Density peaks of paralog pairs in human and mouse genomes

Gene

Volumn 527, Issue 1, 2013, Pages 55-61

  Vinogradov, Alexander E ^a  

^a INSTITUTE OF CYTOLOGY   (Russian Federation)

Author keywords

Complexity; Gene duplication; Olfactory receptors; Orthologs; Paralogs; Zinc fingers

Indexed keywords

ADAPTIVE RADIATION; AMINO ACID SEQUENCE; ANOLIS CAROLINENSIS; ARTICLE; GENE DUPLICATION; GENOME; HUMAN; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OLFACTORY RECEPTOR; OPOSSUM; OREOCHROMIS NILOTICUS; PARALOGY; POLYPLOIDY; PRIORITY JOURNAL; PUFFER FISH; RAT; RHESUS MONKEY; XENOPUS TROPICALIS; ZEBRA FISH; ZINC FINGER MOTIF;

BLOCKS OF AMINO ACID SUBSTITUTION MATRIX; BLOSUM; C2H2; C2H2 ZINC FINGER; C2H2-ZF; COMPLEXITY; CYSTEINE(2)HISTIDINE(2); DISTANCE OF NONSYNONYMOUS SUBSTITUTIONS; DISTANCE OF SYNONYMOUS SUBSTITUTIONS; DN; DS; G PROTEIN COUPLED RECEPTOR A; GENE DUPLICATION; GPCR_A; KRAB; KRUEPPEL-ASSOCIATED BOX DOMAIN; OLFACTORY RECEPTORS; ORTHOLOGS; PAML; PARALOGS; PFAM; PHYLOGENETIC ANALYSIS BY MAXIMUM LIKELIHOOD; PROTEIN FAMILIES (THE DATABASE OF PROTEIN DOMAINS); REFERENCE SEQUENCE (THE DATABASE OF NON-REDUNDANT SEQUENCES); REFSEQ; REVERSE TRANSLATION ALIGNMENT PROGRAM; REVTRANS; ZINC FINGERS;

ALLELES; ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, HUMAN; HUMANS; MICE; MODELS, GENETIC; RECEPTORS, ODORANT; SEQUENCE HOMOLOGY, NUCLEIC ACID; ZINC FINGERS;

MAMMALIA; METATHERIA;

EID: 84881249508     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.05.039     Document Type: Article

References (59)

1. Altenhoff A.M., Dessimoz C. Inferring orthology and paralogy. Methods Mol. Biol. 2012, 855:259-279.
2. Anisimova M., Kosiol C. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol. Biol. Evol. 2009, 26:255-271.
3. Carroll S.B. Evolution at two levels: on genes and form. PLoS Biol. 2005, 3:e245.
4. Carroll S.B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 2008, 134:25-36.
5. Chamary J.V., Parmley J.L., Hurst L.D. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 2006, 7:98-108.
6. Cheng Y., et al. KRAB zinc finger protein ZNF382 is a proapoptotic tumor suppressor that represses multiple oncogenes and is commonly silenced in multiple carcinomas. Cancer Res. 2010, 70:6516-6526.
7. Claverie J.M. Gene number. What if there are only 30,000 human genes?. Science 2001, 291:1255-1257.
8. Davis J.C., Petrov D.A. Do disparate mechanisms of duplication add similar genes to the genome?. Trends Genet. 2005, 21:548-551.
9. Dehal P., Boore J.L. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005, 3:e314.
10. Demetrius L. Of mice and men. When it comes to studying ageing and the means to slow it down, mice are not just small humans. EMBO Rep. 2005, 6:S39-S44.
11. Ding G., Lorenz P., Kreutzer M., Li Y., Thiesen H.J. SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res. 2009, 37:D267-D273.
12. Emerson R.O., Thomas J.H. Adaptive evolution in zinc finger transcription factors. PLoS Genet. 2009, 5:e1000325.
13. Estivill-Castro V. Why So Many Clustering Algorithms. ACM SIGKDD Explorations Newsletter 2002, 4:65-75.
14. Felsenstein J. Inferring Phylogenies 2004, Sinauer Associates, Sunderland, MA.
15. Frankel N., Erezyilmaz D.F., McGregor A.P., Wang S., Payre F., Stern D.L. Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 2011, 474:598-603.
16. Fu F., et al. Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res. 2009, 37:D279-D283.
17. Groner A.C., et al. KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet. 2010, 6:e1000869.
18. Hahn M.W., Wray G.A. The g-value paradox. Evol. Dev. 2002, 4:73-75.
19. Hayden S., Bekaert M., Crider T.A., Mariani S., Murphy W.J., Teeling E.C. Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Res. 2010, 20:1-9.
20. Hurst L.D. The sound of silence. Nature 2011, 471:582-583.
21. Huttley G.A., Wakefield M.J., Easteal S. Rates of genome evolution and branching order from whole genome analysis. Mol. Biol. Evol. 2007, 24:1722-1730.
22. Klug A. The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Q. Rev. Biophys. 2010, 43:1-21.
23. Kondrashov F.A., Rogozin I.B., Wolf Y.I., Koonin E.V. Selection in the evolution of gene duplications. Genome Biol. 2002, 3. (RESEARCH0008).
24. Koonin E.V. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 2005, 39:309-338.
25. Lam K.N., van Bakel H., Cote A.G., van der Ven A., Hughes T.R. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res. 2011, 39:4680-4690.
26. Larkin M.A., et al. Clustal W and Clustal X Version 2.0. Bioinformatics 2007, 23:2947-2948.
27. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 1993, 36:96-99.
28. Li W.H., Wu C.I., Luo C.C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 1985, 2:150-174.
29. Li J., Zhang Z., Vang S., Yu J., Wong G.K., Wang J. Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J. Mol. Evol. 2009, 68:414-423.
30. Lorenz P., et al. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genomics 2010, 11:206.
31. Meylan S., et al. A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing. BMC Genomics 2011, 12:378.
32. Nakatani Y., Takeda H., Kohara Y., Morishita S. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res. 2007, 17:1254-1265.
33. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3:418-426.
34. Pamilo P., Bianchi N.O. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 1993, 10:271-281.
35. Pearson W. Finding protein and nucleotide similarities with FASTA. Curr. Protoc. Bioinformatics 2004, (Chapter 3, Unit 39) (in press). 10.1002/0471250953.bi0309s04.
36. Powell S., et al. EggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 2012, 40:D284-D289.
37. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. Section16.4. Hierarchical Clustering by Phylogenetic Trees in Numerical Recipes: The Art of Scientific Computing 2007, Cambridge University Press, New York. 3rd ed.
38. Pruitt K.D., Tatusova T., Brown G.R., Maglott D.R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012, 40:D130-D135.
39. Punta M., et al. The Pfam protein families database. Nucleic Acids Res. 2012, 40:D290-D301.
40. Rangarajan A., Weinberg R.A. Comparative biology of mouse versus human cells: modelling human cancer in mice. Nat. Rev. Cancer 2003, 3:952-959.
41. Rangarajan A., Hong S.J., Gifford A., Weinberg R.A. Species- and cell type-specific requirements for cellular transformation. Cancer Cell 2004, 6:171-183.
42. Schad E., Tompa P., Hegyi H. The relationship between proteome size, structural disorder and organism complexity. Genome Biol. 2011, 12:R120.
43. Stern D.L., Orgogozo V. The loci of evolution: how predictable is genetic evolution?. Evolution 2008, 62:2155-2177.
44. Szathmary E., Jordan F., Pal C. Can genes explain biological complexity?. Science 2001, 292:1315-1316.
45. Taft R.J., Pheasant M., Mattick J.S. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29:288-299.
46. Van de Peer Y., Maere S., Meyer A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 2009, 10:725-732.
47. Van de Peer Y., Maere S., Meyer A. 2R or not 2R is not the question anymore. Nat. Rev. Genet. 2010, 11:166.
48. Vinogradov A.E. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 2003, 31:1838-1844.
49. Vinogradov A.E. Systemic factors dominate mammal protein evolution. Proc. R. Soc. B 2010, 277:1403-1408.
50. Vinogradov A.E. Large scale of human duplicate genes divergence. J. Mol. Evol. 2012, 75:25-33.
51. Vinogradov A.E. Human more complex than mouse at cellular level. PLoS One 2012, 7:e41753.
52. Vinogradov A.E., Anatskaya O.V. Organismal complexity, cell differentiation and gene expression: human over mouse. Nucleic Acids Res. 2007, 35:6350-6356.
53. Wagner G.P., Pavlicev M., Cheverud J.M. The road to modularity. Nat. Rev. Genet. 2007, 8:921-931.
54. Waterhouse R.M., Tegenfeldt F., Li J., Zdobnov E.M., Kriventseva E.V. OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res. 2013, 41:D358-D365.
55. Wernersson R., Pedersen A.G. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 2003, 31:3537-3539.
56. Wolf D., Goff S.P. Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 2009, 458:1201-1204.
57. Yang Z. Computational Molecular Evolution 2006, Oxford University Press, Oxford.
58. Yang Z. PAML 4: a program package for phylogenetic analysis likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.
59. Yang Z., Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 2000, 17:32-43.