Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla -selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Simmonds, Peter ^a   Xia, Wenjun ^b   Baillie, J K ^a   McKinnon, Ken ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Dinucleotide; Exon; Markov modelling; Methylation; RNA virus

Indexed keywords

CPG DINUCLEOTIDE; DINUCLEOTIDE; GENOMIC DNA; MESSENGER RNA; UNCLASSIFIED DRUG; UPA DINUCLEOTIDE;

ARTICLE; CYTOPLASM; DNA METHYLATION; DNA SEQUENCE; EUKARYOTE; GENE EXPRESSION; GENE MUTATION; GENETIC SELECTION; HUMAN; NONHUMAN; PHYLUM; RNA SEQUENCE; RNA STABILITY; RNA VIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; ANIMAL; BIOLOGICAL MODEL; CPG ISLAND; DNA BASE COMPOSITION; GENETICS; METABOLISM; MUTATION; PROBABILITY;

EUKARYOTA; MAMMALIA; RNA VIRUSES; VERTEBRATA;

ANIMALS; BASE COMPOSITION; CPG ISLANDS; CYTOPLASM; DNA METHYLATION; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MUTATION; RNA VIRUSES; RNA, MESSENGER; SELECTION, GENETIC;

EID: 84883609173     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-610     Document Type: Article

References (37)

1. Russell GJ, Walker PM, Elton RA, Subak-Sharpe JH. Doublet frequency analysis of fractionated vertebrate nuclear DNA. J Mol Biol 1976, 108:1-23. 10.1016/S0022-2836(76)80090-3, 1003479.
2. Schwarz MN, Trautner TA, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid: XI: further studies on nearest neighbor base sequences in deoxyribonucleic acids. J Biol Chem 1962, 237:1961-1967.
3. Josse J, Kaiser AD, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid: VIII: frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J Biol Chem 1961, 236:864-875.
4. Bird AP. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 1980, 8:1499-1504. 10.1093/nar/8.7.1499, 324012, 6253938.
5. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature 1978, 274:775-780. 10.1038/274775a0, 355893.
6. Duan J, Antezana MA. Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J Mol Evol 2003, 57:694-701. 10.1007/s00239-003-2519-1, 14745538.
7. Beutler E, Gelbart T, Han JH, Koziol JA, Beutler B. Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc Natl Acad Sci USA 1989, 86:192-196. 10.1073/pnas.86.1.192, 286430, 2463621.
8. Fryxell KJ, Moon WJ. CpG mutation rates in the human genome are highly dependent on local GC content. Mol Biol Evol 2005, 22:650-658.
9. Fryxell KJ, Zuckerkandl E. Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol Biol Evol 2000, 17:1371-1383. 10.1093/oxfordjournals.molbev.a026420, 10958853.
10. Rima BK, McFerran NV. Dinucleotide and stop codon frequencies in single-stranded RNA viruses. J Gen Virol 1997, 78:2859-2870.
11. Karlin S, Doerfler W, Cardon LR. Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?. J Virol 1994, 68:2889-2897. 236777, 8151759.
12. Belalov IS, Lukashev AN. Causes and implications of codon usage bias in RNA viruses. PLoS One 2013, 8:e56642. 10.1371/journal.pone.0056642, 3581513, 23451064.
13. Simmen MW. Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals. Genomics 2008, 92:33-40. 10.1016/j.ygeno.2008.03.009, 18485662.
14. Duret L, Galtier N. The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact. Mol Biol Evol 2000, 17:1620-1625. 10.1093/oxfordjournals.molbev.a026261, 11070050.
15. Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R. The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol 2010, 8:e1000506. 10.1371/journal.pbio.1000506, 2970541, 21072239.
16. Glastad KM, Hunt BG, Yi SV, Goodisman MA. DNA methylation in insects: on the brink of the epigenomic era. Insect Mol Biol 2011, 20:553-565. 10.1111/j.1365-2583.2011.01092.x, 21699596.
17. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A. Sequence specificity of methylation in higher plant DNA. Nature 1981, 292:860-862. 10.1038/292860a0, 6267477.
18. Jabbari K, Bernardi G. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene 2004, 333:143-149.
19. Lindsay H, Yap VB, Ying H, Huttley GA. Pitfalls of the most commonly used models of context dependent substitution. Biol Direct 2008, 3:52. 10.1186/1745-6150-3-52, 2628887, 19087239.
20. Zhang W, Bouffard GG, Wallace SS, Bond JP. Estimation of DNA sequence context-dependent mutation rates using primate genomic sequences. J Mol Evol 2007, 65:207-214. 10.1007/s00239-007-9000-5, 17676366.
21. Berard J, Gueguen L. Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context. Syst Biol 2012, 61:510-521. 10.1093/sysbio/sys024, 22331438.
22. Sved J, Bird A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci USA 1990, 87:4692-4696. 10.1073/pnas.87.12.4692, 54183, 2352943.
23. Aissani B, Bernardi G. CpG islands, genes and isochores in the genomes of vertebrates. Gene 1991, 106:185-195. 10.1016/0378-1119(91)90198-K, 1937049.
24. Shioiri C, Takahata N. Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry. J Mol Evol 2001, 53:364-376. 10.1007/s002390010226, 11675596.
25. Tomso DJ, Bell DA. Sequence context at human single nucleotide polymorphisms: overrepresentation of CpG dinucleotide at polymorphic sites and suppression of variation in CpG islands. J Mol Biol 2003, 327:303-308. 10.1016/S0022-2836(03)00120-7, 12628237.
26. Zhao Z, Zhang F. Sequence context analysis in the mouse genome: single nucleotide polymorphisms and CpG island sequences. Genomics 2006, 87:68-74. 10.1016/j.ygeno.2005.09.012, 16316740.
27. Qiu L, Moreira A, Kaplan G, Levitz R, Wang JY, Xu C, Drlica K. Degradation of hammerhead ribozymes by human ribonucleases. Mol Gen Genet 1998, 258:352-362. 10.1007/s004380050741, 9648739.
28. Lobo FP, Mota BE, Pena SD, Azevedo V, Macedo AM, Tauch A, Machado CR, Franco GR. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS ONE 2009, 4:e6282. 10.1371/journal.pone.0006282, 2707012, 19617912.
29. Koning FA, Goujon C, Bauby H, Malim MH. Target cell-mediated editing of HIV-1 cDNA by APOBEC3 proteins in human macrophages. J Virol 2011, 85:13448-13452. 10.1128/JVI.00775-11, 3233168, 21957290.
30. Samuel CE. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology 2011, 411:180-193. 10.1016/j.virol.2010.12.004, 3057271, 21211811.
31. Greenbaum BD, Rabadan R, Levine AJ. Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. PLoS ONE 2009, 4:e5969. 10.1371/journal.pone.0005969, 2694999, 19536338.
32. Greenbaum BD, Levine AJ, Bhanot G, Rabadan R. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 2008, 4:e1000079. 10.1371/journal.ppat.1000079, 2390760, 18535658.
33. Sugiyama T, Gursel M, Takeshita F, Coban C, Conover J, Kaisho T, Akira S, Klinman DM, Ishii KJ. CpG RNA: identification of novel single-stranded RNA that stimulates human CD14+CD11c+ monocytes. J Immunol 2005, 174:2273-2279.
34. Burns CC, Campagnoli R, Shaw J, Vincent A, Jorba J, Kew O. Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons. J Virol 2009, 83:9957-9969. 10.1128/JVI.00508-09, 2747992, 19605476.
35. Burns CC, Shaw J, Campagnoli R, Jorba J, Vincent A, Quay J, Kew O. Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. J Virol 2006, 80:3259-3272. 10.1128/JVI.80.7.3259-3272.2006, 1440415, 16537593.
36. Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S. Virus attenuation by genome-scale changes in codon pair bias. Science 2008, 320:1784-1787. 10.1126/science.1155761, 2754401, 18583614.
37. Simmonds P. SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes 2012, 5:50. 10.1186/1756-0500-5-50, 3292810, 22264264.