메뉴 건너뛰기




Volumn 18, Issue 7, 2008, Pages 1030-1042

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; APE; ARTICLE; CERCOPITHECIDAE; CHIMPANZEE; CHROMOSOME DUPLICATION; CHROMOSOME YP; CHROMOSOME YQ; EUCHROMATIN; FLUORESCENCE IN SITU HYBRIDIZATION; HETEROCHROMATIN; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RHESUS MONKEY; Y CHROMOSOME;

EID: 46449091406     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.076711.108     Document Type: Article
Times cited : (29)

References (67)
  • 1
    • 0030011808 scopus 로고    scopus 로고
    • Affara, N., Bishop, C., Brown, W., Cokke, H., Davey, P., Ellis, N., Graves, J.M., Jones, M., Mitchell, M., Rappold, G., et al. 1996. Report of the Second International Workshop on Y Chromosome Mapping 1995. Cytogenet. Cell Genet. 73: 33-76.
    • Affara, N., Bishop, C., Brown, W., Cokke, H., Davey, P., Ellis, N., Graves, J.M., Jones, M., Mitchell, M., Rappold, G., et al. 1996. Report of the Second International Workshop on Y Chromosome Mapping 1995. Cytogenet. Cell Genet. 73: 33-76.
  • 2
    • 34848890323 scopus 로고    scopus 로고
    • Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data
    • doi: 10.1371/journal.pcbi.0030181
    • Alkan, C., Ventura, M., Archidiacono, N., Rocchi, M., Sahinalp, S.C., and Eichler, E.E. 2007. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS Comput. Biol. 3: e181. doi: 10.1371/journal.pcbi.0030181.
    • (2007) PLoS Comput. Biol , vol.3
    • Alkan, C.1    Ventura, M.2    Archidiacono, N.3    Rocchi, M.4    Sahinalp, S.C.5    Eichler, E.E.6
  • 4
    • 3242708463 scopus 로고    scopus 로고
    • Genome-wide detection and analysis of recent segmental duplications within mammalian organisms
    • Bailey, J.A. and Eichler, E.E. 2003. Genome-wide detection and analysis of recent segmental duplications within mammalian organisms. Cold Spring Harb. Symp. Quant. Biol. 68: 115-124.
    • (2003) Cold Spring Harb. Symp. Quant. Biol , vol.68 , pp. 115-124
    • Bailey, J.A.1    Eichler, E.E.2
  • 5
    • 33745373606 scopus 로고    scopus 로고
    • Primate segmental duplications: Crucibles of evolution, diversity and disease
    • Bailey, J.A. and Eichler, E.E. 2006. Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat. Rev. Genet. 7: 552-564.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 552-564
    • Bailey, J.A.1    Eichler, E.E.2
  • 6
    • 0034831138 scopus 로고    scopus 로고
    • Segmental duplications: Organization and impact within the current human genome project assembly
    • Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J., and Eichler, E.E. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11: 1005-1017.
    • (2001) Genome Res , vol.11 , pp. 1005-1017
    • Bailey, J.A.1    Yavor, A.M.2    Massa, H.F.3    Trask, B.J.4    Eichler, E.E.5
  • 9
    • 25444489920 scopus 로고    scopus 로고
    • Duplication and positive selection among hominin-specific PRAME genes
    • doi: 10.1186/1471-2164-6-120
    • Birtle, Z., Goodstadt, L., and Ponting, C. 2005. Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics 6: 120. doi: 10.1186/1471-2164-6-120.
    • (2005) BMC Genomics , vol.6 , pp. 120
    • Birtle, Z.1    Goodstadt, L.2    Ponting, C.3
  • 12
    • 0037837485 scopus 로고    scopus 로고
    • Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence
    • doi: 10.1186/gb-2003-4-4-r25
    • Cheung, V.G., Estivill, X., Khaja, R., MacDonald, J.R., Lau, K., Tsui, L.C., and Scherer, S.W. 2003. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4: R25. doi: 10.1186/gb-2003-4-4-r25.
    • (2003) Genome Biol , vol.4
    • Cheung, V.G.1    Estivill, X.2    Khaja, R.3    MacDonald, J.R.4    Lau, K.5    Tsui, L.C.6    Scherer, S.W.7
  • 13
    • 18244396646 scopus 로고    scopus 로고
    • Human paralogs of KIAA0187 were created through independent pericentromeric-directed and chromosome-specific duplication mechanisms
    • Crosier, M., Viggiano, L., Guy, J., Misceo, D., Stones, R., Wei, W., Hearn, T., Ventura, M., Archidiacono, N., Rocchi, M., et al. 2002. Human paralogs of KIAA0187 were created through independent pericentromeric-directed and chromosome-specific duplication mechanisms. Genome Res. 12: 67-80.
    • (2002) Genome Res , vol.12 , pp. 67-80
    • Crosier, M.1    Viggiano, L.2    Guy, J.3    Misceo, D.4    Stones, R.5    Wei, W.6    Hearn, T.7    Ventura, M.8    Archidiacono, N.9    Rocchi, M.10
  • 14
    • 0035500899 scopus 로고    scopus 로고
    • Recent duplication, domain accretion and the dynamic mutation of the human genome
    • Eichler, E.E. 2001. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 11: 661-669.
    • (2001) Trends Genet , vol.11 , pp. 661-669
    • Eichler, E.E.1
  • 15
    • 0036114001 scopus 로고    scopus 로고
    • Biomedical applications and studies of molecular evolution: A proposal for a primate genomic library resource
    • Eichler, E.E. and DeJong, P.J. 2002. Biomedical applications and studies of molecular evolution: A proposal for a primate genomic library resource. Genome Res. 12: 673-678.
    • (2002) Genome Res , vol.12 , pp. 673-678
    • Eichler, E.E.1    DeJong, P.J.2
  • 18
    • 0031732094 scopus 로고    scopus 로고
    • A computer program for aligning a cDNA sequence with a genomic DNA sequence
    • Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974.
    • (1998) Genome Res , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.M.4    Miller, W.5
  • 19
    • 0037351279 scopus 로고    scopus 로고
    • Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates
    • Frazer, K.A., Chen, X., Hinds, D.A., Pant, P.V., Patil, N., and Cox, D.R. 2003. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 13: 341-346.
    • (2003) Genome Res , vol.13 , pp. 341-346
    • Frazer, K.A.1    Chen, X.2    Hinds, D.A.3    Pant, P.V.4    Patil, N.5    Cox, D.R.6
  • 22
    • 0033360816 scopus 로고    scopus 로고
    • The genomic record of humankind's evolutionary roots
    • Goodman, M. 1999. The genomic record of humankind's evolutionary roots. Am. J. Hum. Genet. 64: 31-39.
    • (1999) Am. J. Hum. Genet , vol.64 , pp. 31-39
    • Goodman, M.1
  • 23
    • 23644459637 scopus 로고    scopus 로고
    • Moving primate genomics beyond the chimpanzee genome
    • Goodman, M. 2005. Moving primate genomics beyond the chimpanzee genome. Trends Genet. 21: 511-517.
    • (2005) Trends Genet , vol.21 , pp. 511-517
    • Goodman, M.1
  • 24
    • 46449106546 scopus 로고    scopus 로고
    • Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q
    • Guy, J., Spalluto, C., McMurray, A., Hearn, T., Crosier, M., Viggiano, L., Miolla, V., Archidiacono, N., Rocchi, M., Scott, C., et al. 2000. Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q. Genome Res. 12: 2029-2042.
    • (2000) Genome Res , vol.12 , pp. 2029-2042
    • Guy, J.1    Spalluto, C.2    McMurray, A.3    Hearn, T.4    Crosier, M.5    Viggiano, L.6    Miolla, V.7    Archidiacono, N.8    Rocchi, M.9    Scott, C.10
  • 25
    • 0037317323 scopus 로고    scopus 로고
    • Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p
    • Guy, J., Hearn, T., Crosier, M., Mudge, J., Viggiano, L., Koczan, D., Thiesen, H.J., Bailey, J.A., Horvath, J.E., Eichler, E.E., et al. 2003. Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. Genome Res. 13: 159-172.
    • (2003) Genome Res , vol.13 , pp. 159-172
    • Guy, J.1    Hearn, T.2    Crosier, M.3    Mudge, J.4    Viggiano, L.5    Koczan, D.6    Thiesen, H.J.7    Bailey, J.A.8    Horvath, J.E.9    Eichler, E.E.10
  • 26
    • 0031828293 scopus 로고    scopus 로고
    • Orangutan alpha-satellite monomers are closely related to the human consensus sequence
    • Haaf, T. and Willard, H.F. 1998. Orangutan alpha-satellite monomers are closely related to the human consensus sequence. Mamm. Genome 9: 440-447.
    • (1998) Mamm. Genome , vol.9 , pp. 440-447
    • Haaf, T.1    Willard, H.F.2
  • 27
    • 18244381274 scopus 로고    scopus 로고
    • Systematics and the origin of species: An introduction
    • Hey, J., Fitch, W.M., and Ayala, F.J. 2005. Systematics and the origin of species: An introduction. Proc. Natl. Acad. Sci. 102 (Suppl. 1): 6515-6519.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , Issue.SUPPL. 1 , pp. 6515-6519
    • Hey, J.1    Fitch, W.M.2    Ayala, F.J.3
  • 28
    • 0029976603 scopus 로고    scopus 로고
    • Using CLUSTALW for multiple sequence alignments
    • Higgins, D.G., Thompson, J.D., and Gibson, T.J. 1996. Using CLUSTALW for multiple sequence alignments. Methods Enzymol. 266: 383-402.
    • (1996) Methods Enzymol , vol.266 , pp. 383-402
    • Higgins, D.G.1    Thompson, J.D.2    Gibson, T.J.3
  • 29
    • 0033916868 scopus 로고    scopus 로고
    • The mosaic structure of human pericentromeric DNA: A strategy for characterizing complex regions of the human genome
    • Horvath, J.E., Schwartz, S., and Eichler, E.E. 2000. The mosaic structure of human pericentromeric DNA: A strategy for characterizing complex regions of the human genome. Genome Res. 10: 839-852.
    • (2000) Genome Res , vol.10 , pp. 839-852
    • Horvath, J.E.1    Schwartz, S.2    Eichler, E.E.3
  • 30
    • 0035475786 scopus 로고    scopus 로고
    • Lessons from the human genome: Transitions between euchromatin and heterochromatin
    • Horvath, J.E., Bailey, J.A., Locke, D.P., and Eichler, E.E. 2001. Lessons from the human genome: Transitions between euchromatin and heterochromatin. Genome Res. 10: 2215-2223.
    • (2001) Genome Res , vol.10 , pp. 2215-2223
    • Horvath, J.E.1    Bailey, J.A.2    Locke, D.P.3    Eichler, E.E.4
  • 33
  • 34
    • 0032928889 scopus 로고    scopus 로고
    • Sequences flanking the centromere of human chromosome 10 are a complex patchwork of arm-specific sequences, stable duplications and unstable sequences with homologies to telomeric and other centromeric locations
    • Jackson, M.S., Rocchi, M., Thompson, G., Hearn, T., Crosier, M., Guy, J., Kirk, D., Mulligan, L., Ricco, A., Piccininni, S., et al. 1999. Sequences flanking the centromere of human chromosome 10 are a complex patchwork of arm-specific sequences, stable duplications and unstable sequences with homologies to telomeric and other centromeric locations. Hum. Mol. Genet. 8: 205-215.
    • (1999) Hum. Mol. Genet , vol.8 , pp. 205-215
    • Jackson, M.S.1    Rocchi, M.2    Thompson, G.3    Hearn, T.4    Crosier, M.5    Guy, J.6    Kirk, D.7    Mulligan, L.8    Ricco, A.9    Piccininni, S.10
  • 36
    • 0034028921 scopus 로고    scopus 로고
    • Structure of chromosomal duplicons and their role in mediating human genomic disorders
    • Ji, Y., Eichler, E.E., Schwartz, S., and Nicholls, R.D. 2000. Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10: 597-610.
    • (2000) Genome Res , vol.10 , pp. 597-610
    • Ji, Y.1    Eichler, E.E.2    Schwartz, S.3    Nicholls, R.D.4
  • 37
  • 38
    • 46449091350 scopus 로고    scopus 로고
    • DupMasker: A tool for annotating primate segmental duplications
    • in press doi: 10.1101/gr.078477.108
    • Jiang, Z., Hubley, R., Smit, A., and Eichler, E.E. 2008. DupMasker: A tool for annotating primate segmental duplications. Genome Res. (in press) doi: 10.1101/gr.078477.108.
    • (2008) Genome Res
    • Jiang, Z.1    Hubley, R.2    Smit, A.3    Eichler, E.E.4
  • 40
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120.
    • (1980) J. Mol. Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 41
    • 0030452917 scopus 로고    scopus 로고
    • Molecular analysis of the genomic structure of the human Y chromosome in the euchromatic part of its long arm (Yq11)
    • Kirsch, S., Keil, R., Edelmann, A., Henegariu, O., Hirschmann, P., LePaslier, D., and Vogt, P.H. 1996. Molecular analysis of the genomic structure of the human Y chromosome in the euchromatic part of its long arm (Yq11). Cytogenet. Cell Genet. 75: 197-206.
    • (1996) Cytogenet. Cell Genet , vol.75 , pp. 197-206
    • Kirsch, S.1    Keil, R.2    Edelmann, A.3    Henegariu, O.4    Hirschmann, P.5    LePaslier, D.6    Vogt, P.H.7
  • 44
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
    • Kumar, S., Tamura, K., and Nei, M. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163.
    • (2004) Brief. Bioinform , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 46
    • 46449122087 scopus 로고    scopus 로고
    • Li, W. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA. Locke, D.P., Jiang, Z., Pertz, L.M., Misceo, D., Archidiacono, N., and Eichler, E.E. 2005. Molecular evolution of the human chromosome 15 pericentromeric region. Cytogenet. Genome Res. 108: 73-82.
    • Li, W. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA. Locke, D.P., Jiang, Z., Pertz, L.M., Misceo, D., Archidiacono, N., and Eichler, E.E. 2005. Molecular evolution of the human chromosome 15 pericentromeric region. Cytogenet. Genome Res. 108: 73-82.
  • 48
    • 3042641037 scopus 로고    scopus 로고
    • Orthologous numbering of great ape and human chromosomes is essential for comparative genomics
    • McConkey, E.H. 2004. Orthologous numbering of great ape and human chromosomes is essential for comparative genomics. Cytogenet. Genome Res. 105: 157-158.
    • (2004) Cytogenet. Genome Res , vol.105 , pp. 157-158
    • McConkey, E.H.1
  • 49
    • 0036244955 scopus 로고    scopus 로고
    • The complex structure and dynamic evolution of human subtelomeres
    • Mefford, H.C. and Trask, B.J. 2002. The complex structure and dynamic evolution of human subtelomeres. Nat. Rev. Genet. 3: 91-102.
    • (2002) Nat. Rev. Genet , vol.3 , pp. 91-102
    • Mefford, H.C.1    Trask, B.J.2
  • 51
    • 0345184332 scopus 로고    scopus 로고
    • The Tre2 (USP6) oncogene is a hominoid-specific gene
    • Paulding, C.A., Ruvolo, M., and Haber, D.A. 2003. The Tre2 (USP6) oncogene is a hominoid-specific gene. Proc. Natl. Acad. Sci. 83: 2934-2938.
    • (2003) Proc. Natl. Acad. Sci , vol.83 , pp. 2934-2938
    • Paulding, C.A.1    Ruvolo, M.2    Haber, D.A.3
  • 53
    • 0026604579 scopus 로고
    • Simultaneous visualization of seven different DNA probes by in situ hybridization using combinatorial fluorescence and digital imaging microscopy
    • Ried, T., Baldini, A., Rand, T.C., and Ward, D.C. 1992. Simultaneous visualization of seven different DNA probes by in situ hybridization using combinatorial fluorescence and digital imaging microscopy. Proc. Natl. Acad. Sci. 89: 1388-1392.
    • (1992) Proc. Natl. Acad. Sci , vol.89 , pp. 1388-1392
    • Ried, T.1    Baldini, A.2    Rand, T.C.3    Ward, D.C.4
  • 61
    • 46449107151 scopus 로고    scopus 로고
    • Implications of human genome architecture for rearrangement-based disorders: The genomic basis of disease
    • Shaw, C.J. and Lupski, J.R. 2004. Implications of human genome architecture for rearrangement-based disorders: The genomic basis of disease. Hum. Mol. Genet. 115: 1-7.
    • (2004) Hum. Mol. Genet , vol.115 , pp. 1-7
    • Shaw, C.J.1    Lupski, J.R.2
  • 63
    • 33745175531 scopus 로고    scopus 로고
    • She, X., Liu, G., Ventura, M., Zhao, S., Misceo, D., Roberto, R., Cardone, M.F., Rocchi, M., NISC Comparative Sequencing Program, Green, E.D., et al. 2006. A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 16: 576-583.
    • She, X., Liu, G., Ventura, M., Zhao, S., Misceo, D., Roberto, R., Cardone, M.F., Rocchi, M., NISC Comparative Sequencing Program, Green, E.D., et al. 2006. A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. Genome Res. 16: 576-583.
  • 65
    • 33646187369 scopus 로고    scopus 로고
    • Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci
    • Steiper, M.E. 2006. Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci. J. Hum. Evol. 50: 509-522.
    • (2006) J. Hum. Evol , vol.50 , pp. 509-522
    • Steiper, M.E.1
  • 66
    • 9244255880 scopus 로고    scopus 로고
    • Fluorescence in situ hybridization to chromosomes as a tool to understand human and primate genome evolution
    • Wienberg, J. 2005. Fluorescence in situ hybridization to chromosomes as a tool to understand human and primate genome evolution. Cytogenet. Genome Res. 108: 139-160.
    • (2005) Cytogenet. Genome Res , vol.108 , pp. 139-160
    • Wienberg, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.