DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria

Bioinformatics

Volumn 20, Issue 18, 2004, Pages 3336-3345

  Wang, Yong ^a   Leung, Frederick C C ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CYSTEINE; GUANINE;

ARTICLE; BACTERIAL GENOME; CONTROLLED STUDY; CORRELATION ANALYSIS; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; DNA STRAND; DNA STRUCTURE; GENETIC SELECTION; HYPOTHESIS; PRIORITY JOURNAL; PROBABILITY; PROTEIN STRUCTURE; SIMULATION;

BACTERIA (MICROORGANISMS);

EID: 12344304270     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth393     Document Type: Article

References (29)

1. Aissani,B. and Bernardi,G. (1991) CpG islands, genes and isochores in the genomes of vertebrates. Gene, 106, 185-195.
2. Almagor,H. (1983) A Markov analysis of DNA sequences. J. Theoret. Biol., 104, 633-645.
3. 31P NMR spectra. Biochemistry, 32, 7079-7088.
4. Antri,S.E., Mauffret,O., Monnot,M., Lescot,E. and Convert,O. (1993b) Structural deviations at CpG provide a plausible explanation for the high frequency of mutation at this site. J. Mol. Biol., 230 373-378.
5. Bernardi,G., Olofsson,B., Filipski,J. and Zerial,M. (1985) The mosaic genome of warm-blooded vertebrates. Science, 228, 953-958.
6. Bestor,T.H. (1990) DNA methylation: evolution of a bacterial immune function into a regulator to gene expression and genome structure in higher eukaryotes. Phil. Trans. R. Soc. Lond. B, 326, 179-187.
7. Bird,A.P. (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res., 8, 1499-1504.
8. Bird,A.P. (2002) DNA methylation patterns and epigenetic memory. Gene. Dev., 16, 6-21.
9. Caccio,S., Jabbari,K., Matassi,G., Guermonprez,F., Desgres,J. and Bernardi,G. (1997) Methylation patterns in the isochores of vertebrate genomes. Gene, 205, 119-124.
10. Cooper,D.N. and Youssoufian,H. (1988) The CpG dinucleotide and human genetic disease. Hum. Genet., 78, 151-155.
11. Duret,L. and Galtier,N. (2000) The covariation between TpA deficiency, CpG deficiency, and G + C content of human isochores is due to a mathematical artifact. Mol. Biol. Evol., 17, 1620-1625.
12. Gelfand,M.S. and Koonin,E.V. (1997) Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res., 25, 2430-2439.
13. Jeltsch,A. (2002) Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembio chem, 3, 274-293.
14. Karlin,S. (1998) Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol., 1, 598-610.
15. Karlin,S. and Burge,C. (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet., 11, 283-290.
16. Karlin,S., Burge,C. and Campbell,A.M. (1992) Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res., 20, 1363-1370.
17. Karlin,S., Doerfler,W. and Cardon,L.R. (1994) Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? J. Virol., 68, 2889-2897.
18. Krieg,A.M. (1996) Lymphocyte activation by CpG dinucleotide motifs in prokaryotic DNA. Trends Microbiol., 4, 73-77.
19. Krieg,A.M. (2002) CpG motifs in bacterial DNA and their immune effects. Annu. Rev. Immunol., 20, 709-760.
20. Lefebvre,A., Mauffret,O., Lescot,E., Bartmann,B. and Fermandjian, S. (1996) Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculation are compatible with a BI/BII equilibrium at CpG. Biochemistry, 35 12560-12569.
21. Levy,D.D., Magee,A.D. and Seidman,M.M. (1996a) Single nucleotide positions have proximal and distal influence on UV mutation hotspots and coldspots. J. Mol. Biol., 258, 251-260.
22. Levy,D.D., Magee,A.D., Namiki,C. and Seidman,M.M. (1996b) The influence of single base changes on UV mutational activity at two translocated hotspots. J. Mol. Biol., 255, 435-445.
23. Merino,E. and Garciarrubio,A. (2000) The global intrinsic curvature of archaeal and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation. Nucleic Acids Res., 28, 2431-2438.
24. Ollila,J., Lappalainen,I. and Vihinen,M. (1996) Sequence specificity in CpG mutation hotspots. FEBS Lett., 396, 119-122.
25. Pesole,G., Luini,S., Grillo,G. and Saccone,C. (1997) Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene, 205, 95-102.
26. Philips,G.J., Arnold,J. and Ivarie,R. (1987) Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis. Nucleic Acids Res., 15, 2611-2626.
27. Rocha,E.P.C., Danchin,A. and Viari,A. (2001) Evolution role of restriction/modification systems as revealed by comparative genome analysis. Genome Res., 11, 946-958.
28. Schbath,S., Prum,B. and Turckheim,E. (1995) Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comput. Biol., 2, 417-437.
29. Wang,Y., Rocha,E.P.C., Leung,F.C.C. and Danchin,A. (2004) Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes. J. Mol. Evol. 58, 692-700.