158
Views
6
CrossRef citations to date
0
Altmetric
Research Article

In silico mapping of polymorphic miRNA–mRNA interactions in autoimmune thyroid diseases

Pages 327-333 | Received 15 Nov 2013, Accepted 09 Feb 2014, Published online: 10 Mar 2014

References

  • Stathatos, N., and G. H. Daniels. 2012. Autoimmune thyroid disease. Curr. Opin. Rheumatol. 24: 70–75
  • McLachlan, S. M., and B. Rapoport. 2014. Breaking tolerance to thyroid antigens: changing concepts in thyroid autoimmunity. Endocr. Rev. 35: 59–105
  • Jacobson, E. M., and Y. Tomer. 2007. The genetic basis of thyroid autoimmunity. Thyroid 17: 949–961
  • Brent, G. A. 2010. Environmental exposures and autoimmune thyroid disease. Thyroid 20: 755–761
  • Davies, T. F., R. Latif, and X. Yin. 2012. New genetic insights from autoimmune thyroid disease. J. Thyroid Res. 2012: Article ID 623852
  • Płoski, R., K. Szymański, and T. Bednarczuk. 2011. The genetic basis of Graves' disease. Curr. Genomics 12: 542–563
  • Tomer, Y., and A. Huber. 2009. The etiology of autoimmune thyroid disease: a story of genes and environment. J. Autoimmun. 32: 231–239
  • Ambros, V. 2004. The functions of animal microRNAs. Nature 431: 350–355
  • Bartel, D. P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297
  • Meola, N., V. Gennarino, and S. Banfi. 2009. MicroRNAs and genetic diseases. Patho. Genetics. 2: 7
  • Sayed, D., and M. Abdellatif. 2011. MicroRNAs in development and disease. Physio.l Rev. 91: 827–887
  • Pasquinelli, A. E. 2012. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat. Rev. Genet. 13: 271–282
  • Saunders, M. A., H. Liang, and W.-H. Li. 2007. Human polymorphism at microRNAs and microRNA target sites. Proc. Natl. Acad. Sci. USA. 104: 3300–3305
  • Sethupathy, P., and F. S. Collins. 2008. MicroRNA target site polymorphisms and human disease. Trends Genet. 24: 489–497
  • Ryan, B. M., A. I. Robles, and C. C. Harris. 2010. Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 10: 389–402
  • Gamazon, E. R., D. Ziliak, H. K. Im, et al. 2012. Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am. J. Hum. Genet. 90: 1046–1063
  • Lu, J., and A. G. Clark. 2012. Impact of microRNA regulation on variation in human gene expression. Genome Res. 22: 1243–1254
  • Mendell, J. T., and E. N. Olson. 2012. MicroRNAs in stress signaling and human disease. Cell 148: 1172–1187
  • Li, J., and Z. Zhang. 2013. miRNA regulatory variation in human evolution. Trends Genet. 29: 116–124
  • Bhattacharya, A., J. D. Ziebarth, and Y. Cui. 2012. Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PLoS ONE 7: e46176
  • Ziebarth, J. D., A. Bhattacharya, and Y. Cui. 2012. Integrative analysis of somatic mutations altering microrna targeting in cancer genomes. PLoS ONE 7: e47137
  • Bhattacharya, A., J. D. Ziebarth, and Y. Cui. 2013. SomamiR: a database for somatic mutations impacting microRNA function in cancer. Nuc. Acids Res. 41: D977–D982
  • Pauley, K. M., S. Cha, and E. K. L. Chan. 2009. MicroRNA in autoimmunity and autoimmune diseases. J. Autoimmun. 32: 189–194
  • Ceribelli, A., M. Satoh, and E. K. L. Chan. 2012. MicroRNAs and autoimmunity. Curr. Opin. Immunol. 24: 686–691
  • Bernecker, C., L. Lenz, M. S. Ostapczuk, et al. 2012. MicroRNAs miR-146a1, miR-155-2, and miR-200a1 are regulated in autoimmune thyroid diseases. Thyroid 22: 1294–1295
  • 1000 Genomes Project Consortium, G. R. Abecasis, A. Auton, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65
  • Hafner, M., M. Landthaler, L. Burger, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129–141
  • Chi, S. W., J. B. Zang, A. Mele, and R. B. Darnell. 2009. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479–486
  • Helwak, A., G. Kudla, T. Dudnakova, and D. Tollervey. 2013. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153: 654–665
  • Reyes-Herrera, P. H., and E. Ficarra. 2012. One decade of development and evolution of microRNA target prediction algorithms. Genomics Proteomics Bioinformatics 10: 254–263
  • Xiao, F., Z. Zuo, G. Cai, et al. 2009. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37: D105–D110
  • Hsu, S. D., F. M. Lin, W. Y. Wu, et al. 2011. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucl. Acids Res. 39: D163–D169
  • Bao, L., M. Zhou, L. Wu, et al. 2007. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucl. Acids Res. 35: D51–D54
  • Ziebarth, J. D., A. Bhattacharya, A. Chen, and Y. Cui. 2012. PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. Nucl. Acids Res. 40: D216–D221
  • Bhattacharya, A., J. D. Ziebarth, and Y. Cui. 2013. PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucl. Acids Res. 42: D86–D91
  • Huang, D. W., B. T. Sherman, and R. A. Lempicki. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucl. Acids Res. 37: 1–13
  • Kanehisa, M., S. Goto, Y. Sato, M. Furumichi, and M. Tanabe. 2012. KEGG for integration and interpretation of large-scale molecular data sets. Nucl. Acids Res. 40: D109–D114
  • Horton, R., L. Wilming, V. Rand, et al. 2004. Gene map of the extended human MHC. Nat. Rev. Genet. 5: 889–899
  • Simmonds, M. J. 2013. GWAS in autoimmune thyroid disease: redefining our understanding of pathogenesis. Nat. Rev. Endocrinol. 9: 277–287
  • Jacobson, E. M., A. Huber, and Y. Tomer. 2008. The HLA gene complex in thyroid autoimmunity: From epidemiology to etiology. J. Autoimmun. 30: 58–62
  • Trowsdale, J. 2011. The MHC, disease and selection. Immunol. Lett. 137: 1–8
  • Giuliani, C., I. Bucci, V. Montani, et al. 2010. Regulation of major histocompatibility complex gene expression in thyroid epithelial cells by methimazole and phenylmethimazole. J. Endocrinol. 204: 57–66
  • Hindorff, L. A., P. Sethupathy, H. A. Junkins, et al. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA. 106: 9362–9367
  • Cooper, J. D., M. J. Simmonds, N. M. Walker, et al. 2012. Seven newly identified loci for autoimmune thyroid disease. Hum. Mol. Genet. 21: 5202–5208
  • Simmonds, M. J., and S. C. L. Gough. 2011. The search for the genetic contribution to autoimmune thyroid disease: the never ending story? Brief. Funct. Genomic. 10: 77–90
  • Edwards, S. L., J. Beesley, et al. 2013. Beyond GWASs: illuminating the dark road from association to function. Am. J. Hum. Genet. 93: 779–797
  • Maurano, M. T., R. Humbert, E. Rynes, et al. 2012. Systematic localization of common disease-associated variation in regulatory dna. Science 337: 1190–1195
  • Bulik-Sullivan, B., S. Selitsky, and P. Sethupathy. 2013. Prioritization of genetic variants in the microRNA regulome as functional candidates in genome-wide association studies. Hum. Mutat. 34: 1049–1056
  • Chu, X., C. M. Pan, S. X. Zhao, et al. 2011. A genome-wide association study identifies two new risk loci for Graves' disease. Nat. Genet. 43: 897–901
  • Eriksson, N., J. Y. Tung, A. K. Kiefer, et al. 2012. Novel associations for hypothyroidism include known autoimmune risk loci. PLoS ONE 7: e34442
  • Gudmundsson, J., P. Sulem, D. F. Gudbjartsson, et al. 2009. Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. Nat. Genet. 41: 460–464
  • Porcu, E., M. Medici, G. Pistis, et al. 2013. A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function. PLoS Genet 9: e1003266
  • Gudmundsson, J., P. Sulem, D. F. Gudbjartsson, et al. (2012). Discovery of common variants associated with low TSH levels and thyroid cancer risk. Nat. Genet. 44: 319–322
  • Teumer, A., R. Rawal, G. Homuth, et al. 2011. Genome-wide association study identifies four genetic loci associated with thyroid volume and goiter risk. Am. J. Hum. Genet. 88: 664–673
  • Rawal, R., A. Teumer, H. Völzke, et al. 2012. Meta-analysis of two genome-wide association studies identifies four genetic loci associated with thyroid function. Hum. Mol. Genet. 21: 3275–3282

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.