The mosaic genome of warm-blooded vertebrates.

Most of the nuclear genome of warm-blooded vertebrates is a mosaic of very long (much greater than 200 kilobases) DNA segments, the isochores; these isochores are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content. The families of DNA molecules derived from such classes can be separated and used to study the genome distribution of any sequence which can be probed. This approach has revealed (i) that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and (ii) that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences. The compositional compartmentalization of the genome of warm-blooded vertebrates is discussed with respect to its evolutionary origin, its causes, and its effects on chromosome structure and function.

[1]  M. A. Goldman,et al.  Replication timing of genes and middle repetitive sequences. , 1984, Science.

[2]  G. Bernardi,et al.  Nucleotide sequence organization in the very small genome of a tetraodontid fish, Arothron diadematus. , 1984, European journal of biochemistry.

[3]  C. Schildkraut,et al.  Changes in gene position are accompanied by a change in time of replication , 1984, Cell.

[4]  L. Ratner,et al.  Human-proto-oncogene nucleotide sequences corresponding to the transforming region of simian sarcoma virus. , 1984, Science.

[5]  R. Stephens,et al.  Nucleotide sequence analysis of the long terminal repeat of integrated bovine leukemia provirus DNA and of adjacent viral and host sequences , 1984, Journal of virology.

[6]  Rosalind C. Lee,et al.  The mouse c-abl locus: Molecular cloning and characterization , 1984, Cell.

[7]  G. Bernardi,et al.  The Bam repeats of the mouse genome belong in several superfamilies the longest of which is over 9 kb in size. , 1984, Nucleic acids research.

[8]  W. Quax,et al.  The structure of the vimentin gene , 1983, Cell.

[9]  G. Bernardi,et al.  The distribution of CR1, and Alu-like family of interspersed repeats, in the chicken genome. , 1983, Biochimica et biophysica acta.

[10]  P. Hofschneider,et al.  Integration of hepatitis B virus DNA: Evidence for integration in the single-stranded gap , 1983, Cell.

[11]  R. Heilig,et al.  Isolation and characterization of cDNA clones for human skeletal muscle alpha actin. , 1983, Nucleic acids research.

[12]  G Bernardi,et al.  The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[13]  E. Chen,et al.  Complete nucleotide sequences of the T24 human bladder carcinoma oncogene and its normal homologue , 1983, Nature.

[14]  E. Chen,et al.  Identification and nucleotide sequence of a human locus homologous to the v-myc oncogene of avian myelocytomatosis virus MC29 , 1983, Nature.

[15]  G. Bernardi,et al.  Organization of nucleotide sequences in the chicken genome. , 1983, European journal of biochemistry.

[16]  D J Lipman,et al.  Contextual constraints on synonymous codon choice. , 1983, Journal of molecular biology.

[17]  G. Holmquist,et al.  Characterization of Giemsa dark- and light-band DNA , 1982, Cell.

[18]  A. Minty,et al.  A fetal skeletal muscle actin mRNA in the mouse and its identity with cardiac actin mRNA , 1982, Cell.

[19]  R. Heilig,et al.  The ovalbumin gene family: complete sequence and structure of the Y gene. , 1982, Nucleic acids research.

[20]  G. V. Vande Woude,et al.  Human DNA sequence homologous to the transforming gene (mos) of Moloney murine sarcoma virus. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[21]  W. Jelinek,et al.  The Alu family of dispersed repetitive sequences. , 1982, Science.

[22]  W. Fiers,et al.  Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. , 1982, Gene.

[23]  Stanley N Cohen,et al.  Characterization of the structural gene and putative 5′-regulatory sequences for human proopiomelanocortin , 1982, Nature.

[24]  P. Chambon,et al.  The complete nucleotide sequence of the chicken ovotransferrin mRNA. , 1982, European journal of biochemistry.

[25]  G. Bernardi,et al.  Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[26]  S. Nakanishi,et al.  Isolation and structural organization of the human corticotropin‐β‐lipotropin precursor gene , 1981, FEBS letters.

[27]  W G Beattie,et al.  Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance. , 1981, Biochemistry.

[28]  J. D. Engel,et al.  Adult chicken alpha-globin genes alpha A and alpha D: no anemic shock alpha-globin exists in domestic chickens. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[29]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.

[30]  V. Ingram,et al.  cDNA sequence of a new chicken embryonic rho-globin. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[31]  J V Maizel,et al.  The nucleotide sequence of a 5.5-kilobase DNA segment containing the mouse kappa immunoglobulin J and C region genes. , 1981, The Journal of biological chemistry.

[32]  G. Bernardi,et al.  The major components of the mouse and human genomes. 2. Reassociation kinetics. , 1981, European journal of biochemistry.

[33]  A. V. van Ooyen,et al.  DNA sequences preceding the rabbit beta-globin gene are required for formation in mouse L cells of beta-globin RNA with the correct 5' terminus. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[34]  G. Modiano,et al.  Nonrandom patterns of codon usage and of nucleotide substitutions in human alpha- and beta-globin genes: an evolutionary strategy reducing the rate of mutations with drastic effects? , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[35]  C. Schildkraut,et al.  alpha-Globulin sequences are located in a region of early-replicating DNA in murine erythroleukemia cells. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[36]  J. Yunis.  Mid-prophase human chromosomes. The attainment of 2000 bands , 1981, Human Genetics.

[37]  Y. Kan,et al.  Cloning and complete nucleotide sequence of human 5'-alpha-globin gene. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[38]  A. Michelson,et al.  The 3′ untranslated regions of the duplicated human α-globin genes are unexpectedly divergent , 1980, Cell.

[39]  G. Bernardi,et al.  An analysis of fish genomes by density gradient centrifugation. , 1980, European journal of biochemistry.

[40]  A. Jeffreys,et al.  The 5' flanking region of human epsilon-globin gene. , 1980, Nucleic acids research.

[41]  Ann E. Blechl,et al.  Human fetal g γ- and A γ-globin genes: Complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes , 1980, Cell.

[42]  Tom Maniatis,et al.  The structure and evolution of the human β-globin gene family , 1980, Cell.

[43]  C. Shoulders,et al.  The primary structure of the human ϵ-globin gene , 1980, Cell.

[44]  S. Weissman,et al.  Complete nucleotide sequence of the human δ-globin gene , 1980, Cell.

[45]  T. Maniatis,et al.  The nucleotide sequence of the human β-globin gene , 1980, Cell.

[46]  Jeffrey G. Williams,et al.  The nucleotide sequence of the major β-globin mRNA from Xenopus laevis , 1980 .

[47]  P. Leder,et al.  Mouse globin system: a functional and evolutionary analysis. , 1980, Science.

[48]  Jeffrey G. Williams,et al.  Internal organization of the major adult α- and β-globin genes of X. laevis , 1980, Cell.

[49]  P. Chambon,et al.  The ovalbumin gene family: Structure of the X gene and evolution of duplicated split genes , 1980, Cell.

[50]  J. D. Engel,et al.  Analysis of the closely linked adult chicken alpha-globin genes in recombinant DNAs. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[51]  P. Leder,et al.  Organization and complete sequence of identical embryonic and plasmacytoma kappa V-region genes. , 1980, The Journal of biological chemistry.

[52]  J. T. Wilson,et al.  Nucleotide sequence of the coding portion of human alpha globin messenger RNA. , 1980, The Journal of biological chemistry.

[53]  A. Meager,et al.  Enhancement of interferon mRNA levels in butyric acid‐treated namalwa cells , 1980, FEBS letters.

[54]  T. Miyata,et al.  Secondary structure of MS2 phage RNA and bias in code word usage. , 1979, Nucleic acids research.

[55]  N. Rosenthal,et al.  The structure and transcription of four linked rabbit β-like globin genes , 1979, Cell.

[56]  A. Ullrich,et al.  Molecular cloning and sequence analysis of adult chicken β globin cDNA , 1979 .

[57]  P. Leder,et al.  The complete sequence of a chromosomal mouse α-globin gene reveals elements conserved throughout vertebrate evolution , 1979, Cell.

[58]  J. Maizel,et al.  The evolution and sequence comparison of two recently diverged mouse chromosomal β-globin genes , 1979, Cell.

[59]  F. Galibert,et al.  Nucleotide sequence of the hepatitis B virus genome (subtype ayw) cloned in E. coli , 1979, Nature.

[60]  A. V. van Ooyen,et al.  Comparison of total sequence of a cloned rabbit beta-globin gene and its flanking regions with a homologous mouse sequence. , 1979, Science.

[61]  G. Bernardi,et al.  Integration of bovine leukemia virus DNA in the bovine genome. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[62]  C Benoist,et al.  No more than seven interruptions in the ovalbumin gene: comparison of genomic and double-stranded cDNA sequences. , 1979, Nucleic acids research.

[63]  G. Bernardi.  The petite mutation in yeast , 1979 .

[64]  J. Dodgson,et al.  Isolation of the chicken β-globin gene and a linked embryonic β-like globin gene from a chicken DNA recombinant library , 1979, Cell.

[65]  G. Bernardi,et al.  THE DNA components of the chicken genome. , 1979, European journal of biochemistry.

[66]  P. Chambon,et al.  The ovalbumin gene region: common features in the organisation of three genes expressed in chicken oviduct under hormonal control , 1979, Nature.

[67]  F Crick,et al.  Split genes and RNA splicing. , 1979, Science.

[68]  J. D. Engel,et al.  Gene localization by chromosome fractionation: globin genes are on at least two chromosomes and three estrogen-inducible genes are on three chromosomes. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[69]  G. Bernardi,et al.  Isolation and organization of calf ribosomal DNA. , 1979, Nucleic acids research.

[70]  J. Vandekerckhove,et al.  At least six different actins are expressed in a higher mammal: an analysis based on the amino acid sequence of the amino-terminal tryptic peptide. , 1978, Journal of molecular biology.

[71]  P. Leder,et al.  The sequence of the chromosomal mouse β-globin major gene: Homologies in capping, splicing and poly(A) sites , 1978, Cell.

[72]  W. Salser,et al.  The primary sequence of rabbit α-globin mRNA , 1978, Cell.

[73]  G. Bernardi,et al.  An analysis of the bovine genome by density-gradient centrifugation. Preparation of the dG+dC-rich DNA components. , 1978, European journal of biochemistry.

[74]  D. Comings.  Mechanisms of chromosome banding and implications for chromosome structure. , 1978, Annual review of genetics.

[75]  S. Weissman,et al.  Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA. , 1977, The Journal of biological chemistry.

[76]  P Berg,et al.  Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. , 1977, Journal of molecular biology.

[77]  G. Bernardi,et al.  An analysis of the bovine genome by density gradient centrifugation: fractionation in Cs2SO4/3,6-bis(acetatomercurimethyl)dioxane density gradient. , 1977, European journal of biochemistry.

[78]  G Bernardi,et al.  An approach to the organization of eukaryotic genomes at a macromolecular level. , 1976, Journal of molecular biology.

[79]  G Bernardi,et al.  An analysis of eukaryotic genomes by density gradient centrifugation. , 1976, Journal of molecular biology.

[80]  G Bernardi,et al.  An analysis of the bovine genome by Cs2SO4-Ag density gradient centrifugation. , 1973, Journal of molecular biology.

[81]  G. Bernardi,et al.  Isolation and characterization of mouse and guinea pig satellite deoxyribonucleic acids. , 1968, Biochemistry.

[82]  A. Kornberg,et al.  Enzymatic synthesis of deoxyribonucleic acid. XI. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. , 1962, The Journal of biological chemistry.