메뉴 건너뛰기




Volumn 395, Issue , 2007, Pages 367-379

Phylogenetic footprinting to find functional DNA elements

Author keywords

Noncoding functional DNA element; Phylogenetic footprinting; Ribosomal DNA; Saccharomyces

Indexed keywords

FUNGAL DNA; RIBOSOME DNA;

EID: 36549034755     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-514-8:367     Document Type: Article
Times cited : (8)

References (35)
  • 1
    • 0037271322 scopus 로고    scopus 로고
    • Cross-species sequence comparisons: A review of methods and available resources
    • Frazer, K. A., Elnitski, L., Church, D. M., Dubchak, I., and Hardison, R. C. (2003) Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 13, 1-12.
    • (2003) Genome Res , vol.13 , pp. 1-12
    • Frazer, K.A.1    Elnitski, L.2    Church, D.M.3    Dubchak, I.4    Hardison, R.C.5
  • 2
    • 3142740663 scopus 로고    scopus 로고
    • Comparative genomics
    • Hardison, R. C. (2003) Comparative genomics. PLoS Biol. 1, 156-160.
    • (2003) PLoS Biol , vol.1 , pp. 156-160
    • Hardison, R.C.1
  • 3
    • 0642368358 scopus 로고    scopus 로고
    • Position specific variation in the rate of evolution in transcription factor binding sites
    • Moses, A. M., Chiang, D. Y., Kellis, M., Lander, E. S., and Eisen, M. B. (2003) Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Biol. 3, 19.
    • (2003) BMC Evol. Biol , vol.3 , pp. 19
    • Moses, A.M.1    Chiang, D.Y.2    Kellis, M.3    Lander, E.S.4    Eisen, M.B.5
  • 4
    • 0034284481 scopus 로고    scopus 로고
    • Conserved noncoding sequences are reliable guides to regulatory elements
    • Hardison, R. C. (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16, 369-372.
    • (2000) Trends Genet , vol.16 , pp. 369-372
    • Hardison, R.C.1
  • 5
    • 0027325017 scopus 로고
    • Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the e-globin gene
    • Gumucio, D. L., Shelton, D. A., Bailey, W. J., Slightom, J. L., and Goodman, M. (1993) Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the e-globin gene. Proc. Natl. Acad. Sci. USA 90, 6018-6022.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 6018-6022
    • Gumucio, D.L.1    Shelton, D.A.2    Bailey, W.J.3    Slightom, J.L.4    Goodman, M.5
  • 6
    • 0037781051 scopus 로고    scopus 로고
    • Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing
    • Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D. (2003) Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing. Plant Cell 15, 1296-1309.
    • (2003) Plant Cell , vol.15 , pp. 1296-1309
    • Hong, R.L.1    Hamaguchi, L.2    Busch, M.A.3    Weigel, D.4
  • 7
    • 0038825775 scopus 로고    scopus 로고
    • Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus
    • Brachat, S., Dietrich, F. S., Voegeli, S., et al. (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol. 4, R45.
    • (2003) Ashbya gossypii. Genome Biol , vol.4
    • Brachat, S.1    Dietrich, F.S.2    Voegeli, S.3
  • 8
    • 23844492486 scopus 로고    scopus 로고
    • Ganley, A. R. D., Hayashi, K., Horiuchi, T., and Kobayashi, T. (2005) Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc. Natl. Acad. Sci. USA 102, 11, 787-11,792.
    • Ganley, A. R. D., Hayashi, K., Horiuchi, T., and Kobayashi, T. (2005) Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc. Natl. Acad. Sci. USA 102, 11, 787-11,792.
  • 9
    • 0242662461 scopus 로고    scopus 로고
    • Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)
    • Dermitzakis, E. T., Reymond, A., Scamuffa, N., et al. (2003) Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302, 1033-1035.
    • (2003) Science , vol.302 , pp. 1033-1035
    • Dermitzakis, E.T.1    Reymond, A.2    Scamuffa, N.3
  • 10
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E. S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 12
    • 1542347045 scopus 로고    scopus 로고
    • zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles
    • Ovcharenko, I., Loots, G. G., Hardison, R. C, Miller, W., and Stubbs, L. (2004) zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14, 472-477.
    • (2004) Genome Res , vol.14 , pp. 472-477
    • Ovcharenko, I.1    Loots, G.G.2    Hardison, R.C.3    Miller, W.4    Stubbs, L.5
  • 13
    • 23144431920 scopus 로고    scopus 로고
    • TOUCAN 2: The all-inclusive open source workbench for regulatory sequence analysis
    • Aerts, S., Van Loo, P., Thijs, G., et al. (2005) TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucl. Acids Res. 33, W393-W396.
    • (2005) Nucl. Acids Res , vol.33
    • Aerts, S.1    Van Loo, P.2    Thijs, G.3
  • 14
    • 13244260826 scopus 로고    scopus 로고
    • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
    • Sinha, S., Blanchette, M., and Tompa, M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinform. 5, 170.
    • (2004) BMC Bioinform , vol.5 , pp. 170
    • Sinha, S.1    Blanchette, M.2    Tompa, M.3
  • 15
    • 13244278001 scopus 로고    scopus 로고
    • GATA: A graphic alignment tool for comparative sequence analysis
    • Nix, D. A. and Eisen, M. B. (2005) GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinform. 6, 9.
    • (2005) BMC Bioinform , vol.6 , pp. 9
    • Nix, D.A.1    Eisen, M.B.2
  • 16
    • 0018814593 scopus 로고
    • Repeated genes in eukaryotes
    • Long, E. O. and Dawid, I. B. (1980) Repeated genes in eukaryotes. Ann. Rev. Biochem. 49, 727-764.
    • (1980) Ann. Rev. Biochem , vol.49 , pp. 727-764
    • Long, E.O.1    Dawid, I.B.2
  • 17
    • 0037540048 scopus 로고    scopus 로고
    • Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses
    • Kurtzman, C. P. and Robnett, C. J. (2003) Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res. 3, 417-432.
    • (2003) FEMS Yeast Res , vol.3 , pp. 417-432
    • Kurtzman, C.P.1    Robnett, C.J.2
  • 18
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
    • (1994) Nucl. Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 20
    • 22144491990 scopus 로고    scopus 로고
    • MONKEY: Identifying conserved transcription-factor binding sites in mulitple alignments using a binding site-specific evolutionary model
    • Moses, A. M., Chiang, D. Y., Pollard, D. A., Iyer, V. N., and Eisen, M. B. (2004) MONKEY: identifying conserved transcription-factor binding sites in mulitple alignments using a binding site-specific evolutionary model. Genome Biol. 5, R98.
    • (2004) Genome Biol , vol.5
    • Moses, A.M.1    Chiang, D.Y.2    Pollard, D.A.3    Iyer, V.N.4    Eisen, M.B.5
  • 21
    • 0035154384 scopus 로고    scopus 로고
    • Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences
    • Göttgens, B., Gilbert, J. G. R., Barton, L. M., et al. (2001) Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res. 11, 87-97.
    • (2001) Genome Res , vol.11 , pp. 87-97
    • Göttgens, B.1    Gilbert, J.G.R.2    Barton, L.M.3
  • 22
    • 0036303443 scopus 로고    scopus 로고
    • Concerted evolution between duplicated genetic elements in Helicobacter pylori
    • Pride, D. T. and Blaser, M. J. (2002) Concerted evolution between duplicated genetic elements in Helicobacter pylori. J. Mol. Biol. 316, 629-642.
    • (2002) J. Mol. Biol , vol.316 , pp. 629-642
    • Pride, D.T.1    Blaser, M.J.2
  • 23
    • 3242891684 scopus 로고    scopus 로고
    • DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ
    • Morgenstern, B. (2004) DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucl. Acids Res. 32, W33-W36.
    • (2004) Nucl. Acids Res , vol.32
    • Morgenstern, B.1
  • 24
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno, M., Do, C. B., Cooper, G. M., et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731.
    • (2003) Genome Res , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.B.2    Cooper, G.M.3
  • 25
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider, T. D. and Stephens, R. M. (1990) Sequence logos: a new way to display consensus sequences. Nucl. Acids Res. 18, 6097-6100.
    • (1990) Nucl. Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 27
    • 0344629438 scopus 로고    scopus 로고
    • The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork
    • Kobayashi, T. (2003) The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork. Mol. Cell. Biol. 23, 9178-9188.
    • (2003) Mol. Cell. Biol , vol.23 , pp. 9178-9188
    • Kobayashi, T.1
  • 28
    • 24644499002 scopus 로고    scopus 로고
    • Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats
    • Kobayashi, T. and Ganley, A. R. D. (2005) Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309, 1581-1584.
    • (2005) Science , vol.309 , pp. 1581-1584
    • Kobayashi, T.1    Ganley, A.R.D.2
  • 30
    • 0024326883 scopus 로고
    • Transcription of the 5S rRNA gene of Saccharomyces cerevisiae requires a promoter element at +1 and a 14-base pair internal control region
    • Challice, J. M. and Segall, J. (1989) Transcription of the 5S rRNA gene of Saccharomyces cerevisiae requires a promoter element at +1 and a 14-base pair internal control region. J. Biol. Chem. 264, 20,060-20,067.
    • (1989) J. Biol. Chem , vol.264
    • Challice, J.M.1    Segall, J.2
  • 31
    • 0027087436 scopus 로고
    • Topography of transcription factor complexes on the Saccharomyces cerevisiae 5S RNA gene
    • Brown, B. R., Bartholomew, B., Kassavetis, G. A., and Geiduschek, E. P. (1992) Topography of transcription factor complexes on the Saccharomyces cerevisiae 5S RNA gene. J. Mol. Biol. 228, 1063-1077.
    • (1992) J. Mol. Biol , vol.228 , pp. 1063-1077
    • Brown, B.R.1    Bartholomew, B.2    Kassavetis, G.A.3    Geiduschek, E.P.4
  • 32
    • 0027290923 scopus 로고
    • cis-Acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae
    • Miller, C. A. and Kowalski, D. (1993) cis-Acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol. Cell. Biol. 13, 5360-5369.
    • (1993) Mol. Cell. Biol , vol.13 , pp. 5360-5369
    • Miller, C.A.1    Kowalski, D.2
  • 33
    • 4143102539 scopus 로고    scopus 로고
    • rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication
    • Burkhalter, M. D. and Sogo, J. M. (2004) rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication. Mol. Cell. 15, 409-421.
    • (2004) Mol. Cell , vol.15 , pp. 409-421
    • Burkhalter, M.D.1    Sogo, J.M.2
  • 34
    • 0034722387 scopus 로고    scopus 로고
    • Chromosomal addresses of the cohesin component Mcd1p
    • Laloraya, S., Guacci, V., and Koshland, D. (2000) Chromosomal addresses of the cohesin component Mcd1p. J. Cell Biol. 151, 1047-1056.
    • (2000) J. Cell Biol , vol.151 , pp. 1047-1056
    • Laloraya, S.1    Guacci, V.2    Koshland, D.3
  • 35
    • 0024380724 scopus 로고
    • Proteins that bind to the yeast rDNA enhancer
    • Morrow, B. E., Johnson, S. P., and Warner, J. R. (1989) Proteins that bind to the yeast rDNA enhancer. J. Biol. Chem. 264, 9061-9068.
    • (1989) J. Biol. Chem , vol.264 , pp. 9061-9068
    • Morrow, B.E.1    Johnson, S.P.2    Warner, J.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.