The evolution of isochores

One of the most striking features of mammalian chromosomes is the variation in G+C content that occurs over scales of hundreds of kilobases to megabases, the so-called 'isochore' structure of the human genome. This variation in base composition affects both coding and non-coding sequences and seems to reflect a fundamental level of genome organization. However, although we have known about isochores for over 25 years, we still have a poor understanding of why they exist. In this article, we review the current evidence for the three main hypotheses.

[1]  Howard Ochman,et al.  Isochores result from mutation not selection , 1999, Nature.

[2]  L. Hurst,et al.  The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. , 1999, Genetics.

[3]  T. Ikemura,et al.  Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. , 1991, Nucleic acids research.

[4]  A. Eyre-Walker,et al.  Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. , 1999, Genetics.

[5]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[6]  Peter D. Keightley,et al.  High genomic deleterious mutation rates in hominids , 1999, Nature.

[7]  L. Hurst,et al.  The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution. , 2001, Molecular biology and evolution.

[8]  W Krone,et al.  An isochore transition in the NF1 gene region coincides with a switch in the extent of linkage disequilibrium. , 2000, American journal of human genetics.

[9]  M. Meuth,et al.  The molecular basis of mutations induced by deoxyribonucleoside triphosphate pool imbalances in mammalian cells. , 1989, Experimental cell research.

[10]  A. Eyre-Walker The role of DNA replication and isochores in generating mutation and silent substitution rate variance in mammals. , 1992, Genetical research.

[11]  A. Clark,et al.  Local rates of recombination are positively correlated with GC content in the human genome. , 2001, Molecular biology and evolution.

[12]  G Bernardi,et al.  The mosaic genome of warm-blooded vertebrates. , 1985, Science.

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

[14]  A. Eyre-Walker DNA mismatch repair and synonymous codon evolution in mammals. , 1994, Molecular biology and evolution.

[15]  M. Meuth,et al.  A novel pathway for transversion mutation induced by dCTP misincorporation in a mutator strain of CHO cells , 1989, Molecular and cellular biology.

[16]  S. Shabalina,et al.  Pattern of selective constraint in C. elegans and C. briggsae genomes. , 1999, Genetical research.

[17]  A. R. Merchant,et al.  High guanine–cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[18]  D. Mccormick Sequence the Human Genome , 1986, Bio/Technology.

[19]  D. Mouchiroud,et al.  Warm-blooded isochore structure in Nile crocodile and turtle. , 1999, Molecular biology and evolution.

[20]  A. Nekrutenko,et al.  Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. , 2000, Gene.

[21]  C. Mathews,et al.  DNA precursor pools and ribonucleotide reductase activity: distribution between the nucleus and cytoplasm of mammalian cells , 1985, Molecular and cellular biology.

[22]  S. Boissinot,et al.  Mutation Pattern Variation Among Regions of the Primate Genome , 1997, Journal of Molecular Evolution.

[23]  J. Jiricny,et al.  Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells , 1988, Cell.

[24]  J. Jurka,et al.  Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[25]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[26]  P. Keightley,et al.  Deleterious mutations and the evolution of sex. , 2000, Science.

[27]  M. Meuth,et al.  The genetic consequences of DNA precursor pool imbalance: sequence analysis of mutations induced by excess thymidine at the hamster aprt locus. , 1989, Mutation research.

[28]  K. J. Fryxell,et al.  Cytosine deamination plays a primary role in the evolution of mammalian isochores. , 2000, Molecular biology and evolution.

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

[30]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[31]  J. Bertram,et al.  Changes in ribo- and deoxyribonucleoside triphosphate pools within the cell cycle of a synchronized mouse fibroblast cell line. , 1983, Biochimica et biophysica acta.

[32]  Z. Yang,et al.  Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions. , 2000, Genetics.

[33]  T. Nagylaki Evolution of a finite population under gene conversion. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Adam Eyre-Walker,et al.  Recombination and mammalian genome evolution , 1993, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[35]  T Gojobori,et al.  Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex , 1997, Molecular and cellular biology.

[36]  G. Holmquist,et al.  Chromosome bands, their chromatin flavors, and their functional features. , 1992, American journal of human genetics.

[37]  J. Filipski,et al.  Correlation between molecular clock ticking, codon usage, fidelity of DNA repair, chromosome banding and chromatin compactness in germline cells , 1987, FEBS letters.

[38]  G Bernardi,et al.  The correlation of protein hydropathy with the base composition of coding sequences. , 1999, Gene.

[39]  A. Eyre-Walker,et al.  Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. , 2001, Molecular biology and evolution.

[40]  Wen-Hsiung Li,et al.  Mutation rates differ among regions of the mammalian genome , 1989, Nature.

[41]  F. Rodier,et al.  Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences. , 1989, Journal of molecular biology.

[42]  G Bernardi,et al.  Isochores and the evolutionary genomics of vertebrates. , 2000, Gene.

[43]  A. Smit Interspersed repeats and other mementos of transposable elements in mammalian genomes. , 1999, Current opinion in genetics & development.

[44]  N. Galtier,et al.  Isochore evolution in mammals: a human-like ancestral structure. , 1998, Genetics.

[45]  M. Tomita,et al.  Characteristic Sequence Pattern in the 5- to 20-bp Upstream Region of Primate Alu Elements , 2000, Journal of Molecular Evolution.

[46]  L. Hurst,et al.  Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores. , 2000, Gene.

[47]  A. Eyre-Walker,et al.  Evidence that both G + C rich and G + C poor isochores are replicated early and late in the cell cycle. , 1992, Nucleic acids research.

[48]  Gen Tamiya,et al.  Complete sequence and gene map of a human major histocompatibility complex , 1999 .

[49]  Elena S. Babaylova,et al.  Complete sequence and gene map of a human major histocompatibility complex , 1999, Nature.

[50]  G Bernardi,et al.  Human coding and noncoding DNA: compositional correlations. , 1996, Molecular phylogenetics and evolution.

[51]  Jef D Boeke,et al.  Human L1 Retrotransposon Encodes a Conserved Endonuclease Required for Retrotransposition , 1996, Cell.

[52]  N. Sueoka Directional mutation pressure and neutral molecular evolution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

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

[54]  A. Eyre-Walker The effect of constraint on the rate of evolution in neutral models with biased mutation. , 1992, Genetics.

[55]  J. Lobry,et al.  Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes , 1997, Journal of Molecular Evolution.

[56]  A. Eyre-Walker Differentiating between selection and mutation bias. , 1997, Genetics.

[57]  K. H. Wolfe,et al.  Mammalian DNA replication: mutation biases and the mutation rate. , 1991, Journal of theoretical biology.

[58]  G. Bernardi,et al.  The gene-richest bands of human chromosomes replicate at the onset of the S-phase , 1998, Cytogenetic and Genome Research.