메뉴 건너뛰기




Volumn 2, Issue 1, 2010, Pages 180-189

Origins and evolution of microRNA genes in Drosophila species

Author keywords

Birth and death evolution; Gene duplication; Gene regulation; Multigene family; Noncoding RNA; Substitution rate

Indexed keywords

DROSOPHILA PROTEIN; MICRORNA; UNTRANSLATED RNA;

EID: 77958462907     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq009     Document Type: Article
Times cited : (94)

References (51)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • Ambros V. 2004. The functions of animal microRNAs. Nature 431:350-355.
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 3
    • 43449118038 scopus 로고    scopus 로고
    • Evolution of plant microRNAs and their targets
    • Axtell MJ, Bowman JL. 2008. Evolution of plant microRNAs and their targets. Trends Plant Sci. 13:343-349.
    • (2008) Trends Plant Sci. , vol.13 , pp. 343-349
    • Axtell, M.J.1    Bowman, J.L.2
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.
    • (2004) Cell. , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215-233.
    • (2009) Cell. , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 6
    • 33845452609 scopus 로고    scopus 로고
    • Insect microRNAs: Structure, function and evolution
    • Behura SK. 2007. Insect microRNAs: structure, function and evolution. Insect Biochem Mol Biol. 37:3-9.
    • (2007) Insect Biochem. Mol. Biol. , vol.37 , pp. 3-9
    • Behura, S.K.1
  • 7
    • 22844440427 scopus 로고    scopus 로고
    • Identification of hundreds of conserved and nonconserved human microRNAs
    • Bentwich I, et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet. 37:766-770.
    • (2005) Nat. Genet. , vol.37 , pp. 766-770
    • Bentwich, I.1
  • 9
    • 73349122299 scopus 로고    scopus 로고
    • Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
    • Berezikov E, et al. 2010. Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat Genet. 42:6-9.
    • (2010) Nat. Genet. , vol.42 , pp. 6-9
    • Berezikov, E.1
  • 10
    • 10244243802 scopus 로고    scopus 로고
    • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    • Bonnet E, Wuyts J, Rouze P, Van de Peer Y. 2004. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20:2911-2917.
    • (2004) Bioinformatics , vol.20 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3    Van De Peer, Y.4
  • 11
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Clark AG, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.
    • (2007) Nature , vol.450 , pp. 203-218
    • Clark, A.G.1
  • 12
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 13
    • 48249142558 scopus 로고    scopus 로고
    • Sequence variation of micro-RNAs and their binding sites in Arabidopsis
    • Ehrenreich IM, Purugganan MD. 2008. Sequence variation of micro-RNAs and their binding sites in Arabidopsis. Plant Physiol. 146:1974-1982.
    • (2008) Plant Physiol. , vol.146 , pp. 1974-1982
    • Ehrenreich, I.M.1    Purugganan, M.D.2
  • 14
    • 0036961560 scopus 로고    scopus 로고
    • Changing effective population size and the McDonald-Kreitman test
    • Eyre-Walker A. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics 162:2017-2024.
    • (2002) Genetics , vol.162 , pp. 2017-2024
    • Eyre-Walker, A.1
  • 15
    • 57049169777 scopus 로고    scopus 로고
    • Evolution of Arabidopsis thaliana microRNAs from random sequences
    • Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D. 2008. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14:2455-2459.
    • (2008) RNA , vol.14 , pp. 2455-2459
    • Felippes, F.F.1    Schneeberger, K.2    Dezulian, T.3    Huson, D.H.4    Weigel, D.5
  • 16
    • 54149095553 scopus 로고    scopus 로고
    • Biological principles of microRNA-mediated regulation: Shared themes amid diversity
    • Flynt AS, Lai EC. 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
  • 18
    • 34548361941 scopus 로고    scopus 로고
    • Molecular evolution of Drosophila odorant receptor genes
    • Guo S, Kim J. 2007. Molecular evolution of Drosophila odorant receptor genes. Mol Biol Evol. 24:1198-1207.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1198-1207
    • Guo, S.1    Kim, J.2
  • 19
    • 33744520104 scopus 로고    scopus 로고
    • Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
    • Han J, et al. 2006. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125:887-901.
    • (2006) Cell. , vol.125 , pp. 887-901
    • Han, J.1
  • 20
    • 45249106003 scopus 로고    scopus 로고
    • Near neutrality leading edge of the neutral theory of molecular evolution
    • Hughes AL. 2008. Near neutrality leading edge of the neutral theory of molecular evolution. Ann N Y Acad Sci. 1133:162-179.
    • (2008) Ann. N. Y. Acad. Sci. , vol.1133 , pp. 162-179
    • Hughes, A.L.1
  • 21
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro HM, editor, New York: Academic
    • Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HM, editor. Mammalian protein metabolism. New York: Academic. p. 21-132
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 22
    • 58649116227 scopus 로고    scopus 로고
    • The molecular machines that mediate microRNA maturation
    • Lau PW, MacRae IJ. 2009. The molecular machines that mediate microRNA maturation. J Cell Mol Med. 13:54-60.
    • (2009) J. Cell. Mol. Med. , vol.13 , pp. 54-60
    • Lau, P.W.1    MacRae, I.J.2
  • 23
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843-854.
    • (1993) Cell. , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 24
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20.
    • (2005) Cell. , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 25
    • 33947309774 scopus 로고    scopus 로고
    • Evolution of plant microRNA gene families
    • Li A, Mao L. 2007. Evolution of plant microRNA gene families. Cell Res. 17:212-218.
    • (2007) Cell. Res. , vol.17 , pp. 212-218
    • Li, A.1    Mao, L.2
  • 26
    • 33751118533 scopus 로고    scopus 로고
    • MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila
    • Li Y, Wang F, Lee JA, Gao FB. 2006. MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev. 20:2793-2805.
    • (2006) Genes Dev. , vol.20 , pp. 2793-2805
    • Li, Y.1    Wang, F.2    Lee, J.A.3    Gao, F.B.4
  • 27
    • 48249150513 scopus 로고    scopus 로고
    • Adaptive evolution of newly emerged micro-RNA genes in Drosophila
    • Lu J, et al. 2008a. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Mol Biol Evol. 25:929-938.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 929-938
    • Lu, J.1
  • 28
    • 39749083331 scopus 로고    scopus 로고
    • The birth and death of microRNA genes in Drosophila
    • Lu J, et al. 2008b. The birth and death of microRNA genes in Drosophila. Nat Genet. 40:351-355.
    • (2008) Nat. Genet. , vol.40 , pp. 351-355
    • Lu, J.1
  • 29
    • 33749153857 scopus 로고    scopus 로고
    • Biological function of unannotated transcription during the early development of Drosophila melanogaster
    • Manak JR, et al. 2006. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet. 38:1151-1158.
    • (2006) Nat. Genet. , vol.38 , pp. 1151-1158
    • Manak, J.R.1
  • 30
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 288:911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 31
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
    • (1991) Nature , vol.351 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 32
    • 0024297806 scopus 로고
    • Jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II
    • Mizrokhi LJ, Georgieva SG, Ilyin YV. 1988. jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II. Cell 54:685-691.
    • (1988) Cell. , vol.54 , pp. 685-691
    • Mizrokhi, L.J.1    Georgieva, S.G.2    Ilyin, Y.V.3
  • 33
    • 27944477670 scopus 로고    scopus 로고
    • Concerted and birth-and-death evolution of multigene families
    • Nei M, Rooney AP. 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet. 39:121-152.
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 121-152
    • Nei, M.1    Rooney, A.P.2
  • 34
    • 34249844953 scopus 로고    scopus 로고
    • Evolutionary dynamics of olfactory receptor genes in Drosophila species
    • Nozawa M, Nei M. 2007. Evolutionary dynamics of olfactory receptor genes in Drosophila species. Proc Natl Acad Sci USA. 104:7122-7127.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 7122-7127
    • Nozawa, M.1    Nei, M.2
  • 35
    • 34447107760 scopus 로고    scopus 로고
    • The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila
    • Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. 2007. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130:89-100.
    • (2007) Cell. , vol.130 , pp. 89-100
    • Okamura, K.1    Hagen, J.W.2    Duan, H.3    Tyler, D.M.4    Lai, E.C.5
  • 36
    • 34250776711 scopus 로고    scopus 로고
    • A family of human microRNA genes from miniature inverted-repeat transposable elements
    • Piriyapongsa J, Jordan IK. 2007. A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One. 2: e203.
    • (2007) PLoS One , vol.2
    • Piriyapongsa, J.1    Jordan, I.K.2
  • 37
    • 42449099982 scopus 로고    scopus 로고
    • Dual coding of siRNAs and miRNAs by plant transposable elements
    • Piriyapongsa J, Jordan IK. 2008. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814-821.
    • (2008) RNA , vol.14 , pp. 814-821
    • Piriyapongsa, J.1    Jordan, I.K.2
  • 38
    • 0034708122 scopus 로고    scopus 로고
    • The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    • Reinhart BJ, et al. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-906.
    • (2000) Nature , vol.403 , pp. 901-906
    • Reinhart, B.J.1
  • 39
    • 34447097693 scopus 로고    scopus 로고
    • Intronic microRNA precursors that bypass Drosha processing
    • Ruby JG, Jan CH, Bartel DP. 2007a. Intronic microRNA precursors that bypass Drosha processing. Nature 448:83-86.
    • (2007) Nature , vol.448 , pp. 83-86
    • Ruby, J.G.1    Jan, C.H.2    Bartel, D.P.3
  • 40
    • 38149071979 scopus 로고    scopus 로고
    • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila micro-RNAs
    • Ruby JG, et al. 2007b. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila micro-RNAs. Genome Res. 17:1850-1864.
    • (2007) Genome Res. , vol.17 , pp. 1850-1864
    • Ruby, J.G.1
  • 41
    • 52049125422 scopus 로고    scopus 로고
    • Polytene chromosomal maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps
    • Schaeffer SW, et al. 2008. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics 179:1601-1655.
    • (2008) Genetics , vol.179 , pp. 1601-1655
    • Schaeffer, S.W.1
  • 42
    • 51449085579 scopus 로고    scopus 로고
    • Origins and evolution of eukaryotic RNA interference
    • Shabalina SA, Koonin EV. 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
  • 44
    • 1242352089 scopus 로고    scopus 로고
    • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
    • Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol. 21:36-44.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 36-44
    • Tamura, K.1    Subramanian, S.2    Kumar, S.3
  • 45
    • 2342450524 scopus 로고    scopus 로고
    • Molecular evolution of a microRNA cluster
    • Tanzer A, Stadler PF. 2004. Molecular evolution of a microRNA cluster. J Mol Biol. 339:327-335.
    • (2004) J. Mol. Biol. , vol.339 , pp. 327-335
    • Tanzer, A.1    Stadler, P.F.2
  • 46
    • 36048973464 scopus 로고    scopus 로고
    • Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: Purifying selection and birth-and-death evolution
    • Vieira FG, Sanchez-Gracia A, Rozas J. 2007. Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol. 8: R235.
    • (2007) Genome Biol. , vol.8
    • Vieira, F.G.1    Sanchez-Gracia, A.2    Rozas, J.3
  • 47
    • 60149086351 scopus 로고    scopus 로고
    • Origin, biogenesis, and activity of plant microRNAs
    • Voinnet O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136:669-687.
    • (2009) Cell. , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 48
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 49
    • 52149090746 scopus 로고    scopus 로고
    • MicroRNAs in the Hox network: An apparent link to posterior prevalence
    • Yekta S, Tabin CJ, Bartel DP. 2008. MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nat Rev Genet. 9:789-796.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 789-796
    • Yekta, S.1    Tabin, C.J.2    Bartel, D.P.3
  • 50
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • Zhang J, Rosenberg HF, Nei M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA. 95:3708-3713.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3708-3713
    • Zhang, J.1    Rosenberg, H.F.2    Nei, M.3
  • 51
    • 50649110065 scopus 로고    scopus 로고
    • A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    • Zhu QH, et al. 2008. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res. 18:1456-1465.
    • (2008) Genome Res. , vol.18 , pp. 1456-1465
    • Zhu, Q.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.