Journal of Biomedicine and Biotechnology
Volume 2009 (2009), Article ID 594738, 9 pages
doi:10.1155/2009/594738
Review Article
An Evolutionary Perspective of Animal MicroRNAs and Their Targets
1Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
Received 27 March 2009; Accepted 17 June 2009
Academic Editor: Bibekanand Mallick
Copyright © 2009 Noam Shomron 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
- V. Ambros, “The functions of animal microRNAs,” Nature, vol. 431, no. 7006, pp. 350–355, 2004. View at Publisher · View at Google Scholar · View at PubMed
- D. P. Bartel, “MicroRNAs: genomics, biogenesis, mechanism, and function,” Cell, vol. 116, no. 2, pp. 281–297, 2004. View at Publisher · View at Google Scholar
- L. He and G. J. Hannon, “MicroRNAs: small RNAs with a big role in gene regulation,” Nature Reviews Genetics, vol. 5, no. 7, pp. 522–531, 2004. View at Publisher · View at Google Scholar · View at PubMed
- T. Du and P. D. Zamore, “microPrimer: the biogenesis and function of microRNA,” Development, vol. 132, no. 21, pp. 4645–4652, 2005. View at Publisher · View at Google Scholar · View at PubMed
- W. Filipowicz, L. Jaskiewicz, F. A. Kolb, and R. S. Pillai, “Post-transcriptional gene silencing by siRNAs and miRNAs,” Current Opinion in Structural Biology, vol. 15, no. 3, pp. 331–341, 2005. View at Publisher · View at Google Scholar · View at PubMed
- R. W. Carthew, “Gene regulation by microRNAs,” Current Opinion in Genetics and Development, vol. 16, no. 2, pp. 203–208, 2006. View at Publisher · View at Google Scholar · View at PubMed
- R. H. A. Plasterk, “Micro RNAs in animal development,” Cell, vol. 124, no. 5, pp. 877–881, 2006. View at Publisher · View at Google Scholar · View at PubMed
- B. P. Lewis, I.-H. Shih, M. W. Jones-Rhoades, D. P. Bartel, and C. B. Burge, “Prediction of mammalian microRNA targets,” Cell, vol. 115, no. 7, pp. 787–798, 2003. View at Publisher · View at Google Scholar
- J. Brennecke, A. Stark, R. B. Russell, and S. M. Cohen, “Principles of microRNA-target recognition,” PLoS Biology, vol. 3, no. 3, article e85, 2005.
- A. Krek, D. Grün, M. N. Poy, et al., “Combinatorial microRNA target predictions,” Nature Genetics, vol. 37, no. 5, pp. 495–500, 2005. View at Publisher · View at Google Scholar · View at PubMed
- C. B. Nielsen, N. Shomron, R. Sandberg, E. Hornstein, J. Kitzman, and C. B. Burge, “Determinants of targeting by endogenous and exogenous microRNAs and siRNAs,” RNA, vol. 13, no. 11, pp. 1894–1910, 2007. View at Publisher · View at Google Scholar · View at PubMed
- S. Ohno, Evolution by Gene Duplication, Springer, New York, NY, USA, 1970.
- P. W. H. Holland, J. Garcia-Fernandez, N. A. Williams, and A. Sidow, “Gene duplications and the origins of vertebrate development,” Development, vol. 120, supplement, pp. 125–133, 1994.
- L.-G. Lundin, “Gene duplications in early metazoan evolution,” Seminars in Cell and Developmental Biology, vol. 10, no. 5, pp. 523–530, 1999. View at Publisher · View at Google Scholar · View at PubMed
- J. Hertel, M. Lindemeyer, K. Missal, et al., “The expansion of the metazoan microRNA repertoire,” BMC Genomics, vol. 7, article 25, 2006. View at Publisher · View at Google Scholar · View at PubMed
- I. Bentwich, A. Avniel, Y. Karov, et al., “Identification of hundreds of conserved and nonconserved human microRNAs,” Nature Genetics, vol. 37, no. 7, pp. 766–770, 2005. View at Publisher · View at Google Scholar · View at PubMed
- R. Zhang, Y. Peng, W. Wang, and B. Su, “Rapid evolution of an X-linked microRNA cluster in primates,” Genome Research, vol. 17, no. 5, pp. 612–617, 2007. View at Publisher · View at Google Scholar · View at PubMed
- J. Piriyapongsa, L. Mariño-Ramírez, and I. K. Jordan, “Origin and evolution of human microRNAs from transposable elements,” Genetics, vol. 176, no. 2, pp. 1323–1337, 2007. View at Publisher · View at Google Scholar · View at PubMed
- F. Ozsolak, L. L. Poling, Z. Wang, et al., “Chromatin structure analyses identify miRNA promoters,” Genes & Development, vol. 22, no. 22, pp. 3172–3183, 2008. View at Publisher · View at Google Scholar · View at PubMed
- J. M. Thomson, M. Newman, J. S. Parker, E. M. Morin-Kensicki, T. Wright, and S. M. Hammond, “Extensive post-transcriptional regulation of microRNAs and its implications for cancer,” Genes & Development, vol. 20, no. 16, pp. 2202–2207, 2006. View at Publisher · View at Google Scholar · View at PubMed
- W. Yang, T. P. Chendrimada, Q. Wang, et al., “Modulation of microRNA processing and expression through RNA editing by ADAR deaminases,” Nature Structural and Molecular Biology, vol. 13, no. 1, pp. 13–21, 2006. View at Publisher · View at Google Scholar · View at PubMed
- Y. Kawahara, B. Zinshteyn, P. Sethupathy, H. Iizasa, A. G. Hatzigeorgiou, and K. Nishikura, “Redirection of silencing targets by adenosine-to-inosine editing of miRNAs,” Science, vol. 315, no. 5815, pp. 1137–1140, 2007. View at Publisher · View at Google Scholar · View at PubMed
- E. Lund, S. Güttinger, A. Calado, J. E. Dahlberg, and U. Kutay, “Nuclear export of microRNA precursors,” Science, vol. 303, no. 5654, pp. 95–98, 2004. View at Publisher · View at Google Scholar · View at PubMed
- R. Yi, B. P. Doehle, Y. Qin, I. G. Macara, and B. R. Cullen, “Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs,” RNA, vol. 11, no. 2, pp. 220–226, 2005. View at Publisher · View at Google Scholar · View at PubMed
- H.-W. Hwang, E. A. Wentzel, and J. T. Mendell, “A hexanucleotide element directs microRNA nuclear import,” Science, vol. 315, no. 5808, pp. 97–100, 2007. View at Publisher · View at Google Scholar · View at PubMed
- A. Tanzer and P. F. Stadler, “Molecular evolution of a microRNA cluster,” Journal of Molecular Biology, vol. 339, no. 2, pp. 327–335, 2004. View at Publisher · View at Google Scholar · View at PubMed
- A. Rodriguez, S. Griffiths-Jones, J. L. Ashurst, and A. Bradley, “Identification of mammalian microRNA host genes and transcription units,” Genome Research, vol. 14, no. 10A, pp. 1902–1910, 2004. View at Publisher · View at Google Scholar · View at PubMed
- N. Iwai and H. Naraba, “Polymorphisms in human pre-miRNAs,” Biochemical and Biophysical Research Communications, vol. 331, no. 4, pp. 1439–1444, 2005. View at Publisher · View at Google Scholar · View at PubMed
- B. Weber, C. Stresemann, B. Brueckner, and F. Lyko, “Methylation of human MicroRNA genes in normal and neoplastic cells,” Cell Cycle, vol. 6, no. 9, pp. 1001–1005, 2007.
- S. Tan, J. Guo, Q. Huang, et al., “Retained introns increase putative microRNA targets within UTRs of human mRNA,” FEBS Letters, vol. 581, no. 6, pp. 1081–1086, 2007. View at Publisher · View at Google Scholar · View at PubMed
- R. I. Gregory, K.-P. Yan, G. Amuthan, et al., “The Microprocessor complex mediates the genesis of microRNAs,” Nature, vol. 432, no. 7014, pp. 235–240, 2004. View at Publisher · View at Google Scholar · View at PubMed
- A. M. Denli, B. B. J. Tops, R. H. A. Plasterk, R. F. Ketting, and G. J. Hannon, “Processing of primary microRNAs by the microprocessor complex,” Nature, vol. 432, no. 7014, pp. 231–235, 2004. View at Publisher · View at Google Scholar · View at PubMed
- E. Berezikov, W.-J. Chung, J. Willis, E. Cuppen, and E. C. Lai, “Mammalian mirtron genes,” Molecular Cell, vol. 28, no. 2, pp. 328–336, 2007. View at Publisher · View at Google Scholar · View at PubMed
- D. J. Luciano, H. Mirsky, N. J. Vendetti, and S. Maas, “RNA editing of a miRNA precursor,” RNA, vol. 10, no. 8, pp. 1174–1177, 2004. View at Publisher · View at Google Scholar · View at PubMed
- R. Matsuoka, “Study of the vertebrate MHC multigene family during heart development,” Advances in Experimental Medicine and Biology, vol. 538, pp. 17–30, 2003.
- B. A. Janowski, S. T. Younger, D. B. Hardy, R. Ram, K. E. Huffman, and D. R. Corey, “Activating gene expression in mammalian cells with promoter-targeted duplex RNAs,” Nature Chemical Biology, vol. 3, no. 3, pp. 166–173, 2007. View at Publisher · View at Google Scholar · View at PubMed
- D. S. Schwarz, G. Hutvágner, T. Du, Z. Xu, N. Aronin, and P. D. Zamore, “Asymmetry in the assembly of the RNAi enzyme complex,” Cell, vol. 115, no. 2, pp. 199–208, 2003. View at Publisher · View at Google Scholar
- T. Hirose, M.-D. Shu, and J. A. Steitz, “Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells,” Molecular Cell, vol. 12, no. 1, pp. 113–123, 2003. View at Publisher · View at Google Scholar
- A. Clop, F. Marcq, H. Takeda, et al., “A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep,” Nature Genetics, vol. 38, no. 7, pp. 813–818, 2006. View at Publisher · View at Google Scholar · View at PubMed
- A. Grishok, A. E. Pasquinelli, D. Conte, et al., “Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing,” Cell, vol. 106, no. 1, pp. 23–34, 2001. View at Publisher · View at Google Scholar
- G. Hutvágner, J. McLachlan, A. E. Pasquinelli, E. Bálint, T. Tuschl, and P. D. Zamore, “A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA,” Science, vol. 293, no. 5531, pp. 834–838, 2001. View at Publisher · View at Google Scholar · View at PubMed
- R. C. Lee and V. Ambros, “An extensive class of small RNAs in Caenorhabditis elegans,” Science, vol. 294, no. 5543, pp. 862–864, 2001. View at Publisher · View at Google Scholar · View at PubMed
- J. W. Pham, J. L. Pellino, Y. S. Lee, R. W. Carthew, and E. J. Sontheimer, “A Dicer-2-dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila,” Cell, vol. 117, no. 1, pp. 83–94, 2004. View at Publisher · View at Google Scholar
- J. Winter, S. Jung, S. Keller, R. I. Gregory, and S. Diederichs, “Many roads to maturity: microRNA biogenesis pathways and their regulation,” Nature Cell Biology, vol. 11, no. 3, pp. 228–234, 2009. View at Publisher · View at Google Scholar · View at PubMed
- P. Bertone, V. Stolc, T. E. Royce, et al., “Global identification of human transcribed sequences with genome tiling arrays,” Science, vol. 306, no. 5705, pp. 2242–2246, 2004. View at Publisher · View at Google Scholar · View at PubMed
- J. S. Pedersen, G. Bejerano, A. Siepel, et al., “Identification and classification of conserved RNA secondary structures in the human genome,” PLoS Computational Biology, vol. 2, no. 4, article e33, 2006.
- P. Landgraf, M. Rusu, R. Sheridan, et al., “A mammalian microRNA expression atlas based on small RNA library sequencing,” Cell, vol. 129, no. 7, pp. 1401–1414, 2007. View at Publisher · View at Google Scholar · View at PubMed
- R. Yelin, D. Dahary, R. Sorek, et al., “Widespread occurrence of antisense transcription in the human genome,” Nature Biotechnology, vol. 21, no. 4, pp. 379–386, 2003. View at Publisher · View at Google Scholar · View at PubMed
- G. Lavorgna, D. Dahary, B. Lehner, R. Sorek, C. M. Sanderson, and G. Casari, “In search of antisense,” Trends in Biochemical Sciences, vol. 29, no. 2, pp. 88–94, 2004. View at Publisher · View at Google Scholar · View at PubMed
- K. Okamura, J. W. Hagen, H. Duan, D. M. Tyler, and E. C. Lai, “The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila,” Cell, vol. 130, no. 1, pp. 89–100, 2007. View at Publisher · View at Google Scholar · View at PubMed
- J. G. Ruby, C. H. Jan, and D. P. Bartel, “Intronic microRNA precursors that bypass Drosha processing,” Nature, vol. 448, no. 7149, pp. 83–86, 2007. View at Publisher · View at Google Scholar · View at PubMed
- M. Lagos-Quintana, R. Rauhut, W. Lendeckel, and T. Tuschl, “Identification of novel genes coding for small expressed RNAs,” Science, vol. 294, no. 5543, pp. 853–858, 2001. View at Publisher · View at Google Scholar · View at PubMed
- E. C. Lai, P. Tomancak, R. W. Williams, and G. M. Rubin, “Computational identification of Drosophila microRNA genes,” Genome Biology, vol. 4, no. 7, article R42, 2003.
- Y. Altuvia, P. Landgraf, G. Lithwick, et al., “Clustering and conservation patterns of human microRNAs,” Nucleic Acids Research, vol. 33, no. 8, pp. 2697–2706, 2005. View at Publisher · View at Google Scholar · View at PubMed
- S. Baskerville and D. P. Bartel, “Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes,” RNA, vol. 11, no. 3, pp. 241–247, 2005. View at Publisher · View at Google Scholar · View at PubMed
- M. J. Weber, “New human and mouse microRNA genes found by homology search,” FEBS Journal, vol. 272, no. 1, pp. 59–73, 2005. View at Publisher · View at Google Scholar · View at PubMed
- E. Berezikov, G. van Tetering, M. Verheul, et al., “Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis,” Genome Research, vol. 16, no. 10, pp. 1289–1298, 2006. View at Publisher · View at Google Scholar · View at PubMed
- S.-L. Lin, J. D. Miller, and S.-Y. Ying, “Intronic microRNA (miRNA),” Journal of Biomedicine and Biotechnology, vol. 2006, no. 4, p. 26818, 2006. View at Publisher · View at Google Scholar · View at PubMed
- Y.-K. Kim and V. N. Kim, “Processing of intronic microRNAs,” The EMBO Journal, vol. 26, no. 3, pp. 775–783, 2007. View at Publisher · View at Google Scholar · View at PubMed
- Y. Liang, D. Ridzon, L. Wong, and C. Chen, “Characterization of microRNA expression profiles in normal human tissues,” BMC Genomics, vol. 8, article 166, 2007. View at Publisher · View at Google Scholar · View at PubMed
- A. Sewer, N. Paul, P. Landgraf, et al., “Identification of clustered microRNAs using an ab initio prediction method,” BMC Bioinformatics, vol. 6, article 267, 2005. View at Publisher · View at Google Scholar · View at PubMed
- H. Seitz, H. Royo, M.-L. Bortolin, S.-P. Lin, A. C. Ferguson-Smith, and J. Cavaillé, “A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain,” Genome Research, vol. 14, no. 9, pp. 1741–1748, 2004. View at Publisher · View at Google Scholar · View at PubMed
- B. Zhang, X. Pan, C. H. Cannon, G. P. Cobb, and T. A. Anderson, “Conservation and divergence of plant microRNA genes,” Plant Journal, vol. 46, no. 2, pp. 243–259, 2006. View at Publisher · View at Google Scholar · View at PubMed
- U. Ohler, S. Yekta, L. P. Lim, D. P. Bartel, and C. B. Burge, “Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification,” RNA, vol. 10, no. 9, pp. 1309–1322, 2004. View at Publisher · View at Google Scholar · View at PubMed
- J. Lee, Z. Li, R. Brower-Sinning, and B. John, “Regulatory circuit of human microRNA biogenesis,” PLoS Computational Biology, vol. 3, no. 4, article e67, 2007. View at Publisher · View at Google Scholar · View at PubMed
- X. Zhou, J. Ruan, G. Wang, and W. Zhang, “Characterization and identification of microRNA core promoters in four model species,” PLoS Computational Biology, vol. 3, no. 3, article e37, 2007. View at Publisher · View at Google Scholar · View at PubMed
- B. Ason, D. K. Darnell, B. Wittbrodt, et al., “Differences in vertebrate microRNA expression,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 39, pp. 14385–14389, 2006. View at Publisher · View at Google Scholar · View at PubMed
- W. Filipowicz and V. Pogacic, “Biogenesis of small nucleolar ribonucleoproteins,” Current Opinion in Cell Biology, vol. 14, no. 3, pp. 319–327, 2002. View at Publisher · View at Google Scholar
- S. Vincenti, V. de Chiara, I. Bozzoni, and C. Presutti, “The position of yeast snoRNA-coding regions within host introns is essential for their biosynthesis and for efficient splicing of the host pre-mRNA,” RNA, vol. 13, no. 1, pp. 138–150, 2007. View at Publisher · View at Google Scholar · View at PubMed
- E. van Rooij, L. B. Sutherland, X. Qi, J. A. Richardson, J. Hill, and E. N. Olson, “Control of stress-dependent cardiac growth and gene expression by a microRNA,” Science, vol. 316, no. 5824, pp. 575–579, 2007. View at Publisher · View at Google Scholar · View at PubMed
- J. M. Pawlicki and J. A. Steitz, “Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production,” Journal of Cell Biology, vol. 182, no. 1, pp. 61–76, 2008. View at Publisher · View at Google Scholar · View at PubMed
- J. M. Pawlicki and J. A. Steitz, “Subnuclear compartmentalization of transiently expressed polyadenylated pri-microRNAs: processing at transcription sites or accumulation in SC35 foci,” Cell Cycle, vol. 8, no. 3, pp. 345–356, 2009.
- M. Morlando, M. Ballarino, N. Gromak, F. Pagano, I. Bozzoni, and N. J. Proudfoot, “Primary microRNA transcripts are processed co-transcriptionally,” Nature Structural and Molecular Biology, vol. 15, no. 9, pp. 902–909, 2008. View at Publisher · View at Google Scholar · View at PubMed
- N. Shomron and C. Levy, “MicroRNA-biogenesis and pre-mRNA splicing crosstalk,” Journal of Biomedicine and Biotechnology, vol. 2009, Article ID 594678, 6 pages, 2009. View at Publisher · View at Google Scholar · View at PubMed
- S. Butenas, R. F. Branda, C. Van't Veer, K. M. Cawthern, and K. G. Mann, “Platelets and phospholipids in tissue factor-initiated thrombin generation,” Thrombosis and Haemostasis, vol. 86, no. 2, pp. 660–667, 2001.
- 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 PubMed
- E. Morkin, “Control of cardiac myosin heavy chain gene expression,” Microscopy Research and Technique, vol. 50, no. 6, pp. 522–531, 2000. View at Publisher · View at Google Scholar
- 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. View at Publisher · View at Google Scholar · View at PubMed
- R. Revilla-i-Domingo and E. H. Davidson, “Developmental gene network analysis,” International Journal of Developmental Biology, vol. 47, no. 7-8, pp. 695–703, 2003.
- L. F. Sempere, C. N. Cole, M. A. Mcpeek, and K. J. Peterson, “The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint,” Journal of Experimental Zoology Part B, vol. 306, no. 6, pp. 575–588, 2006. View at Publisher · View at Google Scholar · View at PubMed
- 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. View at Publisher · View at Google Scholar · View at PubMed
- 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. View at Publisher · View at Google Scholar · View at PubMed
- K. K.-H. Farh, A. Grimson, C. Jan, et al., “The widespread impact of mammalian microRNAs on mRNA repression and evolution,” Science, vol. 310, no. 5755, pp. 1817–1821, 2005. View at Publisher · View at Google Scholar · View at PubMed
- R. C. Friedman, K. K.-H. Farh, C. B. Burge, and D. P. Bartel, “Most mammalian mRNAs are conserved targets of microRNAs,” Genome Research, vol. 19, no. 1, pp. 92–105, 2009. View at Publisher · View at Google Scholar · View at PubMed
- J. L. Umbach and B. R. Cullen, “The role of RNAi and microRNAs in animal virus replication and antiviral immunity,” Genes & Development, vol. 23, no. 10, pp. 1151–1164, 2009. View at Publisher · View at Google Scholar · View at PubMed
- B. R. Cullen, “Viral and cellular messenger RNA targets of viral microRNAs,” Nature, vol. 457, no. 7228, pp. 421–425, 2009. View at Publisher · View at Google Scholar · View at PubMed
- B. John, A. J. Enright, A. Aravin, T. Tuschl, C. Sander, and D. S. Marks, “Human microRNA targets,” PLoS Biology, vol. 2, no. 11, article e363, 2004. View at Publisher · View at Google Scholar · View at PubMed
- R. Shalgi, D. Lieber, M. Oren, and Y. Pilpel, “Global and local architecture of the mammalian microRNA-transcription factor regulatory network,” PLoS Computational Biology, vol. 3, no. 7, article e131, 2007.
- S. Artzi, A. Kiezun, and N. Shomron, “miRNAminer: a tool for homologous microRNA gene search,” BMC Bioinformatics, vol. 9, article 39, 2008. View at Publisher · View at Google Scholar · View at PubMed
- Q. Jing, S. Huang, S. Guth, et al., “Involvement of microRNA in AU-rich element-mediated mRNA instability,” Cell, vol. 120, no. 5, pp. 623–634, 2005. View at Publisher · View at Google Scholar · View at PubMed
- C. A. Beelman and R. Parker, “Degradation of mRNA in eukaryotes,” Cell, vol. 81, no. 2, pp. 179–183, 1995.
- R. Ashfield, P. Enriquez-Harris, and N. J. Proudfoot, “Transcriptional termination between the closely linked human complement genes C2 and factor B: common termination factor for C2 and c-myc?” The EMBO Journal, vol. 10, no. 13, pp. 4197–4207, 1991.
- M. Yonaha and N. J. Proudfoot, “Transcriptional termination and coupled polyadenylation in vitro,” The EMBO Journal, vol. 19, no. 14, pp. 3770–3777, 2000.
- N. R. Smalheiser and V. I. Torvik, “Alu elements within human mRNAs are probable microRNA targets,” Trends in Genetics, vol. 22, no. 10, pp. 532–536, 2006. View at Publisher · View at Google Scholar · View at PubMed
- K. Newcombe, T. Glassco, and C. Mueller, “Regulation of the DBP promoter by PAR proteins and in leukemic cells bearing an E2A/HLF translocation,” Biochemical and Biophysical Research Communications, vol. 245, no. 2, pp. 633–639, 1998. View at Publisher · View at Google Scholar · View at PubMed
- M. Lapidot and Y. Pilpel, “Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms,” EMBO Reports, vol. 7, no. 12, pp. 1216–1222, 2006. View at Publisher · View at Google Scholar · View at PubMed
- L.-C. Li, S. T. Okino, H. Zhao, et al., “Small dsRNAs induce transcriptional activation in human cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 46, pp. 17337–17342, 2006. View at Publisher · View at Google Scholar · View at PubMed
- F. Saatcioglu, D. J. Perry, D. S. Pasco, and J. B. Fagan, “Multiple DNA-binding factors interact with overlapping specificities at the aryl hydrocarbon response element of the cytochrome P450IA1 gene,” Molecular and Cellular Biology, vol. 10, no. 12, pp. 6408–6416, 1990.
- K. Chen and N. Rajewsky, “The evolution of gene regulation by transcription factors and microRNAs,” Nature Reviews Genetics, vol. 8, no. 2, pp. 93–103, 2007. View at Publisher · View at Google Scholar · View at PubMed
- E. S. Lander, L. M. Linton, B. Birren, et al., “Initial sequencing and analysis of the human genome,” Nature, vol. 409, no. 6822, pp. 860–921, 2001. View at Publisher · View at Google Scholar · View at PubMed
- J. F. Abelson, K. Y. Kwan, B. J. O'Roak, et al., “Sequence variants in SLITRK1 are associated with Tourette's syndrome,” Science, vol. 310, no. 5746, pp. 317–320, 2005. View at Publisher · View at Google Scholar · View at PubMed
- R. Durrett and D. Schmidt, “Waiting for regulatory sequences to appear,” Annals of Applied Probability, vol. 17, no. 1, pp. 1–32, 2007. View at Publisher · View at Google Scholar · View at MathSciNet
- A. Stark, J. Brennecke, N. Bushati, R. B. Russell, and S. M. Cohen, “Animal microRNAs confer robustness to gene expression and have a significant impact on UTR evolution,” Cell, vol. 123, no. 6, pp. 1133–1146, 2005. View at Publisher · View at Google Scholar · View at PubMed