메뉴 건너뛰기




Volumn 5, Issue 1, 2015, Pages 905-920

The expansion of animal microRNA families revisited

Author keywords

Dollo parsimony; Gene loss; Genome duplication; Innovation; Metazoa; MicroRNA

Indexed keywords

ANIMALIA; ENOPLEA; EUKARYOTA; EUTHERIA; INVERTEBRATA; METAZOA; RHABDITOIDEA; UROCHORDATA; VERTEBRATA;

EID: 84924658050     PISSN: None     EISSN: 20751729     Source Type: Journal    
DOI: 10.3390/life5010905     Document Type: Article
Times cited : (43)

References (58)
  • 1
    • 84880770383 scopus 로고    scopus 로고
    • Diversifying microRNA sequence and function
    • Ameres, S. L.; Zamore, P. D. Diversifying microRNA sequence and function. Nat. Rev. Mol. Cell Biol. 2013, 14, 475–488.
    • (2013) Nat. Rev. Mol. Cell Biol , vol.14 , pp. 475-488
    • Ameres, S.L.1    Zamore, P.D.2
  • 2
    • 33745951984 scopus 로고    scopus 로고
    • On the origin and functions of RNA-mediated silencing: From protists to man
    • Cerutti, H.; Casas-Mollano, J. A. On the origin and functions of RNA-mediated silencing: From protists to man. Curr. Genet. 2006, 50, 81–99.
    • (2006) Curr. Genet , vol.50 , pp. 81-99
    • Cerutti, H.1    Casas-Mollano, J.A.2
  • 3
    • 51449085579 scopus 로고    scopus 로고
    • Origins and evolution of eukaryotic RNA interference
    • Shabalina, S. A.; Koonin, E. V. Origins and evolution of eukaryotic RNA interference. Trends Ecol. Evol. 2008, 23, 578–587.
    • (2008) Trends Ecol. Evol , vol.23 , pp. 578-587
    • Shabalina, S.A.1    Koonin, E.V.2
  • 5
    • 38049141363 scopus 로고    scopus 로고
    • Antisense RNA and RNAi in protozoan parasites: Working hard or hardly working?
    • Militello, K. T.; Refour, P.; Comeaux, C. A.; Duraisingh, M. T. Antisense RNA and RNAi in protozoan parasites: Working hard or hardly working? Mol. Biochem. Parasitol. 2008, 157, 117–126.
    • (2008) Mol. Biochem. Parasitol , vol.157 , pp. 117-126
    • Militello, K.T.1    Refour, P.2    Comeaux, C.A.3    Duraisingh, M.T.4
  • 6
    • 77954063506 scopus 로고    scopus 로고
    • A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a Metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii
    • Braun, L.; Cannella, D.; Ortet, P.; Barakat, M.; Sautel, C. F.; Kieffer, S.; Garin, J.; Bastien, O.; Voinnet, O.; Hakimi, M.A.; et al. A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a Metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathog. 2010, 6, e1000920.
    • (2010) Plos Pathog , vol.6
    • Braun, L.1    Cannella, D.2    Ortet, P.3    Barakat, M.4    Sautel, C.F.5    Kieffer, S.6    Garin, J.7    Bastien, O.8    Voinnet, O.9    Hakimi, M.A.10
  • 7
    • 84866631065 scopus 로고    scopus 로고
    • MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs
    • Avesson, L.; Reimegård, J.; Wagner, E. G.; Söderbom, F. MicroRNAs in Amoebozoa: Deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs. RNA 2012, 18, 1771–1782.
    • (2012) RNA , vol.18 , pp. 1771-1782
    • Avesson, L.1    Reimegård, J.2    Wagner, E.G.3    Söderbom, F.4
  • 8
    • 57149094023 scopus 로고    scopus 로고
    • SnoRNA, a novel precursor of microRNA in Giardia lamblia
    • Saraiya, A. A.; Wang, C.C. snoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog. 2008, 4, e1000224.
    • (2008) Plos Pathog , vol.4
    • Saraiya, A.A.1    Wang, C.C.2
  • 9
    • 78650480483 scopus 로고    scopus 로고
    • High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis
    • Chen, X. S.; Collins, L. J.; Biggs, P. J.; Penny, D. High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol. Evol. 2009, 1, 165–175.
    • (2009) Genome Biol. Evol , vol.1 , pp. 165-175
    • Chen, X.S.1    Collins, L.J.2    Biggs, P.J.3    Penny, D.4
  • 10
    • 79959439535 scopus 로고    scopus 로고
    • Neutral evolution of robustness in Drosophila microRNA precursors
    • Price, N.; Cartwright, R. A.; Sabath, N.; Graur, D.; Azevedo, R. B. Neutral evolution of robustness in Drosophila microRNA precursors. Mol. Biol. Evol. 2011, 28, 2115–2123.
    • (2011) Mol. Biol. Evol , vol.28 , pp. 2115-2123
    • Price, N.1    Cartwright, R.A.2    Sabath, N.3    Graur, D.4    Azevedo, R.B.5
  • 11
    • 33644772270 scopus 로고    scopus 로고
    • The Students of Bioinformatics Computer Labs 2004 and 2005. The Expansion of the Metazoan MicroRNA Repertoire
    • Hertel, J.; Lindemeyer, M.; Missal, K.; Fried, C.; Tanzer, A.; Flamm, C.; Hofacker, I. L.; Stadler, P. F.; The Students of Bioinformatics Computer Labs 2004 and 2005. The Expansion of the Metazoan MicroRNA Repertoire. BMC Genomics 2006, 7, doi:10.1186/1471-2164-7-25.
    • (2006) BMC Genomics , pp. 7
    • Hertel, J.1    Lindemeyer, M.2    Missal, K.3    Fried, C.4    Tanzer, A.5    Flamm, C.6    Hofacker, I.L.7    Stadler, P.F.8
  • 12
    • 2342450524 scopus 로고    scopus 로고
    • Molecular Evolution of a MicroRNA Cluster
    • Tanzer, A.; Stadler, P. F. Molecular Evolution of a MicroRNA Cluster. J. Mol. Biol. 2004, 339, 327–335.
    • (2004) J. Mol. Biol , vol.339 , pp. 327-335
    • Tanzer, A.1    Stadler, P.F.2
  • 15
    • 33845608152 scopus 로고    scopus 로고
    • The phylogenetic distribution of Metazoan microRNAs: Insights into evolutionary complexity and constraint
    • Sempere, L. F.; Cole, C. N.; McPeek, M. A.; Peterson, K. J. The phylogenetic distribution of Metazoan microRNAs: Insights into evolutionary complexity and constraint. J. Exp. Zool. B Mol. Dev. Evol. 2006, 306B, 575–588.
    • (2006) J. Exp. Zool. B Mol. Dev. Evol , vol.306B , pp. 575-588
    • Sempere, L.F.1    Cole, C.N.2    McPeek, M.A.3    Peterson, K.J.4
  • 17
    • 78650592620 scopus 로고    scopus 로고
    • MicroRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate
    • Heimberg, A. M.; Cowper-Sallari, R.; Sémon, M.; Donoghue, P. C.; Peterson, K. J. MicroRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate. Proc. Natl. Acad. Sci. USA 2010, 107, 19379–19383.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 19379-19383
    • Heimberg, A.M.1    Cowper-Sallari, R.2    Sémon, M.3    Donoghue, P.C.4    Peterson, K.J.5
  • 19
    • 44649088993 scopus 로고    scopus 로고
    • Altered miRNA Repertoire in the Simplified Chordate, Oikopleura dioica
    • Fu, X.; Adamski, M.; Thompson, E. M. Altered miRNA Repertoire in the Simplified Chordate, Oikopleura dioica. Mol. Biol. Evol. 2008, 25, 1067–1080.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 1067-1080
    • Fu, X.1    Adamski, M.2    Thompson, E.M.3
  • 24
    • 78650942892 scopus 로고    scopus 로고
    • MicroRNA complements in deuterostomes: Origin and evolution of microRNAs
    • Campo-Paysaa, F.; Sémon, M.; Cameron, R. A.; Peterson, K. J.; Schubert, M. MicroRNA complements in deuterostomes: Origin and evolution of microRNAs. Evol. Dev. 2011, 13, 15–27.
    • (2011) Evol. Dev , vol.13 , pp. 15-27
    • Campo-Paysaa, F.1    Sémon, M.2    Cameron, R.A.3    Peterson, K.J.4    Schubert, M.5
  • 25
    • 84880530293 scopus 로고    scopus 로고
    • Clusters of microRNAs emerge by new hairpins in existing transcripts
    • Marco, A.; Ninova, M.; Ronshaugen, M.; Griffiths-Jones, S. Clusters of microRNAs emerge by new hairpins in existing transcripts. Nucleic Acids Res. 2013, 41, 7745–7752.
    • (2013) Nucleic Acids Res , vol.41 , pp. 7745-7752
    • Marco, A.1    Ninova, M.2    Ronshaugen, M.3    Griffiths-Jones, S.4
  • 26
    • 66249117657 scopus 로고    scopus 로고
    • Lowly expressed human microRNA genes evolve rapidly
    • Liang, H.; Li, W. Lowly expressed human microRNA genes evolve rapidly. Mol. Biol. Evol. 2009, 26, 1195–1198.
    • (2009) Mol. Biol. Evol , vol.26 , pp. 1195-1198
    • Liang, H.1    Li, W.2
  • 28
    • 34248638447 scopus 로고    scopus 로고
    • Evolutionary conservation of microRNA regulatory circuits: An examination of microRNA gene complexity and conserved microRNA-target interactions through Metazoan phylogeny
    • Lee, C. T.; Risom, T.; Strauss, W. M. Evolutionary conservation of microRNA regulatory circuits: An examination of microRNA gene complexity and conserved microRNA-target interactions through Metazoan phylogeny. DNA Cell Biol. 2007, 26, 209–218.
    • (2007) DNA Cell Biol , vol.26 , pp. 209-218
    • Lee, C.T.1    Risom, T.2    Strauss, W.M.3
  • 29
    • 34147147595 scopus 로고    scopus 로고
    • The evolution of animal microRNA function
    • Niwa, R.; Slack, F. J. The evolution of animal microRNA function. Curr. Opin. Genet. Dev. 2007, 17, 145–150.
    • (2007) Curr. Opin. Genet. Dev , vol.17 , pp. 145-150
    • Niwa, R.1    Slack, F.J.2
  • 30
    • 33846052292 scopus 로고    scopus 로고
    • Evidence for a microRNA expansion in the bilaterian ancestor
    • Prochnik, S. E.; Rokhsar, D. S.; Aboobaker, A. A. Evidence for a microRNA expansion in the bilaterian ancestor. Dev. Genes Evol. 2007, 217, 73–77.
    • (2007) Dev. Genes Evol , vol.217 , pp. 73-77
    • Prochnik, S.E.1    Rokhsar, D.S.2    Aboobaker, A.A.3
  • 31
    • 81355123438 scopus 로고    scopus 로고
    • Evolution of microRNA diversity and regulation in animals
    • Berezikov, E. Evolution of microRNA diversity and regulation in animals. Nat. Rev. Genet. 2011, 12, 846–860.
    • (2011) Nat. Rev. Genet , vol.12 , pp. 846-860
    • Berezikov, E.1
  • 32
    • 58549099701 scopus 로고    scopus 로고
    • Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution
    • Dai, Z.; Chen, Z.; Ye, H.; Zhou, L.; Cao, L.; Wang, Y.; Peng, S.; Chen, L. Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution. Evol. Dev. 2009, 11, 41–49.
    • (2009) Evol. Dev , vol.11 , pp. 41-49
    • Dai, Z.1    Chen, Z.2    Ye, H.3    Zhou, L.4    Cao, L.5    Wang, Y.6    Peng, S.7    Chen, L.8
  • 34
    • 84891818318 scopus 로고    scopus 로고
    • MiRBase: Annotating high confidence microRNAs using deep sequencing data
    • Kozomara, A. K.; Griffiths-Jones, S. miRBase: Annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014, 42, D68–D73.
    • (2014) Nucleic Acids Res , vol.42 , pp. D68-D73
    • Kozomara, A.K.1    Griffiths-Jones, S.2
  • 36
    • 34247598415 scopus 로고    scopus 로고
    • Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
    • Will, S.; Reiche, K.; Hofacker, I. L.; Stadler, P. F.; Backofen, R. Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. 2007, 3, e65.
    • (2007) Plos Comput. Biol , pp. 3
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 38
    • 19444367079 scopus 로고    scopus 로고
    • Mammalian microRNAs derived from genomic repeats
    • Smalheiser, N. R.; Torvik, V. I. Mammalian microRNAs derived from genomic repeats. Trends Genet. 2005, 21, 322–326.
    • (2005) Trends Genet , vol.21 , pp. 322-326
    • Smalheiser, N.R.1    Torvik, V.I.2
  • 39
    • 34250776711 scopus 로고    scopus 로고
    • A family of human microRNA genes from miniature inverted-repeat transposable elements
    • Piriyapongsa, J.; Jordan, I. K. A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One 2007, 2, e203.
    • (2007) Plos One , pp. 2
    • Piriyapongsa, J.1    Jordan, I.K.2
  • 40
    • 84959795073 scopus 로고
    • Phylogenetic analysis under Dollo’s law
    • Farris, J. S. Phylogenetic analysis under Dollo’s law. Syst. Zool. 1977, 26, 77–88.
    • (1977) Syst. Zool , vol.26 , pp. 77-88
    • Farris, J.S.1
  • 41
    • 0016424695 scopus 로고
    • Minimal mutation trees of sequences
    • Sankoff, D. Minimal mutation trees of sequences. SIAM J. Appl. Math. 1975, 28, 35–42.
    • (1975) SIAM J. Appl. Math , vol.28 , pp. 35-42
    • Sankoff, D.1
  • 42
    • 84924681429 scopus 로고    scopus 로고
    • Available online, (accessed on 11 February 2015)
    • ePoPE: efficient Prediction of Paralog Evolution. Available online: http://www.bioinf.uni-leipzig.de/Software/ePoPE/(accessed on 11 February 2015).
    • Efficient Prediction of Paralog Evolution
  • 43
    • 84875275813 scopus 로고    scopus 로고
    • Impact of whole-genome duplication on vertebrate development and evolution
    • Kasahara, M. Impact of whole-genome duplication on vertebrate development and evolution. Semin. Cell Dev. Biol. 2013, 24, 81–82.
    • (2013) Semin. Cell Dev. Biol , vol.24 , pp. 81-82
    • Kasahara, M.1
  • 44
    • 84857924074 scopus 로고    scopus 로고
    • Hypothesis for the modern RNA world: A pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence 2 of multicellular complexity
    • Lozada-Chávez, I.; Stadler, P. F.; Prohaska, S.J. “Hypothesis for the modern RNA world”: A pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence 2 of multicellular complexity. Orig. Life Evol. Biosph. 2011, 41, 587–607.
    • (2011) Orig. Life Evol. Biosph , vol.41 , pp. 587-607
    • Lozada-Chávez, I.1    Stadler, P.F.2    Prohaska, S.J.3
  • 45
    • 70349320089 scopus 로고    scopus 로고
    • MicroRNAs and Metazoan macroevolution: Insights into canalization, complexity, and the Cambrian explosion
    • Peterson, K. J.; Dietrich, M. R.; McPeek, M. A. MicroRNAs and Metazoan macroevolution: Insights into canalization, complexity, and the Cambrian explosion. BioEssays 2009, 31, 736–747.
    • (2009) Bioessays , vol.31 , pp. 736-747
    • Peterson, K.J.1    Dietrich, M.R.2    McPeek, M.A.3
  • 47
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch, M.; Conery, J. S. The evolutionary fate and consequences of duplicate genes. Science 2000, 290, 1151–1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 49
    • 79956329403 scopus 로고    scopus 로고
    • Evolutionary crossroads in developmental biology
    • Lemaire, P. Evolutionary crossroads in developmental biology: The tunicates. Development 2011, 138, 2143–2152.
    • (2011) The Tunicates. Development , vol.138 , pp. 2143-2152
    • Lemaire, P.1
  • 50
    • 69949132925 scopus 로고    scopus 로고
    • Embryogenesis of Romanomermis culicivorax: An alternative way to construct a nematode
    • Schulze, J.; Schierenberg, E. Embryogenesis of Romanomermis culicivorax: An alternative way to construct a nematode. Dev. Biol. 2009, 334, 10–21.
    • (2009) Dev. Biol , vol.334 , pp. 10-21
    • Schulze, J.1    Schierenberg, E.2
  • 51
    • 72749120240 scopus 로고    scopus 로고
    • MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record
    • Sperling, E.; Vinther, J.; Moy, V.; Wheeler, B.; Semon, M.; Briggs, D.; Peterson, K. MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record. Proc. Biol. Sci. 2009, 276, 4315–4322.
    • (2009) Proc. Biol. Sci , vol.276 , pp. 4315-4322
    • Sperling, E.1    Vinther, J.2    Moy, V.3    Wheeler, B.4    Semon, M.5    Briggs, D.6    Peterson, K.7
  • 52
    • 84867088834 scopus 로고    scopus 로고
    • The oyster genome reveals stress adaptation and complexity of shell formation
    • Zhang, G.; Fang, X.; Guo, X.; Li, L.; Luo, R.; Xu, F.; Yang, P.; Zhang, L.; Wang, X.; Qi, H., et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 2012, 490, 49–54.
    • (2012) Nature , vol.490 , pp. 49-54
    • Zhang, G.1    Fang, X.2    Guo, X.3    Li, L.4    Luo, R.5    Xu, F.6    Yang, P.7    Zhang, L.8    Wang, X.9    Qi, H.10
  • 55
    • 71849109186 scopus 로고    scopus 로고
    • The Tedious Task of Finding Homologous Non-coding RNA Genes
    • Menzel, P.; Gorodkin, J.; Stadler, P. F. The Tedious Task of Finding Homologous Non-coding RNA Genes. RNA 2009, 15, 2075–2082.
    • (2009) RNA , vol.15 , pp. 2075-2082
    • Menzel, P.1    Gorodkin, J.2    Stadler, P.F.3
  • 56
    • 33644919969 scopus 로고    scopus 로고
    • Primate MicroRNAs miR-220 and miR-492 Lie within Processed Pseudogenes
    • Devor, E. J. Primate MicroRNAs miR-220 and miR-492 Lie within Processed Pseudogenes. J. Hered. 2005, 97, 186–190.
    • (2005) J. Hered , vol.97 , pp. 186-190
    • Devor, E.J.1
  • 57
    • 84924743283 scopus 로고    scopus 로고
    • Pitfalls of Ascertainment Biases in Genome Annotations—Computing Comparable Protein Domain Distributions in Eukarya. Malays
    • Parikesit, A. A.; Steiner, L.; Stadler, P. F.; Prohaska, S. J. Pitfalls of Ascertainment Biases in Genome Annotations—Computing Comparable Protein Domain Distributions in Eukarya. Malays. J. Fundam. Appl. Sci. 2014, 10, 65–75.
    • (2014) J. Fundam. Appl. Sci , vol.10 , pp. 65-75
    • Parikesit, A.A.1    Steiner, L.2    Stadler, P.F.3    Prohaska, S.J.4
  • 58
    • 84860779005 scopus 로고    scopus 로고
    • Evolution and function of the extended miR-2 microRNA family
    • Marco, A.; Hooks, K.; Griffiths-Jones, S. Evolution and function of the extended miR-2 microRNA family. RNA Biol. 2012, 9, 242–248.
    • (2012) RNA Biol , vol.9 , pp. 242-248
    • Marco, A.1    Hooks, K.2    Griffiths-Jones, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.