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Volumn 40, Issue 13, 2012, Pages 5890-5900

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

EID: 84864449330     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks279     Document Type: Article
Times cited : (46)

References (76)
  • 1
    • 60149088848 scopus 로고    scopus 로고
    • Origins and mechanisms of mirnas and sirnas
    • Carthew, R.W. and Sontheimer, E.J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell, 136, 642-655.
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 2
    • 77956275374 scopus 로고    scopus 로고
    • MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain
    • Somel, M., Guo, S., Fu, N., Yan, Z., Hu, H.Y., Xu, Y., Yuan, Y., Ning, Z., Hu, Y., Menzel, C. et al. (2010) MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res., 20, 1207-1218.
    • (2010) Genome Res. , vol.20 , pp. 1207-1218
    • Somel, M.1    Guo, S.2    Fu, N.3    Yan, Z.4    Hu, H.Y.5    Xu, Y.6    Yuan, Y.7    Ning, Z.8    Hu, Y.9    Menzel, C.10
  • 3
    • 33748928159 scopus 로고    scopus 로고
    • The diverse functions of MicroRNAs in animal development and disease
    • Kloosterman, W.P. and Plasterk, R.H.A. (2006) The diverse functions of MicroRNAs in animal development and disease. Dev Cell, 11, 441-450.
    • (2006) Dev Cell , vol.11 , pp. 441-450
    • Kloosterman, W.P.1    Plasterk, R.H.A.2
  • 4
    • 84855175650 scopus 로고    scopus 로고
    • MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates
    • Somel, M., Liu, X., Tang, L., Yan, Z., Hu, H., Guo, S., Jiang, X., Zhang, X., Xu, G., Xie, G. et al. (2011) MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PLoS Biol., 9, e1001214.
    • (2011) PLoS Biol. , vol.9
    • Somel, M.1    Liu, X.2    Tang, L.3    Yan, Z.4    Hu, H.5    Guo, S.6    Jiang, X.7    Zhang, X.8    Xu, G.9    Xie, G.10
  • 6
    • 34248196026 scopus 로고    scopus 로고
    • Rapid evolution of an X-linked MicroRNA cluster in primates
    • Zhang, R., Peng, Y., Wang, W. and Su, B. (2007) Rapid evolution of an X-linked MicroRNA cluster in primates. Genome Res., 17, 612-617.
    • (2007) Genome Res. , vol.17 , pp. 612-617
    • Zhang, R.1    Peng, Y.2    Wang, W.3    Su, B.4
  • 7
    • 34147147595 scopus 로고    scopus 로고
    • The evolution of animal MicroRNA function
    • Niwa, R. and Slack, F.J. (2007) The evolution of animal MicroRNA function. Curr. Opin. Genet. Dev., 17, 145-150.
    • (2007) Curr. Opin. Genet. Dev. , vol.17 , pp. 145-150
    • Niwa, R.1    Slack, F.J.2
  • 8
    • 37249025294 scopus 로고    scopus 로고
    • Systematic discovery and characterization of fly MicroRNAs using 12 drosophila genomes
    • Stark, A., Kheradpour, P., Parts, L., Brennecke, J., Hodges, E., Hannon, G.J. and Kellis, M. (2007) Systematic discovery and characterization of fly MicroRNAs using 12 Drosophila genomes. Genome Res., 17, 1865-1879.
    • (2007) Genome Res. , vol.17 , pp. 1865-1879
    • Stark, A.1    Kheradpour, P.2    Parts, L.3    Brennecke, J.4    Hodges, E.5    Hannon, G.J.6    Kellis, M.7
  • 9
    • 66049153398 scopus 로고    scopus 로고
    • Evolution under canalization and the dual roles of MicroRNAs: A hypothesis
    • Wu, C.I., Shen, Y. and Tang, T. (2009) Evolution under canalization and the dual roles of MicroRNAs: a hypothesis. Genome Res., 19, 734-743.
    • (2009) Genome Res. , vol.19 , pp. 734-743
    • Wu, C.I.1    Shen, Y.2    Tang, T.3
  • 10
    • 54149095553 scopus 로고    scopus 로고
    • Biological principles of MicroRNA-mediated regulation: Shared themes amid diversity
    • Flynt, A.S. and Lai, E.C. (2008) Biological principles of MicroRNA-mediated regulation: shared themes amid diversity. Nat. Rev. Genet., 9, 831-842.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 831-842
    • Flynt, A.S.1    Lai, E.C.2
  • 11
    • 1942435249 scopus 로고    scopus 로고
    • Micromanagers of gene expression: The potentially widespread influence of metazoan MicroRNAs
    • Bartel, D.P. and Chen, C.-Z. (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan MicroRNAs. Nat. Rev. Genet., 5, 396-400.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 396-400
    • Bartel, D.P.1    Chen, C.-Z.2
  • 12
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAs confer robustness to gene expression and have a significant impact on 30UTR evolution
    • 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 30UTR evolution. Cell, 123, 1133-1146.
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 13
    • 0037819447 scopus 로고    scopus 로고
    • Transcription regulation and animal diversity
    • Levine, M. and Tjian, R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
    • (2003) Nature , vol.424 , pp. 147-151
    • Levine, M.1    Tjian, R.2
  • 15
    • 33846052292 scopus 로고    scopus 로고
    • Evidence for a MicroRNA expansion in the bilaterian ancestor
    • Prochnik, S., Rokhsar, D. and Aboobaker, A. (2007) Evidence for a MicroRNA expansion in the bilaterian ancestor. Dev. Genes Evol., 217, 73-77.
    • (2007) Dev. Genes Evol. , vol.217 , pp. 73-77
    • Prochnik, S.1    Rokhsar, D.2    Aboobaker, A.3
  • 18
    • 70349320089 scopus 로고    scopus 로고
    • MicroRNAs and metazoan macroevolution: Insights into canalization, complexity, and the cambrian explosion
    • Peterson, K.J., Dietrich, M.R. and McPeek, M.A. (2009) MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion. BioEssays, 31, 736-747.
    • (2009) BioEssays , vol.31 , pp. 736-747
    • Peterson, K.J.1    Dietrich, M.R.2    McPeek, M.A.3
  • 20
    • 78650942892 scopus 로고    scopus 로고
    • MicroRNA complements in deuterostomes: Origin and evolution of MicroRNAs
    • Campo-Paysaa, F., Semon, M., Cameron, R.A., Peterson, K.J. and Schubert, M. (2011) MicroRNA complements in deuterostomes: origin and evolution of MicroRNAs. Evol. Dev., 13, 15-27.
    • (2011) Evol. Dev. , vol.13 , pp. 15-27
    • Campo-Paysaa, F.1    Semon, M.2    Cameron, R.A.3    Peterson, K.J.4    Schubert, M.5
  • 21
    • 33846283385 scopus 로고    scopus 로고
    • The evolution of gene regulation by transcription factors and MicroRNAs
    • Chen, K. and Rajewsky, N. (2007) The evolution of gene regulation by transcription factors and MicroRNAs. Nat. Rev. Genet., 8, 93-103.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 93-103
    • Chen, K.1    Rajewsky, N.2
  • 23
    • 51449085579 scopus 로고    scopus 로고
    • Origins and evolution of eukaryotic RNA interference
    • Shabalina, S.A. and Koonin, E.V. (2008) Origins and evolution of eukaryotic RNA interference. Trends Ecol. Evol., 23, 578-587.
    • (2008) Trends Ecol. Evol. , vol.23 , pp. 578-587
    • Shabalina, S.A.1    Koonin, E.V.2
  • 24
    • 53349180220 scopus 로고    scopus 로고
    • The evolution and functional diversification of animal MicroRNA genes
    • Liu, N., Okamura, K., Tyler, D.M., Phillips, M.D., Chung, W.J. and Lai, E.C. (2008) The evolution and functional diversification of animal MicroRNA genes. Cell Res., 18, 985-996.
    • (2008) Cell Res. , vol.18 , pp. 985-996
    • Liu, N.1    Okamura, K.2    Tyler, D.M.3    Phillips, M.D.4    Chung, W.J.5    Lai, E.C.6
  • 25
    • 67049119074 scopus 로고    scopus 로고
    • Simultaneous Expansions of MicroRNAs and protein-coding genes by gene/genome duplications in early vertebrates
    • Gu, X., Su, Z. and Huang, Y. (2009) Simultaneous expansions of MicroRNAs and protein-coding genes by gene/genome duplications in early vertebrates. J. Exp. Zool. B Mol. Dev. Evol., 312B, 164-170.
    • (2009) J. Exp. Zool. B Mol. Dev. Evol. , vol.312 B , pp. 164-170
    • Gu, X.1    Su, Z.2    Huang, Y.3
  • 26
    • 66249117657 scopus 로고    scopus 로고
    • Lowly expressed human MicroRNA genes evolve rapidly
    • Liang, H. and Li, W.-H. (2009) Lowly expressed human MicroRNA genes evolve rapidly. Mol. Biol. Evol., 26, 1195-1198.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1195-1198
    • Liang, H.1    Li, W.-H.2
  • 28
    • 77958462907 scopus 로고    scopus 로고
    • Origins and evolution of MicroRNA genes in Drosophila species
    • Nozawa, M., Miura, S. and Nei, M. (2010) Origins and evolution of MicroRNA genes in Drosophila species. Genome Biol. Evol., 2, 180-189.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 180-189
    • Nozawa, M.1    Miura, S.2    Nei, M.3
  • 29
    • 38149071979 scopus 로고    scopus 로고
    • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila MicroRNAs
    • Ruby, J.G., Stark, A., Johnston, W.K., Kellis, M., Bartel, D.P. and Lai, E.C. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila MicroRNAs. Genome Res., 17, 1850-1864.
    • (2007) Genome Res. , vol.17 , pp. 1850-1864
    • Ruby, J.G.1    Stark, A.2    Johnston, W.K.3    Kellis, M.4    Bartel, D.P.5    Lai, E.C.6
  • 33
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating MicroRNA annotation and deep-sequencing data
    • Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating MicroRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 35
    • 33751381461 scopus 로고    scopus 로고
    • Timetree: A public knowledge-base of divergence times among organisms
    • Hedges, S.B., Dudley, J. and Kumar, S. (2006) TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics, 22, 2971-2972.
    • (2006) Bioinformatics , vol.22 , pp. 2971-2972
    • Hedges, S.B.1    Dudley, J.2    Kumar, S.3
  • 38
    • 1342345645 scopus 로고    scopus 로고
    • McEntyre, J. and Ostell, J. (eds) National Library of Medicine, US, NCBI, Bethesda, MD
    • Pontius, J.U., Wagner, L. and Schuler, G.D. (2003) In: McEntyre, J. and Ostell, J. (eds), The NCBI Handbook. National Library of Medicine, US, NCBI, Bethesda, MD.
    • (2003) The NCBI Handbook
    • Pontius, J.U.1    Wagner, L.2    Schuler, G.D.3
  • 41
    • 79959813870 scopus 로고    scopus 로고
    • A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
    • Kishore, S., Jaskiewicz, L., Burger, L., Hausser, J., Khorshid, M. and Zavolan, M. (2011) A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat. Methods, 8, 559-564.
    • (2011) Nat. Methods , vol.8 , pp. 559-564
    • Kishore, S.1    Jaskiewicz, L.2    Burger, L.3    Hausser, J.4    Khorshid, M.5    Zavolan, M.6
  • 42
    • 77954522638 scopus 로고    scopus 로고
    • Homolonto: Generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy
    • Parmentier, G., Bastian, F.B. and Robinson-Rechavi, M. (2010) Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics, 26, 1766-1771.
    • (2010) Bioinformatics , vol.26 , pp. 1766-1771
    • Parmentier, G.1    Bastian, F.B.2    Robinson-Rechavi, M.3
  • 44
    • 0030681260 scopus 로고    scopus 로고
    • The significance of digital gene expression profiles
    • Audic, S. and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res., 7, 986-995.
    • (1997) Genome Res. , vol.7 , pp. 986-995
    • Audic, S.1    Claverie, J.M.2
  • 45
    • 34347398567 scopus 로고    scopus 로고
    • Inference of mirna targets using evolutionary conservation and pathway analysis
    • Gaidatzis, D., van Nimwegen, E., Hausser, J. and Zavolan, M. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8, 69.
    • (2007) BMC Bioinformatics , vol.8 , pp. 69
    • Gaidatzis, D.1    Van Nimwegen, E.2    Hausser, J.3    Zavolan, M.4
  • 46
    • 79957579613 scopus 로고    scopus 로고
    • Characterizing the role of mirnas within gene regulatory networks using integrative genomics techniques
    • Su, W.-L., Kleinhanz, R.R. and Schadt, E.E. (2011) Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol. Syst. Biol., 7, 490.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 490
    • Su, W.-L.1    Kleinhanz, R.R.2    Schadt, E.E.3
  • 51
    • 70350212463 scopus 로고    scopus 로고
    • In situ hybridization is a necessary experimental complement to MicroRNA (miRNA) expression profiling in the human brain
    • Nelson, P.T. and Wilfred, B.R. (2009) In situ hybridization is a necessary experimental complement to MicroRNA (miRNA) expression profiling in the human brain. Neurosci. Lett., 466, 69-72.
    • (2009) Neurosci. Lett. , vol.466 , pp. 69-72
    • Nelson, P.T.1    Wilfred, B.R.2
  • 54
    • 33748793116 scopus 로고    scopus 로고
    • Analysis of short RNAs in the malaria parasite and its red blood cell host
    • Rathjen, T., Nicol, C., McConkey, G. and Dalmay, T. (2006) Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett., 580, 5185-5188.
    • (2006) FEBS Lett , vol.580 , pp. 5185-5188
    • Rathjen, T.1    Nicol, C.2    McConkey, G.3    Dalmay, T.4
  • 55
    • 34548013932 scopus 로고    scopus 로고
    • The evolution of sex-biased genes and sex-biased gene expression
    • Ellegren, H. and Parsch, J. (2007) The evolution of sex-biased genes and sex-biased gene expression. Nat. Rev. Genet., 8, 689-698.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 689-698
    • Ellegren, H.1    Parsch, J.2
  • 56
    • 84864453726 scopus 로고    scopus 로고
    • The evolution of the neocortex in mammals: Intrinsic and extrinsic contributions to the cortical phenotype
    • Novartis Foundation Symposium 270, John Wiley & Sons, Ltd, Chichester, UK
    • Karlen, S.J. and Krubitzer, L. (2008) The Evolution of the Neocortex in Mammals: Intrinsic and Extrinsic Contributions to the Cortical Phenotype. In Percept, Decision, Action: Bridging the Gaps. Novartis Foundation Symposium 270, John Wiley & Sons, Ltd, Chichester, UK, pp. 146-163.
    • (2008) Percept, Decision, Action: Bridging the Gaps , pp. 146-163
    • Karlen, S.J.1    Krubitzer, L.2
  • 59
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Ser. B, 57, 289-300.
    • (1995) J. Roy. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 63
    • 77955101812 scopus 로고    scopus 로고
    • Computational methods to identify mirna targets
    • Hammell, M. (2010) Computational methods to identify miRNA targets. Semin. Cell Dev. Biol., 21, 738-744.
    • (2010) Semin. Cell Dev. Biol. , vol.21 , pp. 738-744
    • Hammell, M.1
  • 64
    • 74049088856 scopus 로고    scopus 로고
    • Lost in translation: An assessment and perspective for computational MicroRNA target identification
    • Alexiou, P., Maragkakis, M., Papadopoulos, G.L., Reczko, M. and Hatzigeorgiou, A.G. (2009) Lost in translation: an assessment and perspective for computational MicroRNA target identification. Bioinformatics, 25, 3049-3055.
    • (2009) Bioinformatics , vol.25 , pp. 3049-3055
    • Alexiou, P.1    Maragkakis, M.2    Papadopoulos, G.L.3    Reczko, M.4    Hatzigeorgiou, A.G.5
  • 65
    • 66249106716 scopus 로고    scopus 로고
    • Predicting MicroRNA targets and functions: Traps for the unwary
    • Ritchie, W., Flamant, S. and Rasko, J.E.J. (2009) Predicting MicroRNA targets and functions: traps for the unwary. Nat. Methods, 6, 397-398.
    • (2009) Nat. Methods , vol.6 , pp. 397-398
    • Ritchie, W.1    Flamant, S.2    Rasko, J.E.J.3
  • 67
    • 66149123308 scopus 로고    scopus 로고
    • The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
    • Wolf, Y.I., Novichkov, P.S., Karev, G.P., Koonin, E.V. and Lipman, D.J. (2009) The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc. Natl Acad. Sci. USA, 106, 7273-7280.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 7273-7280
    • Wolf, Y.I.1    Novichkov, P.S.2    Karev, G.P.3    Koonin, E.V.4    Lipman, D.J.5
  • 69
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond, D.A. and Wilke, C.O. (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell, 134, 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 70
    • 58149149757 scopus 로고    scopus 로고
    • Developmental constraints on vertebrate genome evolution
    • Roux, J. and Robinson-Rechavi, M. (2008) Developmental constraints on vertebrate genome evolution. PLoS Genet., 4, e1000311.
    • (2008) PLoS Genet. , vol.4
    • Roux, J.1    Robinson-Rechavi, M.2
  • 71
    • 77953212314 scopus 로고    scopus 로고
    • Paramecium post-genomics, C. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution
    • Gout, J.-F., Kahn, D. and Duret, L. (2010) Paramecium Post-Genomics, C. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet., 6, e1000944.
    • (2010) PLoS Genet , vol.6
    • Gout, J.-F.1    Kahn, D.2    Duret, L.3
  • 73
    • 33846675660 scopus 로고    scopus 로고
    • Global analysis of MicroRNA target gene expression reveals that mirna targets are lower expressed in mature mouse and drosophila tissues than in the embryos
    • Yu, Z., Jian, Z., Shen, S.-H., Purisima, E. and Wang, E. (2007) Global analysis of MicroRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res., 35, 152-164.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 152-164
    • Yu, Z.1    Jian, Z.2    Shen, S.-H.3    Purisima, E.4    Wang, E.5
  • 74
    • 33644499134 scopus 로고    scopus 로고
    • Cell-type-specific signatures of MicroRNAs on target mRNA expression
    • Sood, P., Krek, A., Zavolan, M., Macino, G. and Rajewsky, N. (2006) Cell-type-specific signatures of MicroRNAs on target mRNA expression. Proc. Natl Acad. Sci. USA, 103, 2746-2751.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 2746-2751
    • Sood, P.1    Krek, A.2    Zavolan, M.3    Macino, G.4    Rajewsky, N.5
  • 75
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer MicroRNA target sites
    • Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A. and Burge, C.B. (2008) Proliferating cells express mRNAs with shortened 30 untranslated regions and fewer MicroRNA target sites. Science, 320, 1643-1647.
    • (2008) Science , vol.320 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3    Sharp, P.A.4    Burge, C.B.5
  • 76
    • 39749149956 scopus 로고    scopus 로고
    • Housekeeping genes tend to show reduced upstream sequence conservation
    • Farre, D., Bellora, N., Mularoni, L., Messeguer, X. and Alba, M.M. (2007) Housekeeping genes tend to show reduced upstream sequence conservation. Genome Biol., 8, R140.
    • (2007) Genome Biol , vol.8
    • Farre, D.1    Bellora, N.2    Mularoni, L.3    Messeguer, X.4    Alba, M.M.5


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