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Volumn 32, Issue 5, 2003, Pages 418-426

Using analytical ultracentrifugation to study compositional variation in vertebrate genomes

Author keywords

Analytical ultracentrifugation; Base composition; Density gradients; Isochores; Phylogeny

Indexed keywords

CESIUM CHLORIDE; CYTOSINE; DNA FRAGMENT; GUANINE;

EID: 0041357134     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-003-0294-y     Document Type: Conference Paper
Times cited : (14)

References (55)
  • 1
    • 0037162885 scopus 로고    scopus 로고
    • Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    • Aparicio S, Chapman J, Stupka E, et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310
    • (2002) Science , vol.297 , pp. 1301-1310
    • Aparicio, S.1    Chapman, J.2    Stupka, E.3
  • 3
    • 0033991967 scopus 로고    scopus 로고
    • Isochores and the evolutionary genomics of vertebrates
    • Bernardi G (2000a) Isochores and the evolutionary genomics of vertebrates. Gene 241:3-17
    • (2000) Gene , vol.241 , pp. 3-17
    • Bernardi, G.1
  • 4
    • 0034707199 scopus 로고    scopus 로고
    • The compositional evolution of vertebrate genomes
    • Bernardi G (2000b) The compositional evolution of vertebrate genomes. Gene 259:31-43
    • (2000) Gene , vol.259 , pp. 31-43
    • Bernardi, G.1
  • 5
    • 0035802410 scopus 로고    scopus 로고
    • Misunderstandings about isochores. Part I
    • Bernardi G (2001) Misunderstandings about isochores. Part I. Gene 276:3-13
    • (2001) Gene , vol.276 , pp. 3-13
    • Bernardi, G.1
  • 6
    • 0022914759 scopus 로고
    • Compositional constraints and genome evolution
    • Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1-11
    • (1986) J Mol Evol , vol.24 , pp. 1-11
    • Bernardi, G.1    Bernardi, G.2
  • 7
    • 0025104361 scopus 로고
    • Compositional patterns in the nuclear genome of cold-blooded vertebrates
    • Bernadi G, Bernardi G (1990) Compositional patterns in the nuclear genome of cold-blooded vertebrates. J Mol Evol 31:265-281
    • (1990) J Mol Evol , vol.31 , pp. 265-281
    • Bernadi, G.1    Bernardi, G.2
  • 9
    • 0027051693 scopus 로고
    • Compositional mapping of the human dystrophin-encoding gene
    • Bettecken T, Aissani B, Müller C, Bernardi G (1992) Compositional mapping of the human dystrophin-encoding gene. Gene 122:329-335
    • (1992) Gene , vol.122 , pp. 329-335
    • Bettecken, T.1    Aissani, B.2    Müller, C.3    Bernardi, G.4
  • 10
    • 0037036937 scopus 로고    scopus 로고
    • An ultracentrifugation analysis of two hundred fish genomes
    • Bucciarelli G, Bernardi G, Bernardi G (2002) An ultracentrifugation analysis of two hundred fish genomes. Gene 295:153-162
    • (2002) Gene , vol.295 , pp. 153-162
    • Bucciarelli, G.1    Bernardi, G.2    Bernardi, G.3
  • 11
    • 0035802425 scopus 로고    scopus 로고
    • Standard deviations and correlations of GC levels in DNA sequences
    • Clay O (2001) Standard deviations and correlations of GC levels in DNA sequences. Gene 276:33-38
    • (2001) Gene , vol.276 , pp. 33-38
    • Clay, O.1
  • 12
    • 0035802430 scopus 로고    scopus 로고
    • Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses
    • Clay O, Carels N, Douady C, Macaya G, Bernardi G (2001) Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses. Gene 276:15-24
    • (2001) Gene , vol.276 , pp. 15-24
    • Clay, O.1    Carels, N.2    Douady, C.3    Macaya, G.4    Bernardi, G.5
  • 13
    • 0014385247 scopus 로고
    • Isolation and characterization of mouse and guinea pig satellite DNAs
    • Corneo G, Ginelli E, Soave C, Bernardi G (1968) Isolation and characterization of mouse and guinea pig satellite DNAs. Biochemistry 7:4373-4379
    • (1968) Biochemistry , vol.7 , pp. 4373-4379
    • Corneo, G.1    Ginelli, E.2    Soave, C.3    Bernardi, G.4
  • 14
    • 0019470162 scopus 로고
    • The major components of the mouse and human genomes. I. Preparation, basic properties and compositional heterogeneity
    • Cuny G, Soriano P, Macaya G, Bernardi G (1981) The major components of the mouse and human genomes. I. Preparation, basic properties and compositional heterogeneity. Eur J Biochem 115:227-233
    • (1981) Eur J Biochem , vol.115 , pp. 227-233
    • Cuny, G.1    Soriano, P.2    Macaya, G.3    Bernardi, G.4
  • 15
    • 0028817934 scopus 로고
    • A rapid procedure for the compositional analysis of yeast artificial chromosomes
    • De Sario A, Geigl E-M, Bernardi G (1995) A rapid procedure for the compositional analysis of yeast artificial chromosomes. Nucleic Acids Res 23:4013-4014
    • (1995) Nucleic Acids Res , vol.23 , pp. 4013-4014
    • De Sario, A.1    Geigl, E.-M.2    Bernardi, G.3
  • 17
    • 0001772466 scopus 로고    scopus 로고
    • Collection and storage of tissues
    • Hillis DM, Moritz C, Mable BK (eds). Sinauer, Sunderland, Mass
    • Dessauer HC, Coles CJ, Hafner MS (1996) Collection and storage of tissues. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. 2nd edn. Sinauer, Sunderland, Mass., pp 29-47
    • (1996) Molecular Systematics. 2nd Edn. , pp. 29-47
    • Dessauer, H.C.1    Coles, C.J.2    Hafner, M.S.3
  • 19
    • 0013787912 scopus 로고
    • The native, denatured and renatured states of deoxyribonucleic acid
    • Eigner J, Doty P (1965) The native, denatured and renatured states of deoxyribonucleic acid. J Mol Biol 12:549-580
    • (1965) J Mol Biol , vol.12 , pp. 549-580
    • Eigner, J.1    Doty, P.2
  • 22
    • 0015870552 scopus 로고
    • Density gradient sedimentation equilibrium
    • Hearst JE, Schmid CW (1973) Density gradient sedimentation equilibrium. Methods Enzymol 27:111-127
    • (1973) Methods Enzymol , vol.27 , pp. 111-127
    • Hearst, J.E.1    Schmid, C.W.2
  • 23
    • 0042344216 scopus 로고
    • The effects of pressure on the buoyant behavior of deoxyribonucleic acid and tobacco mosaic virus in a density gradient at equilibrium in the ultracentrifuge
    • Hearst JE, Ifft J, Vinograd J (1961) The effects of pressure on the buoyant behavior of deoxyribonucleic acid and tobacco mosaic virus in a density gradient at equilibrium in the ultracentrifuge. Proc Natl Acad Sci USA 47:1015-1025
    • (1961) Proc Natl Acad Sci USA , vol.47 , pp. 1015-1025
    • Hearst, J.E.1    Ifft, J.2    Vinograd, J.3
  • 24
    • 0004114076 scopus 로고
    • Cambridge University Press, Cambridge
    • Holliday R (1995) Understanding ageing. Cambridge University Press, Cambridge
    • (1995) Understanding Ageing
    • Holliday, R.1
  • 25
    • 0037036936 scopus 로고    scopus 로고
    • Compositional patterns in reptilian genomes
    • Hughes S, Clay O, Bernardi G (2002) Compositional patterns in reptilian genomes. Gene 295:323-329
    • (2002) Gene , vol.295 , pp. 323-329
    • Hughes, S.1    Clay, O.2    Bernardi, G.3
  • 26
    • 11844287403 scopus 로고
    • The determination of density distributions and density gradients in binary solutions at equilibrium in the ultracentrifuge
    • Ifft J, Voet D, Vinograd J (1961) The determination of density distributions and density gradients in binary solutions at equilibrium in the ultracentrifuge. J Phys Chem 65:1138-1145
    • (1961) J Phys Chem , vol.65 , pp. 1138-1145
    • Ifft, J.1    Voet, D.2    Vinograd, J.3
  • 27
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • IHGSC (International Human Genome Sequencing Consortium) (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
    • (2001) Nature , vol.409 , pp. 860-921
  • 28
    • 0031593251 scopus 로고    scopus 로고
    • Evolutionary changes in CpG and methylation levels in the genome of vertebrates
    • Jabbari K, Cacciò S, Pa de Barros J, Desgrès J, Bernardi G (1997) Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205:109-118
    • (1997) Gene , vol.205 , pp. 109-118
    • Jabbari, K.1    Cacciò, S.2    Pa de Barros, J.3    Desgrès, J.4    Bernardi, G.5
  • 29
    • 0027369473 scopus 로고
    • The compositional patterns of the avian genomes and their evolutionary implications
    • Kadi F, Mouchiroud D, Sabeur G, Bernardi G (1993) The compositional patterns of the avian genomes and their evolutionary implications. J Mol Evol 37:544-551
    • (1993) J Mol Evol , vol.37 , pp. 544-551
    • Kadi, F.1    Mouchiroud, D.2    Sabeur, G.3    Bernardi, G.4
  • 30
    • 0014219784 scopus 로고
    • Effect of methylation of cytosine residues on the buoyant density of DNA in caesium chloride solution
    • Kirk JT (1967) Effect of methylation of cytosine residues on the buoyant density of DNA in caesium chloride solution. J Mol Biol 28:171-172
    • (1967) J Mol Biol , vol.28 , pp. 171-172
    • Kirk, J.T.1
  • 31
  • 32
    • 0035802384 scopus 로고    scopus 로고
    • Delineating relative homogeneous G + C domains in DNA sequences
    • Li W (2001) Delineating relative homogeneous G + C domains in DNA sequences. Gene 276:57-72
    • (2001) Gene , vol.276 , pp. 57-72
    • Li, W.1
  • 33
    • 0017173987 scopus 로고
    • An approach to the organization of eukaryotic genomes at a macromolecular level
    • Macaya G, Thiery JP, Bernardi G (1976) An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108:237-254
    • (1976) J Mol Biol , vol.108 , pp. 237-254
    • Macaya, G.1    Thiery, J.P.2    Bernardi, G.3
  • 35
    • 36949082598 scopus 로고
    • Heterogeneity in deoxyribonucleic acids: I. Dependence on composition of the configurational stability of deoxyribonucleic acids
    • Marmur J, Doty P (1959) Heterogeneity in deoxyribonucleic acids: I. Dependence on composition of the configurational stability of deoxyribonucleic acids. Nature 183:1427-1429
    • (1959) Nature , vol.183 , pp. 1427-1429
    • Marmur, J.1    Doty, P.2
  • 37
    • 0001172501 scopus 로고
    • Equilibrium sedimentation of macromolecules in density gradients
    • Meselson M, Stahl F, Vinograd J (1957) Equilibrium sedimentation of macromolecules in density gradients. Proc Natl Acad Sci USA 43:581-588
    • (1957) Proc Natl Acad Sci USA , vol.43 , pp. 581-588
    • Meselson, M.1    Stahl, F.2    Vinograd, J.3
  • 40
    • 0037196383 scopus 로고    scopus 로고
    • A compact view of isochores in the draft human genome sequence
    • Pavlíček A, Paces J, Clay O, Bernardi G (2002a) A compact view of isochores in the draft human genome sequence. FEBS Lett 511:165-169
    • (2002) FEBS Lett , vol.511 , pp. 165-169
    • Pavlíček, A.1    Paces, J.2    Clay, O.3    Bernardi, G.4
  • 41
    • 0037196423 scopus 로고    scopus 로고
    • Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17
    • Pavlíček A, Clay O, Jabbari K, Paces J, Bernardi G (2002b) Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17. FEBS Lett 511:175-177
    • (2002) FEBS Lett , vol.511 , pp. 175-177
    • Pavlíček, A.1    Clay, O.2    Jabbari, K.3    Paces, J.4    Bernardi, G.5
  • 42
    • 0000968381 scopus 로고
    • The relative homogeneity of microbial DNA
    • Rolfe R, Meselson M (1959) The relative homogeneity of microbial DNA. Proc Natl Acad Sci USA 45:1039-1043
    • (1959) Proc Natl Acad Sci USA , vol.45 , pp. 1039-1043
    • Rolfe, R.1    Meselson, M.2
  • 43
    • 0037202372 scopus 로고    scopus 로고
    • Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds
    • Saccone S, Federico C, Bernardi G (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300:169-178
    • (2002) Gene , vol.300 , pp. 169-178
    • Saccone, S.1    Federico, C.2    Bernardi, G.3
  • 44
    • 0035824030 scopus 로고    scopus 로고
    • Unexpected solute aggregation in water on dilution
    • Samal S, Geckeler K (2001) Unexpected solute aggregation in water on dilution. Chem Commun 2224-2225
    • (2001) Chem Commun , pp. 2224-2225
    • Samal, S.1    Geckeler, K.2
  • 45
    • 0011933622 scopus 로고
    • Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl
    • Schildkraut CL, Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol 4:430-443
    • (1962) J Mol Biol , vol.4 , pp. 430-443
    • Schildkraut, C.L.1    Marmur, J.2    Doty, P.3
  • 46
    • 0014694082 scopus 로고
    • Molecular weights of homogeneous coliphage DNAs from density-gradient sedimentation equilibrium
    • Schmid CW, Hearst JE (1969) Molecular weights of homogeneous coliphage DNAs from density-gradient sedimentation equilibrium. J Mol Biol 44:143-160
    • (1969) J Mol Biol , vol.44 , pp. 143-160
    • Schmid, C.W.1    Hearst, J.E.2
  • 47
    • 84985734133 scopus 로고
    • Density-gradient sedimentation equilibrium of DNA and the effective density gradient of several salts
    • Schmid CW, Hearst JE (1971) Density-gradient sedimentation equilibrium of DNA and the effective density gradient of several salts. Biopolymers 10:1901-1924
    • (1971) Biopolymers , vol.10 , pp. 1901-1924
    • Schmid, C.W.1    Hearst, J.E.2
  • 48
    • 0015272818 scopus 로고
    • Sedimentation equilibrium of DNA samples heterogeneous in density
    • Schmid CW, Hearst JE (1972) Sedimentation equilibrium of DNA samples heterogeneous in density. Biopolymers 11:1913-1918
    • (1972) Biopolymers , vol.11 , pp. 1913-1918
    • Schmid, C.W.1    Hearst, J.E.2
  • 49
    • 0000969637 scopus 로고
    • A statistical analysis of deoxyribonucleic acid distribution in density gradient centrifugation
    • Sueoka N (1959) A statistical analysis of deoxyribonucleic acid distribution in density gradient centrifugation. Proc Natl Acad Sci USA 45:1480-1490
    • (1959) Proc Natl Acad Sci USA , vol.45 , pp. 1480-1490
    • Sueoka, N.1
  • 50
    • 36949078842 scopus 로고
    • Heterogeneity in deoxyribonucleic acids. II. Dependence of the density of deoxyribonucleic acids on guanine-cytosine content
    • Sueoka N, Marmur J, Doty P (1959) Heterogeneity in deoxyribonucleic acids. II. Dependence of the density of deoxyribonucleic acids on guanine-cytosine content. Nature 183:1429-1433
    • (1959) Nature , vol.183 , pp. 1429-1433
    • Sueoka, N.1    Marmur, J.2    Doty, P.3
  • 51
    • 77956994114 scopus 로고
    • Use of cesium sulfate for equilibrium density gradient ultracentrifugation
    • Szybalski W (1968) Use of cesium sulfate for equilibrium density gradient ultracentrifugation. Methods Enzymol 12:330-360
    • (1968) Methods Enzymol , vol.12 , pp. 330-360
    • Szybalski, W.1
  • 53
    • 0017105287 scopus 로고
    • An analysis of eukaryotic genomes by density gradient centrifugation
    • Thiery JP, Macaya G, Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108:219-235
    • (1976) J Mol Biol , vol.108 , pp. 219-235
    • Thiery, J.P.1    Macaya, G.2    Bernardi, G.3
  • 55
    • 0030603239 scopus 로고    scopus 로고
    • The gene distribution of the human genome
    • Zoubak S, Clay O, Bernardi G (1996) The gene distribution of the human genome, Gene 174:95-102
    • (1996) Gene , vol.174 , pp. 95-102
    • Zoubak, S.1    Clay, O.2    Bernardi, G.3


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