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Volumn 106, Issue 31, 2009, Pages 12855-12860

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

Author keywords

BovB; Cow; Microsatellite; Repetitive DNA

Indexed keywords

ARTICLE; CATTLE; CONTROLLED STUDY; CORRELATION ANALYSIS; COW; GENE SEQUENCE; GENE TRANSFER; GENETIC ANALYSIS; GENETIC TRAIT; GENOME; GENOME ANALYSIS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; RETROPOSON; ANIMAL; DNA BASE COMPOSITION; DNA METHYLATION; GENETICS; LONG INTERSPERSED REPEAT;

EID: 69149106357     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0901282106     Document Type: Article
Times cited : (89)

References (51)
  • 1
    • 0030479536 scopus 로고    scopus 로고
    • The origin of interspersed repeats in the human genome
    • Smit AF (1996) The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6:743-748.
    • (1996) Curr Opin Genet Dev , vol.6 , pp. 743-748
    • Smit, A.F.1
  • 2
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander ES, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1
  • 4
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston RH, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1
  • 5
    • 0028804572 scopus 로고
    • MIRs are classic, transfer-RNA-derived SINEs that amplified before the mammalian radiation
    • Smit AFA, Riggs AD (1995) MIRs are classic, transfer-RNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res 23:98-102.
    • (1995) Nucleic Acids Res , vol.23 , pp. 98-102
    • Smit, A.F.A.1    Riggs, A.D.2
  • 7
    • 34547609849 scopus 로고    scopus 로고
    • Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation
    • Giordano J, et al. (2007) Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation. PLoS Comput Biol 3:e137.
    • (2007) PLoS Comput Biol , vol.3
    • Giordano, J.1
  • 8
    • 1542513556 scopus 로고    scopus 로고
    • Mobile elements: Drivers of genome evolution
    • Kazazian HH, Jr (2004) Mobile elements: Drivers of genome evolution. Science 303:1626-1632.
    • (2004) Science , vol.303 , pp. 1626-1632
    • Kazazian Jr, H.H.1
  • 9
    • 0032102720 scopus 로고    scopus 로고
    • Mobile elements and disease
    • Kazazian HH, Jr (1998) Mobile elements and disease. Curr Opin Genet Dev 8:343-350.
    • (1998) Curr Opin Genet Dev , vol.8 , pp. 343-350
    • Kazazian Jr, H.H.1
  • 11
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • Birney E, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1
  • 12
    • 34547643930 scopus 로고    scopus 로고
    • Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs)
    • Krull M, Petrusma M, Makalowski W, Brosius J, Schmitz J (2007) Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). Genome Res 17:1139-1145.
    • (2007) Genome Res , vol.17 , pp. 1139-1145
    • Krull, M.1    Petrusma, M.2    Makalowski, W.3    Brosius, J.4    Schmitz, J.5
  • 13
    • 28644447707 scopus 로고    scopus 로고
    • Genome sequence, comparative analysis and haplotype structure of the domestic dog
    • Lindblad-Toh K, et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-819.
    • (2005) Nature , vol.438 , pp. 803-819
    • Lindblad-Toh, K.1
  • 14
    • 34248512741 scopus 로고    scopus 로고
    • Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
    • Gentles AJ, et al. (2007) Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res 17:992-1004.
    • (2007) Genome Res , vol.17 , pp. 992-1004
    • Gentles, A.J.1
  • 15
    • 0041353551 scopus 로고    scopus 로고
    • LINE-mediated retrotransposition of marked Alu sequences
    • Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41-48.
    • (2003) Nat Genet , vol.35 , pp. 41-48
    • Dewannieux, M.1    Esnault, C.2    Heidmann, T.3
  • 16
    • 23844437243 scopus 로고    scopus 로고
    • SINEs and LINEs: Symbionts of eukaryotic genomes with a common tail
    • Ohshima K, Okada N (2005) SINEs and LINEs: Symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res 110:475-490.
    • (2005) Cytogenet Genome Res , vol.110 , pp. 475-490
    • Ohshima, K.1    Okada, N.2
  • 17
    • 0033290719 scopus 로고    scopus 로고
    • Horizontal transfer of non-LTR retrotransposons in vertebrates
    • Kordis D, Gubensek F (1999) Horizontal transfer of non-LTR retrotransposons in vertebrates. Genetica 107:121-128.
    • (1999) Genetica , vol.107 , pp. 121-128
    • Kordis, D.1    Gubensek, F.2
  • 18
    • 0032168623 scopus 로고    scopus 로고
    • Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes
    • Kordis D, Gubensek F (1998) Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc Natl Acad Sci USA 95:10704 -10709.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 10704-10709
    • Kordis, D.1    Gubensek, F.2
  • 19
    • 0032802198 scopus 로고    scopus 로고
    • Genealogy of families of SINEs in cetaceans and artiodactyls: The presence of a huge superfamily of tRNA(Glu)-derived families of SINEs
    • Shimamura M, Abe H, Nikaido M, Ohshima K, Okada N (1999) Genealogy of families of SINEs in cetaceans and artiodactyls: The presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. Mol Biol Evol 16:1046-1060.
    • (1999) Mol Biol Evol , vol.16 , pp. 1046-1060
    • Shimamura, M.1    Abe, H.2    Nikaido, M.3    Ohshima, K.4    Okada, N.5
  • 20
    • 0029049425 scopus 로고
    • Evolution and recombination of bovine DNA repeats
    • Jobse C, et al. (1995) Evolution and recombination of bovine DNA repeats. J Mol Evol 41:277-283.
    • (1995) J Mol Evol , vol.41 , pp. 277-283
    • Jobse, C.1
  • 21
    • 0031857142 scopus 로고    scopus 로고
    • The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs
    • Malik HS, Eickbush TH (1998) The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol Biol Evol 15:1123-1134.
    • (1998) Mol Biol Evol , vol.15 , pp. 1123-1134
    • Malik, H.S.1    Eickbush, T.H.2
  • 24
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100:11484-11489.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5
  • 25
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignments with BLASTZ
    • Schwartz S, et al. (2003) Human-mouse alignments with BLASTZ. Genome Res 13:103-107.
    • (2003) Genome Res , vol.13 , pp. 103-107
    • Schwartz, S.1
  • 26
    • 55949134735 scopus 로고    scopus 로고
    • Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods
    • Pace JK, II, Gilbert C, Clark MS, Feschotte C (2008) Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci USA 105:17023-17028.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 17023-17028
    • Pace II, J.K.1    Gilbert, C.2    Clark, M.S.3    Feschotte, C.4
  • 27
    • 33644920974 scopus 로고    scopus 로고
    • A Tandem Gene Duplication Followed by Recruitment of a Retrotransposon Created the Paralogous Bucentaur Gene (bcntp97) in the Ancestral Ruminant
    • Iwashita S, et al. (2006) A Tandem Gene Duplication Followed by Recruitment of a Retrotransposon Created the Paralogous Bucentaur Gene (bcntp97) in the Ancestral Ruminant. Mol Biol Evol 23:798-806.
    • (2006) Mol Biol Evol , vol.23 , pp. 798-806
    • Iwashita, S.1
  • 28
    • 55249100313 scopus 로고    scopus 로고
    • Evolutionary History of LINE-1 in the Major Clades of Placental Mammals
    • Waters PD, Dobigny G, Waddell PJ, Robinson TJ (2007) Evolutionary History of LINE-1 in the Major Clades of Placental Mammals. PLoS ONE 2:e158.
    • (2007) PLoS ONE , vol.2
    • Waters, P.D.1    Dobigny, G.2    Waddell, P.J.3    Robinson, T.J.4
  • 29
    • 0030903621 scopus 로고    scopus 로고
    • Many human L1 elements are capable of retrotransposition
    • Sassaman DM, et al. (1997) Many human L1 elements are capable of retrotransposition. Nat Genet 16:37-43.
    • (1997) Nat Genet , vol.16 , pp. 37-43
    • Sassaman, D.M.1
  • 30
    • 33744947040 scopus 로고    scopus 로고
    • Molecular mechanisms for maintenance of G-rich short tandem repeats capable of adopting G4 DNA structures
    • Nakagama H, et al. (2006) Molecular mechanisms for maintenance of G-rich short tandem repeats capable of adopting G4 DNA structures. Mutat Res-Fund Mol M 598:120-131.
    • (2006) Mutat Res-Fund Mol M , vol.598 , pp. 120-131
    • Nakagama, H.1
  • 31
    • 33746637933 scopus 로고    scopus 로고
    • Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences
    • Liu GE, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP (2006) Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. BMC Genomics 7:140.
    • (2006) BMC Genomics , vol.7 , pp. 140
    • Liu, G.E.1    Matukumalli, L.K.2    Sonstegard, T.S.3    Shade, L.L.4    Van Tassell, C.P.5
  • 32
  • 33
    • 34547664096 scopus 로고    scopus 로고
    • Genomic Disorders: Molecular Mechanisms for Rearrangements and Conveyed Phenotypes
    • Lupski JR, Stankiewicz P (2005) Genomic Disorders: Molecular Mechanisms for Rearrangements and Conveyed Phenotypes. PLoS Genet 1:e49.
    • (2005) PLoS Genet , vol.1
    • Lupski, J.R.1    Stankiewicz, P.2
  • 34
    • 1842717954 scopus 로고    scopus 로고
    • Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps
    • Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ (2003) Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics 1:30-40.
    • (2003) Hum Genomics , vol.1 , pp. 30-40
    • Murphy, W.J.1    Bourque, G.2    Tesler, G.3    Pevzner, P.4    O'Brien, S.J.5
  • 35
    • 22744440499 scopus 로고    scopus 로고
    • Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
    • Murphy WJ, et al. (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-617.
    • (2005) Science , vol.309 , pp. 613-617
    • Murphy, W.J.1
  • 36
    • 0033780450 scopus 로고    scopus 로고
    • A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression
    • Cohen BA, Mitra RD, Hughes JD, Church GM (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26:183-186.
    • (2000) Nat Genet , vol.26 , pp. 183-186
    • Cohen, B.A.1    Mitra, R.D.2    Hughes, J.D.3    Church, G.M.4
  • 37
    • 34248218111 scopus 로고    scopus 로고
    • Radial chromatin positioning is shaped by local gene density, not by gene expression
    • Kupper K, et al. (2007) Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116:285-306.
    • (2007) Chromosoma , vol.116 , pp. 285-306
    • Kupper, K.1
  • 38
    • 29244433734 scopus 로고    scopus 로고
    • Gamete imprinting: Setting epigenetic patterns for the next generation
    • Trasler JM (2006) Gamete imprinting: Setting epigenetic patterns for the next generation. Reprod Fertil Dev 18:63-69.
    • (2006) Reprod Fertil Dev , vol.18 , pp. 63-69
    • Trasler, J.M.1
  • 39
    • 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
  • 40
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 41
    • 84860513986 scopus 로고    scopus 로고
    • PILER: Identification and classification of genomic repeats
    • Edgar RC, Myers EW (2005) PILER: Identification and classification of genomic repeats. Bioinformatics 21:I152-I158.
    • (2005) Bioinformatics , vol.21
    • Edgar, R.C.1    Myers, E.W.2
  • 42
    • 33846224659 scopus 로고    scopus 로고
    • Improved repeat identification and masking in Dipterans
    • Smith CD, et al. (2007) Improved repeat identification and masking in Dipterans. Gene 389:1-9.
    • (2007) Gene , vol.389 , pp. 1-9
    • Smith, C.D.1
  • 43
    • 29144455282 scopus 로고    scopus 로고
    • De novo identification of repeat families in large genomes
    • Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21:I351-I358.
    • (2005) Bioinformatics , vol.21
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 44
    • 0027399530 scopus 로고
    • Identification of protein coding regions by database similarity search
    • Gish W, States DJ (1993) Identification of protein coding regions by database similarity search. Nat Genet 3:266-272.
    • (1993) Nat Genet , vol.3 , pp. 266-272
    • Gish, W.1    States, D.J.2
  • 45
    • 38549097071 scopus 로고    scopus 로고
    • The UniProt C (2008) The Universal Protein Resource (UniProt). Nucl. Acids Res 36:D190-D195.
    • The UniProt C (2008) The Universal Protein Resource (UniProt). Nucl. Acids Res 36:D190-D195.
  • 46
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 47
    • 21244454414 scopus 로고    scopus 로고
    • Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific effects
    • Arndt PF, Hwa T, Petrov DA (2005) Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific effects. J Mol Evol 60:748-763.
    • (2005) J Mol Evol , vol.60 , pp. 748-763
    • Arndt, P.F.1    Hwa, T.2    Petrov, D.A.3
  • 48
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • ed Munro HN Academic, New York, pp
    • Jukes TH, Cantor CR (1969) Evolution of protein molecules. Mammalian Protein Metabolism, ed Munro HN (Academic, New York), pp 21-123.
    • (1969) Mammalian Protein Metabolism , pp. 21-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 49
    • 34547781750 scopus 로고    scopus 로고
    • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24:1596-1599
    • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24:1596-1599.
  • 50
    • 69249106445 scopus 로고    scopus 로고
    • Mayer C (2008) PHOBOS. Available at http://www.ruhr-uni-bochum.de/ spezzoo/cm/cm-phobos.htm.
    • Mayer C (2008) PHOBOS. Available at http://www.ruhr-uni-bochum.de/ spezzoo/cm/cm-phobos.htm.
  • 51
    • 0035051542 scopus 로고    scopus 로고
    • Mutation and recombination in cattle satellite DNA: A feedback model for the evolution of satellite DNA repeats
    • Nijman IJ, Lenstra JA (2001) Mutation and recombination in cattle satellite DNA: A feedback model for the evolution of satellite DNA repeats. J Mol Evol 52:361-371.
    • (2001) J Mol Evol , vol.52 , pp. 361-371
    • Nijman, I.J.1    Lenstra, J.A.2


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