,” Nature Biotechnology, vol. 26, no. 5, pp. 578–583, 2008.
- M. Kertesz, N. Iovino, U. Unnerstall, U. Gaul, and E. Segal, “The role of site accessibility in microRNA target recognition,” Nature Genetics, vol. 39, no. 10, pp. 1278–1284, 2007.
- R. Duan, C. H. Pak, and P. Jin, “Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA,” Human Molecular Genetics, vol. 16, no. 9, pp. 1124–1131, 2007.
- L. Li, T. Meng, Z. Jia, G. Zhu, and B. Shi, “Single nucleotide polymorphism associated with nonsyndromic cleft palate influences the processing of miR-140,” The American Journal of Medical Genetics, Part A, vol. 152, no. 4, pp. 856–862, 2010.
- K. Jazdzewski, E. L. Murray, K. Franssila, B. Jarzab, D. R. Schoenberg, and A. de la Chapelle, “Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 20, pp. 7269–7274, 2008.
- M. Wu, N. Jolicoeur, Z. Li et al., “Genetic variations of microRNAs in human cancer and their effects on the expression of miRNAs,” Carcinogenesis, vol. 29, no. 9, pp. 1710–1716, 2008.
- Y. Ye, K. K. Wang, J. Gu et al., “Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk,” Cancer Prevention Research, vol. 1, no. 6, pp. 460–469, 2008.
- P. Sethupathy, C. Borel, M. Gagnebin et al., “Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes,” The American Journal of Human Genetics, vol. 81, no. 2, pp. 405–413, 2007.
- D. W. Dickson, M. Baker, and R. Rademakers, “Common variant in GRN is a genetic risk factor for hippocampal sclerosis in the elderly,” Neurodegenerative Diseases, vol. 7, pp. 170–174, 2010.
- L. J. Chin, E. Ratner, S. Leng et al., “A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk,” Cancer Research, vol. 68, no. 20, pp. 8535–8540, 2008.
- G. Wang, J. M. van der Walt, G. Mayhew et al., “Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein,” The American Journal of Human Genetics, vol. 82, no. 2, pp. 283–289, 2008.
- D. Landi, F. Gemignani, R. Barale, and S. Landi, “A catalog of polymorphisms falling in microRNA-binding regions of cancer genes,” DNA and Cell Biology, vol. 27, no. 1, pp. 35–43, 2008.
- P. J. Mishra, R. Humeniuk, G. S. A. Longo-Sorbello, D. Banerjee, and J. R. Bertino, “A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 33, pp. 13513–13518, 2007.
- K. Chen and N. Rajewsky, “Natural selection on human microRNA binding sites inferred from SNP data,” Nature Genetics, vol. 38, no. 12, pp. 1452–1456, 2006.
- M. A. Saunders, H. Liang, and W. H. Li, “Human polymorphism at microRNAs and microRNA target sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 9, pp. 3300–3305, 2007.
- B. E. Stranger, A. C. Nica, M. S. Forrest et al., “Population genomics of human gene expression,” Nature Genetics, vol. 39, no. 10, pp. 1217–1224, 2007.
- I. H. Consortium, “A haplotype map of the human genome,” Nature, vol. 437, pp. 1299–1320, 2005.
- B. F. Voight, S. Kudaravalli, X. Wen, and J. K. Pritchard, “A map of recent positive selection in the human genome,” PLoS Biology, vol. 4, no. 4, article e72, 2006.
- M. Kærn, T. C. Elston, W. J. Blake, and J. J. Collins, “Stochasticity in gene expression: from theories to phenotypes,” Nature Reviews Genetics, vol. 6, no. 6, pp. 451–464, 2005.
- Z. Hu, “Insight into microRNA regulation by analyzing the characteristics of their targets in humans,” BMC Genomics, vol. 10, article 594, 2009.
- G. Grillo, A. Turi, F. Licciulli et al., “UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs,” Nucleic Acids Research, vol. 38, no. 1, pp. D75–D80, 2010.
- Z. Yu, Z. Li, N. Jolicoeur et al., “Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers,” Nucleic Acids Research, vol. 35, no. 13, pp. 4535–4541, 2007.