Compositional bias in DNA

Current Opinion in Genetics and Development

Volumn 10, Issue 6, 2000, Pages 656-661

  Gautier, Christian ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

BACTERIAL GENETICS; COMPUTER ANALYSIS; DNA BASE COMPOSITION; DNA SEQUENCE; GENE SEQUENCE; GENETIC VARIABILITY; ISOCHORE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; TAXONOMY;

BACTERIA (MICROORGANISMS);

EID: 0033675259     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(00)00144-1     Document Type: Review

References (75)

1. On the genetic basis of variation and heterogeneity of DNA base composition
2. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes
3. The unusual mutagenic specificity of an E. coli mutator gene
4. Codon base randomness and composition drift in coliphage
5. Correlation between the abundance of E. 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 translation system
6. Codon usage in bacteria: Correlation with gene expressivity
7. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes
8. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtillis tRNAs: Gene expression level and species-species diversity of codon usage based on multivariate analysis
9. 'Silent' sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons
10. Codon usage and gene function are related in sequences of Arabidopsis thaliana
11. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
12. tRNA gene number and codon usage in C. elegans genome are co-adapted for the optimal translation of highly expressed genes
13. Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A=T and C=G
14. Codon usage and genome evolution
15. Translational selection and molecular evolution
16. Coding sequence evolution
17. The genome sequence of the plant pathogen Xylella fastidiosa
18. Oriloc: Prediction of replication boundaries in unannotated bacterial chromosomes
19. Analysing genomes with cumulative skew diagrams
20. Strand asymetries in DNA evolution
21. Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms
22. When polymerase collide: Replication and the transcriptional organization of the E. coli chromosome
23. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
24. Properties of a general model of DNA evolution under no-strand-bias conditions
25. Asymetrical substitution patterns in the two DNA strands of bacteria
26. Evolution of DNA base composition under no-strand-bias conditions when the subtitution rates are not constant
27. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals
28. Proteome composition and codon usage in spirochaetes: Species-specific and DNA strand-specific mutational biases
29. The contribution of replication orientation, gene direction, and signal sequences to base composition asymmetries in bacterial genomes
30. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
31. Influence of genomic G+C content on average amino-acid composition of protein from 59 bacterial species
32. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
33. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
34. Universal replication biases in bacteria
35. Functional polarization of the Escherichia coli chromosome terminus: The dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity
36. An analysis of eukaryotic genomes by density gradient centrifugation
37. Isochores and the evolutionary genomics of vertebrates
38. Diversity in G+C content at the third position of codons in vertebrate genes and its cause
39. Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins
40. Human coding and non coding DNA: Copositional correlations
41. The gene distribution of the human genome
42. The distribution of genes in the human genome
43. The distribution of interspersed repeats is non uniform and conserved in the mouse and human genomes
44. The isopycnic, compartmentalized integration of Rous sarcoma virus sequences
45. Regional specificity of HTLV-I proviral integration in the human genome
46. CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families
47. Global variation in G+C content along vertebrate genome DNA. Possible correlation with chromosome band structures
48. Evident diversity of codon usage pattern of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data
49. Compositional properties of telomeric regions from human chromosomes
50. Correlation between isochore and chromosomal bands in the human genome
51. Identification of the gene-richest bands in human chromosomes
52. Recombination and mammalian genome evolution
53. The DNA sequence of human chromosome 21. The chromosome 21 mapping and sequencing consortium
54. The DNA sequence of human chromosome 22
55. A boundary of long range G+C% mosaic domains in the human MHC locus: Pseudoautosomal boundary-like sequence exists near the boundary
56. Complete sequence and gene map of a human major histocompatibility complex
57. Gene organisation, sequence variation and isochore structure at the centromeric boundary of the human MHC
58. The isochore organization and the compositional distribution of homologous coding sequences in the nuclear genome of plants
59. Compositional patterns in the nuclear genome of cold-blooded vertebrates
60. Evolution of genome size and DNA base composition in reptiles
61. Warm-blooded isochore structure in Nile crocodile and turtle
62. The compositional distribution of coding sequences and DNA molecules in human and murids
63. Codon usage changes and sequence dissimilarity between human and rat
64. Pattern in the genome
65. Evidence for higher rates of nucleotide substitution in rodents than in man
66. Recombination and mammalian genome evolution
67. Isochore evolution in mammals: A human-like ancestral structure
68. Evidence of selection on silent site base composition in mammals: Potential implications for the evolution of junk DNA
69. 'Silent' sites in Drosophila are not neutral: Evidence of selection among synonymous codons
70. Mutation rates differ among regions of the mammalian genome
71. Chromosomal location effects on gene sequences evolution in mammals
72. Isochores results from mutation not selection
73. Mutation pattern variation among regions of the primate genome
74. Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex
75. The evolution of base composition and phylogenetic inference