Abstract
The point mutations in the form of single nucleotide replacements occurring during the human–chimpanzee divergence process are analyzed in order to obtain an insight into the nature of the constraints that are imposed on various levels of cellular machinery upon the mutational events. The replacement patterns were examined separately for CpG islands (CGI), coding DNA regions, repetitive and nonrepetitive regions and for average genomic regions. The replacement counts were processed by the algebra based upon the rate equations. The starting point was the replacement count matrix. On this basis the replacement probability matrices were calculated. A model replacement probability matrix with three free parameters was constructed and the optimization procedure was used to determine the parameters. The replacements within the CGI and non-CGI regions were reproduced to the extent where the correlation coefficients attained values close to r = 0.9. For the exonic sequences the relative matrix of mutation rejections was calculated and it was found that the differences in the amino acid polarities and their opposites—the hydrophobicities—correlate in the greatest extent with the mutation rejection probabilities.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Arndt PF, Petrov DA, Hwa T (2003) Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation. Mol Biol Evol 20:1887–1896
Borštnik B, Pumpernik D (2002) Tandem repeats in protein coding regions of primate genes. Genome Res 12:909–915
Borštnik B, Pumpernik D (2005) Evidence on DNA slippage step-length distribution. Phys Rev E—Stat, Nonlinear, Soft Matter Phys 71:031913/1–031913/7
De Amicic F, Marchetti S (2000) Intercodon dinucleotides affect codon choice in plant genes. Nucleic Acids Res 28:3339–3345
Duret L, 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
Frappat L, Sciarrino A (2005) Sum rules for free energy and frequency distribution of DNA. dinucleotides. Physica A 351:448–460
Fryxell KJ, Moon W-J (2005) CpG mutation rates in the human genome are highly dependent on local GC content. Mol Biol Evol 22:650–658
Fryxell KJ, Zuckerkandl E (2000) Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol Biol Evol 17:1371–1383
Gibbs RA, Rogers J, et al (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222–234
Jiang C, Zhao Z (2006a) Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. BMC Genomics 7:316 doi:10.1186/1471–2164–7–316
Jiang C, Zhao Z (2006b) Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics 88:527–534
Karro JE, Pfeifer M, Hardison RC, Kollmann M, von Gruenberg HH (2008) Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Mol Biol Evol 25:362–374
Kawashima S, Ogata H, Kanehisa M (1999) AAindex: Amino acid index database. Nucleic Acids Res 27:368–369
Lander ES, Linton LM, et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Michel CJ (2007) Evolution probabilities and phylogenetic distance of dinucleotides. J Theor Biol 249:271–277
Mikkelsen TS, Hillier LW, et al (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69–87
Ollila J, Lappalainen I, et al (1996) Sequence specificity in CpG mutation hotspots. FEBS Lett 396:119–122
Ponger L, Duret L, Mouchiroud D (2001) Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res, 11:1854–1860
Saxonov S, Berg P and Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 103:1412–1417
Siepel A, Haussler D (2004) Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood. Mol Biol Evol 21:468–488
Shabalina SA, Ogurtsov AY, Spiridonov NA (2006) A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res 34:2428–2437
Yampolsky LY, Kondrashov FA, Kondrashov AS (2005) Distribution of the strength of selection against amino acid replacements in human proteins. Human Mol Genetics 14:3191–3201
Ye S, Asaithambi A, Liu Y (2008) CpGIF: an algorithm for the identification of CpG islands. Bioinformation 2:335–338
Zhao Z, Boerwinkle E (2002) Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2.6 million polymorphisms across the human genome. Genome Res 12:1679–1686
Zhao Z, Zhang F (2006) Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome. Gene 366:316–324
Acknowledgments
This work was financed by the Slovenian Research Agency.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Borštnik, B., Oblak, B., Pumpernik, D. (2009). The Evolutionary Constraints in Mutational Replacements. In: Pontarotti, P. (eds) Evolutionary Biology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00952-5_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-00952-5_15
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00951-8
Online ISBN: 978-3-642-00952-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)