Different functional classes of genes are characterized by different compositional properties

FEBS Letters

Volumn 581, Issue 30, 2007, Pages 5819-5824

  D'Onofrio, Giuseppe ^a   Ghosh, Tapash Chandra ^b   Saccone, Salvatore ^c  

^a STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

^b BOSE INSTITUTE   (India)

^c UNIVERSITY OF CATANIA   (Italy)

Author keywords

Base composition (GC); Biased gene conversion (BGC); Chromosomal band; Codon usage; Intron; Isochore

Indexed keywords

GUANYLATE CYCLASE;

ARTICLE; CELL FUNCTION; CELL METABOLISM; CODON; CONTROLLED STUDY; GENE FUNCTION; GENETIC ANALYSIS; GENOME; HUMAN; INTRON; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; XENOPUS;

ANIMALS; BASE COMPOSITION; CHROMOSOMES, HUMAN; CODON; GENES; HUMANS; INTRONS; SEQUENCE HOMOLOGY, NUCLEIC ACID; XENOPUS;

EID: 37049031424     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2007.11.052     Document Type: Article

References (39)

1. Mouchiroud D., Fichant G., and Bernardi G. Compositional compartmentalization and gene composition in the genome of vertebrates. J. Mol. Evol. 26 (1987) 198-204
2. D'Onofrio G., Mouchiroud D., Ai{dotless}̈ssani B., Gautier C., and Bernardi G. Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J. Mol. Evol. 32 (1991) 504-510
3. Bernardi G. Compositional patterns in the nuclear genome of coldblooded vertebrates. J. Mol. Evol. 31 (1990) 265-281
4. D'Onofrio G., Jabbari K., Musto H., Alvarez-Valin F., Cruveiller S., and Bernardi G. Evolutionary genomics of vertebrates and its implications. Ann. NY Acad. Sci. 870 (1999) 81-94
5. Bernardi G. Structural and Evolutionary Genomics. Natural Selection in Genome Evolution (2004), Elsevier, Amsterdam pp. 434
6. Bernardi G., Mouchiroud D., and Gautier C. Compositional patterns in vertebrate genomes: conservation and change in evolution. J. Mol. Evol. 28 (1988) 7-18
7. Bernardi G. The neoselectionist theory of genome evolution. Proc. Natl. Acad. Sci. USA 104 (2007) 8385-8390
8. Bernardi G., Olofson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., and Rodier F. The mosaic genome of warmblooded vertebrates. Science 228 (1985) 953-958
9. Aissani B., D'Onofrio G., Mouchiroud D., Gardiner K., Gautier C., and Bernardi G. The compositional properties of human genes. J. Mol. Evol. 32 (1991) 493-503
10. Mouchiroud D., D'Onofrio G., Aissani B., Macaya G., Gautier C., and Bernardi G. The distribution of genes in the human genome. Gene 100 (1991) 181-187
11. Clay O., Caccio S., Zoubak S., Mouchiroud D., and Bernardi G. Human coding and noncoding DNA: compositional correlations. Mol. Phylogenet. Evol. 5 (1996) 2-12
12. Vinogradov A.E. Bendable genes of warm-blooded vertebrates. Mol. Biol. Evol. 18 (2001) 2195-2200
13. Vinogradov A.E. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 31 (2003) 1838-1844
14. Duret L., Mouchiroud D., and Gauthier C. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40 (1995) 308-317
15. Eyre-Walker A.C. An analysis of codon usage in mammals: selection or mutation bias?. J. Mol. Evol. 33 (1991) 442-449
16. Kotlar D., and Lavner Y. The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids. BMC Genom. 7 (2006) 67
17. Lercher M.J., Urrutia A.O., and Hurst L.D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31 (2002) 180-183
18. Vinogradov A.E. Isochores and tissue-specificity. Nucleic Acids Res. 31 (2003) 5212-5220
19. Vinogradov A.E. Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth. Trends Genet. 21 (2005) 639-643
20. Goncalves I., Duret L., and Mouchiroud D. Nature and structure of human genes that generate retropseudogenes. Genome Res. 10 (2000) 672-678
21. Arhondakis S., Auletta F., Torelli G., and D'Onofrio G. Base composition and expression level of human genes. Gene 325 (2004) 165-169
22. Semon M., and Duret L. Evidence that functional transcription units cover at least half of the human genome. Trends Genet. 20 (2004) 229-232
23. Federico C., Andreozzi L., Saccone S., and Bernardi G. Gene density in the Giemsa bands of human chromosomes. Chromosome Res. 8 (2000) 737-746
24. Saccone S., Federico C., and Bernardi G. Localization of the generichest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300 (2002) 169-178
25. Federico C., Scavo C., Cantarella C.D., Motta S., Saccone S., and Bernardi G. Gene-rich and gene-poor chromosomal regions have different locations in the interphase nuclei of cold-blooded vertebrates. Chromosoma 115 (2006) 123-128
26. Chiusano M.L., D'Onofrio G., Alvarez-Valin F., Jabbari K., Colonna G., and Bernardi G. Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure [In Process Citation]. Gene 238 (1999) 23-31
27. Alvarez-Valin F., Lamolle G., and Bernardi G. Isochores, GC3 and mutation biases in the human genome. Gene 300 (2002) 161-168
28. Galtier N., and Duret L. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 23 (2007) 273-277
29. Press W.H., and Robins H. Isochores exhibit evidence of genes interacting with the large-scale genomic environment. Genetics 174 (2006) 1029-1040
30. Vinogradov A.E. Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res. 33 (2005) 559-563
31. Grillo G., Attimonelli M., Liuni S., and Pesole G. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. Comput. Appl. Biosci. 12 (1996) 1-8
32. Tatusov R.L., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29 (2001) 22-28
33. Tatusov R.L., et al. The COG database: an updated version includes eukaryotes. BMC Bioinf. 4 (2003) 41
34. Costantini M., Clay O., Federico C., Saccone S., Auletta F., and Bernardi G. Human chromosomal bands: nested structure, high-definition map and molecular basis. Chromosoma 116 (2007) 29-40
35. Duret L., Mouchiroud D., and Gouy M. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res. 22 (1994) 2360-2365
36. Galtier N., Piganeau G., Mouchiroud D., and Duret L. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159 (2001) 907-911
37. Ptak S.E., et al. Fine-scale recombination patterns differ between chimpanzees and humans. Nat. Genet. 37 (2005) 429-434
38. Lavner Y., and Kotlar D. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345 (2005) 127-138
39. Kimura M. The Neutral Theory of Molecular Evolution (1983), Cambridge Univ. Press, UK, Cambridge