Bioinformatic resources of microRNA sequences, gene targets, and genetic variation

Frontiers in Genetics

Volumn 3, Issue MAR, 2012, Pages

  Mu, Wenbo ^a   Zhang, Wei ^b  

^a University of Illinois at Chicago   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

Gene expression; Gene regulation; Genetic variation; MicroRNA; RNA sequencing; Single nucleotide polymorphism

Indexed keywords

EID: 84866900491     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00031     Document Type: Review

References (76)

1. 1000 Genomes Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.
2. Ambros, V. (2001). microRNAs: tiny regulators with great potential. Cell 107, 823-826.
3. Ambros, V., Bartel, B., Bartel, D. P., Burge, C. B., Carrington, J. C., Chen, X., Dreyfuss, G., Eddy, S. R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G., and Tuschl, T. (2003). A uniform system for microRNA annotation. RNA 9, 277-279.
4. Amin, N., Byrne, E., Johnson, J., Chenevix-Trench, G., Walter, S., Nolte, I. M., Vink, J. M., Rawal, R., Mangino, M., Teumer, A., Keers, J. C., Verwoert, G., Baumeister, S., Biffar, R., Petersmann, A., Dahmen, N., Doering, A., Isaacs, A., Broer, L., Wray, N. R., Montgomery, G. W., Levy, D., Psaty, B. M., Gudnason, V., Chakravarti, A., Sulem, P., Gudbjartsson, D. F., Kiemeney, L. A., Thorsteinsdottir, U., Stefansson, K., Van Rooij, F. J., Aulchenko, Y. S., Hottenga, J. J., Rivadeneira, F. R., Hofman, A., Uitterlinden, A. G., Hammond, C. J., Shin, S. Y., Ikram, A., Witteman, J. C., Janssens, A. C., Snieder, H., Tiemeier, H., Wolfenbuttel, B. H., Oostra, B. A., Heath, A. C., Wichmann, E., Spector, T. D., Grabe, H. J., Boomsma, D. I., Martin, N. G., and Van Duijn, C. M. (2011). Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM. Mol. Psychiatry. doi: 10.1038/mp.2011.101. [Epub ahead of print].
5. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29.
6. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
7. Betel, D., Wilson, M., Gabow, A., Marks, D. S., and Sander, C. (2008). The microRNA.org resource: targets and expression. Nucleic Acids Res. 36, D149-D153.
8. Bhartiya, D., Laddha, S. V., Mukhopadhyay, A., and Scaria, V. (2011). miRvar: a comprehensive database for genomic variations in microRNAs. Hum. Mutat. 32, E2226-E2245.
9. Chen, K., and Rajewsky, N. (2006). Natural selection on human microRNA binding sites inferred from SNP data. Nat. Genet. 38, 1452-1456.
10. Chen, K., Song, F., Calin, G. A., Wei, Q., Hao, X., and Zhang, W. (2008). Polymorphisms in microRNA targets: a gold mine for molecular epidemiology. Carcinogenesis 29, 1306-1311.
11. Cheung, V. G., Conlin, L. K., Weber, T. M., Arcaro, M., Jen, K. Y., Morley, M., and Spielman, R. S. (2003a). Natural variation in human gene expression assessed in lymphoblastoid cells. Nat. Genet. 33, 422-425.
12. Cheung, V. G., Jen, K. Y., Weber, T., Morley, M., Devlin, J. L., Ewens, K. G., and Spielman, R. S. (2003b). Genetics of quantitative variation in human gene expression. Cold Spring Harb. Symp. Quant. Biol. 68, 403-407.
13. Dhahbi, J. M., Atamna, H., Boffelli, D., Magis, W., Spindler, S. R., and Martin, D. I. (2011). Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence. PLoS ONE 6, e20509. doi:10.1371/journal.pone.0020509
14. Duan, S., Huang, R. S., Zhang, W., Bleibel, W. K., Roe, C. A., Clark, T. A., Chen, T. X., Schweitzer, A. C., Blume, J. E., Cox, N. J., and Dolan, M. E. (2008). Genetic architecture of transcript-level variation in humans. Am. J. Hum. Genet. 82, 1101-1113.
15. Duan, S., Mi, S., Zhang, W., and Dolan, M. E. (2009). Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. RNA Biol. 6, 412-425.
16. Eipper-Mains, J. E., Kiraly, D. D., Palakodeti, D., Mains, R. E., Eipper, B. A., and Graveley, B. R. (2011). microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA 17, 1529-1543.
17. Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D. S. (2003). MicroRNA targets in Drosophila. Genome Biol. 5, R1.
18. Esteller, M. (2011). Non-coding RNAs in human disease. Nat. Rev. Genet. 12, 861-874.
19. Friedlander, M. R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., and Rajewsky, N. (2008). Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol. 26, 407-415.
20. Friedman, R. C., Farh, K. K., Burge, C. B., and Bartel, D. P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105.
21. Gamazon, E. R., Im, H. K., Duan, S., Lussier, Y. A., Cox, N. J., Dolan, M. E., and Zhang, W. (2010). Exprtarget: an integrative approach to predicting human microRNA targets. PLoS ONE 5, e13534. doi:10.1371/journal.pone.0013534
22. Garcia, D. M., Baek, D., Shin, C., Bell, G. W., Grimson, A., and Bartel, D. P. (2011). Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 18, 1139-1146.
23. Griffiths-Jones, S. (2004). The microRNA registry. Nucleic Acids Res. 32, D109-D111.
24. Griffiths-Jones, S., Grocock, R. J., Van Dongen, S., Bateman, A., and Enright, A. J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34, D140-D144.
25. Griffiths-Jones, S., Saini, H. K., Van Dongen, S., and Enright, A. J. (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154-D158.
26. Grimson, A., Farh, K. K., Johnston, W. K., Garrett-Engele, P., Lim, L. P., and Bartel, D. P. (2007). MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105.
27. Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R., and Hofacker, I. L. (2008). The Vienna RNA websuite. Nucleic Acids Res. 36, W70-W74.
28. Grun, D., Wang, Y. L., Langenberger, D., Gunsalus, K. C., and Rajewsky, N. (2005). microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol. 1, e13. doi:10.1371/journal.pcbi.0010013
29. Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., Cabili, M. N., Jaenisch, R., Mikkelsen, T. S., Jacks, T., Hacohen, N., Bernstein, B. E., Kellis, M., Regev, A., Rinn, J. L., and Lander, E. S. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227.
30. HapMap. (2003). The International HapMap Project. Nature 426, 789-796.
31. HapMap. (2005). A haplotype map of the human genome. Nature 437, 1299-1320.
32. Hartford, C. M., Duan, S., Delaney, S. M., Mi, S., Kistner, E. O., Lamba, J. K., Huang, R. S., and Dolan, M. E. (2009). Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity. Blood 113, 2145-2153.
33. Hofacker, I. L. (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429-3431.
34. Huang, R. S., Duan, S., Bleibel, W. K., Kistner, E. O., Zhang, W., Clark, T. A., Chen, T. X., Schweitzer, A. C., Blume, J. E., Cox, N. J., and Dolan, M. E. (2007a). A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc. Natl. Acad. Sci. U.S.A. 104, 9758-9763.
35. Huang, R. S., Duan, S., Shukla, S. J., Kistner, E. O., Clark, T. A., Chen, T. X., Schweitzer, A. C., Blume, J. E., and Dolan, M. E. (2007b). Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach. Am. J. Hum. Genet. 81, 427-437.
36. Huang, R. S., Duan, S., Kistner, E. O., Bleibel, W. K., Delaney, S. M., Fackenthal, D. L., Das, S., and Dolan, M. E. (2008a). Genetic variants contributing to daunorubicin-induced cytotoxicity. Cancer Res. 68, 3161-3168.
37. Huang, R. S., Duan, S., Kistner, E. O., Hartford, C. M., and Dolan, M. E. (2008b). Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans. Mol. Cancer Ther. 7, 3038-3046.
38. Huang, R. S., Gamazon, E. R., Ziliak, D., Wen, Y., Im, H. K., Zhang, W., Wing, C., Duan, S., Bleibel, W. K., Cox, N. J., and Dolan, M. E. (2011). Population differences in microRNA expression and biological implications. RNA Biol. 8, 692-701.
39. Idaghdour, Y., Storey, J. D., Jadallah, S. J., and Gibson, G. (2008). A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet. 4, e1000052. doi:10.1371/journal.pgen.1000052
40. John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004). Human microRNA targets. PLoS Biol. 2, e363. doi:10.1371/journal.pbio.0020363
41. Kaikkonen, M. U., Lam, M. T., and Glass, C. K. (2011). Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc. Res. 90, 430-440.
42. Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002). The human genome browser at UCSC. Genome Res. 12, 996-1006.
43. Kozomara, A., and Griffiths-Jones, S. (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157.
44. Krek, A., Grun, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., Macmenamin, P., Da Piedade, I., Gunsalus, K. C., Stoffel, M., and Rajewsky, N. (2005). Combinatorial microRNA target predictions. Nat. Genet. 37, 495-500.
45. Lai, E. C., Wiel, C., and Rubin, G. M. (2004). Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes. RNA 10, 171-175.
46. Lall, S., Grun, D., Krek, A., Chen, K., Wang, Y. L., Dewey, C. N., Sood, P., Colombo, T., Bray, N., Macmenamin, P., Kao, H. L., Gunsalus, K. C., Pachter, L., Piano, F., and Rajewsky, N. (2006). A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol. 16, 460-471.
47. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A. O., Landthaler, M., Lin, C., Socci, N. D., Hermida, L., Fulci, V., Chiaretti, S., Foa, R., Schliwka, J., Fuchs, U., Novosel, A., Muller, R. U., Schermer, B., Bissels, U., Inman, J., Phan, Q., Chien, M., Weir, D. B., Choksi, R., De Vita, G., Frezzetti, D., Trompeter, H. I., Hornung, V., Teng, G., Hartmann, G., Palkovits, M., Di Lauro, R., Wernet, P., Macino, G., Rogler, C. E., Nagle, J. W., Ju, J., Papavasiliou, F. N., Benzing, T., Lichter, P., Tam, W., Brownstein, M. J., Bosio, A., Borkhardt, A., Russo, J. J., Sander, C., Zavolan, M., and Tuschl, T. (2007). A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414.
48. Landi, D., Gemignani, F., Barale, R., and Landi, S. (2008). A catalog of polymorphisms falling in microRNA-binding regions of cancer genes. DNA Cell Biol. 27, 35-43.
49. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P., and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798.
50. Lewohl, J. M., Nunez, Y. O., Dodd, P. R., Tiwari, G. R., Harris, R. A., and Mayfield, R. D. (2011). Up-regulation of MicroRNAs in brain of human alcoholics. Alcohol. Clin. Exp. Res. 35, 1928-1937.
51. Mardis, E. R. (2008). Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402.
52. Maziere, P., and Enright, A. J. (2007). Prediction of microRNA targets. Drug Discov. Today 12, 452-458.
53. McDonagh, E. M., Whirl-Carrillo, M., Garten, Y., Altman, R. B., and Klein, T. E. (2011). From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark. Med. 5, 795-806.
54. Mishra, P. J., Humeniuk, R., Mishra, P. J., Longo-Sorbello, G. S., Banerjee, D., and Bertino, J. R. (2007). A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc. Natl. Acad. Sci. U.S.A. 104, 13513-13518.
55. Papadopoulos, G. L., Reczko, M., Simossis, V. A., Sethupathy, P., and Hatzigeorgiou, A. G. (2009). The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res. 37, D155-D158.
56. Prosser, H. M., Koike-Yusa, H., Cooper, J. D., Law, F. C., and Bradley, A. (2011). A resource of vectors and ES cells for targeted deletion of microRNAs in mice. Nat. Biotechnol. 29, 840-845.
57. Rehmsmeier, M., Steffen, P., Hochsmann, M., and Giegerich, R. (2004). Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507-1517.
58. Sethupathy, P., Borel, C., Gagnebin, M., Grant, G. R., Deutsch, S., Elton, T. S., Hatzigeorgiou, A. G., and Antonarakis, S. E. (2007). 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. Am. J. Hum. Genet. 81, 405-413.
59. Spielman, R. S., Bastone, L. A., Burdick, J. T., Morley, M., Ewens, W. J., and Cheung, V. G. (2007). Common genetic variants account for differences in gene expression among ethnic groups. Nat. Genet. 39, 226-231.
60. Stark, A., Brennecke, J., Bushati, N., Russell, R. B., and Cohen, S. M. (2005). Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123, 1133-1146.
61. Storey, J. D., Madeoy, J., Strout, J. L., Wurfel, M., Ronald, J., and Akey, J. M. (2007). Gene-expression variation within and among human populations. Am. J. Hum. Genet. 80, 502-509.
62. Stranger, B. E., Forrest, M. S., Clark, A. G., Minichiello, M. J., Deutsch, S., Lyle, R., Hunt, S., Kahl, B., Antonarakis, S. E., Tavare, S., Deloukas, P., and Dermitzakis, E. T. (2005). Genome-wide associations of gene expression variation in humans. PLoS Genet. 1, e78. doi:10.1371/journal.pgen.0010078
63. Stranger, B. E., Forrest, M. S., Dunning, M., Ingle, C. E., Beazley, C., Thorne, N., Redon, R., Bird, C. P., De Grassi, A., Lee, C., Tyler-Smith, C., Carter, N., Scherer, S. W., Tavare, S., Deloukas, P., Hurles, M. E., and Dermitzakis, E. T. (2007a). Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853.
64. Stranger, B. E., Nica, A. C., Forrest, M. S., Dimas, A., Bird, C. P., Beazley, C., Ingle, C. E., Dunning, M., Flicek, P., Koller, D., Montgomery, S., Tavare, S., Deloukas, P., and Dermitzakis, E. T. (2007b). Population genomics of human gene expression. Nat. Genet. 39, 1217-1224.
65. Taft, R. J., Pang, K. C., Mercer, T. R., Dinger, M., and Mattick, J. S. (2010). Non-coding RNAs: regulators of disease. J. Pathol. 220, 126-139.
66. Vaz, C., Ahmad, H. M., Sharma, P., Gupta, R., Kumar, L., Kulshreshtha, R., and Bhattacharya, A. (2012). Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics 11, 288. doi:10.1186/1471-2164-11-288
67. Wang, X. (2008). miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14, 1012-1017.
68. Wang, X., and El Naqa, I. M. (2008). Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24, 325-332.
69. Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., and Li, T. (2009). miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 37, D105-D110.
70. Yang, J. H., Shao, P., Zhou, H., Chen, Y. Q., and Qu, L. H. (2010). deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 38, D123-D130.
71. Yu, Z., Li, Z., Jolicoeur, N., Zhang, L., Fortin, Y., Wang, E., Wu, M., and Shen, S. H. (2007). Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers. Nucleic Acids Res. 35, 4535-4541.
72. Zhang, W., and Dolan, M. E. (2009). Use of cell lines in the investigation of pharmacogenetic loci. Curr. Pharm. Des. 15, 3782-3795.
73. Zhang, W., and Dolan, M. E. (2010). The emerging role of microRNAs in drug responses. Curr. Opin. Mol. Ther. 12, 695-702.
74. Zhang, W., Duan, S., Bleibel, W. K., Wisel, S. A., Huang, R. S., Wu, X., He, L., Clark, T. A., Chen, T. X., Schweitzer, A. C., Blume, J. E., Dolan, M. E., and Cox, N. J. (2009). Identification of common genetic variants that account for transcript isoform variation between human populations. Hum. Genet. 125, 81-93.
75. Zhang, W., Duan, S., Kistner, E. O., Bleibel, W. K., Huang, R. S., Clark, T. A., Chen, T. X., Schweitzer, A. C., Blume, J. E., Cox, N. J., and Dolan, M. E. (2008). Evaluation of genetic variation contributing to differences in gene expression between populations. Am. J. Hum. Genet. 82, 631-640.
76. Zhou, T., Garcia, J. G., and Zhang, W. (2011). Integrating microRNAs into a system biology approach to acute lung injury. Transl. Res. 157, 180-190.