Insights into the genomic features and evolutionary impact of the genes configuring duplicated pseudogenes in human

FEBS Letters

Volumn 584, Issue 18, 2010, Pages 4015-4018

  Sen, Kamalika ^a   Podder, Soumita ^a   Ghosh, Tapash Chandra ^a  

^a BOSE INSTITUTE   (India)

Author keywords

CpG Island; Duplicated pseudogenes; Evolutionary rate; Functional distance; Hub protein; Recombination rate

Indexed keywords

CELL PROTEIN; PROTEIN HUB; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA CONTENT; EVOLUTIONARY RATE; GENE DOSAGE; GENE DUPLICATION; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENOME SIZE; MOLECULAR EVOLUTION; MUTATION RATE; PARALOGY; PRIORITY JOURNAL; PSEUDOGENE; HUMAN; HUMAN GENOME;

CPG ISLANDS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, HUMAN; HUMANS; PSEUDOGENES; RECOMBINATION, GENETIC;

EID: 77956920064     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2010.08.012     Document Type: Article

References (37)

1. Zhang Z.L., Carriero N., Gerstein M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet. 2004, 20:62-67.
2. Mighell A.J., Smith N.R., Robinson P.A., Markham A.F. Vertebrate pseudogenes. FEBS Lett. 2000, 468:109-114.
3. Zhang Z.L., Gerstein M. Large-scale analysis of pseudogenes in the human genome. Curr. Opin. Genet. Dev. 2004, 14:328-335.
4. Ding W.Y., Lin L., Cheh B., Dai J.W. L19 elements, processed pseudogenes and retrogenes in mammalian genomes. IUBMB Life 2006, 58:677-685.
5. Vanin E.F. Processed pseudogenes - characteristics and evolution. Annu. Rev. Genet. 1985, 19:253-272.
6. Zhang Z.D., Frankish A., Hunt T., Harrow J., Gerstein M. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol. 2010, 11:R26.
7. Li W.H., Gojobori T., Nei M. Pseudogenes as a paradigm of neutral evolution. Nature 1981, 292:237-239.
8. Hubbard T.J.P., et al. Ensembl 2009. Nucleic Acids Res. 2009, 37:D690-D697.
9. Karro J.E., et al. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res. 2007, 35(Database issue):D55-D60.
10. Mishra G.R., et al. Human protein reference database - 2006 update. Nucleic Acids Res. 2006, 34:D411-D414.
11. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.
12. PG islands as gene markers in the human genome. Genomics 1992, 13:1095-1107.
13. Thorisson G.A., Smith A.V., Krishnan L., Stein L.D. The international HapMap project web site. Genome Res. 2005, 15:1592-1593.
14. Kato M., Miya F., Kanemura Y., Tanaka T., Nakamura Y., Tsunoda T. Recombination rates of genes expressed in human tissues. Hum. Mol. Genet. 2008, 17:577-586.
15. Su A.I., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 2004, 101:6062-6067.
16. Baudot A., Jacq B., Brun C. A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol. 2004, 5.
17. He X., Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genet. 2006, 2(6):e88.
18. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., Barabasi A.L. The human disease network. Proc. Natl. Acad. Sci. USA 2007, 104:8685-8690.
19. Liang H., Li W.H. Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet. 2007, 23:375-378.
20. Zhang L.Q., Lu H.H.S., Chung W.Y., Yang J., Li W.H. Patterns of segmental duplication in the human genome. Mol. Biol. Evol. 2005, 22:135-141.
21. Kimura M., Ohta T. On some principles governing molecular evolution. Proc. Natl. Acad. Sci. USA 1974, 71:2848-2852.
22. Miyata T., Hayashida H. Extraordinarily high evolutionary rate of pseudogenes - evidence for the presence of selective pressure against changes between synonymous codons. Proc. Natl. Acad. Sci. USA 1981, 78:5739-5743.
23. Hardison R.C., et al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 2003, 13:13-26.
24. Subramanian S., Kumar S. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 2003, 13:838-844.
25. Kim S.-H., Yi S.V. Understanding relationship between sequence and functional evolution in yeast proteins. Genetica 2007, 131:151-156.
26. Khachane A.N., Harrison P.M. Strong association between pseudogenization mechanisms and gene sequence length. Biol. Direct 2009, 4:38.
27. Wu X.D., Qi X.Q. Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homologs through whole genome duplication. BMC Evol. Biol. 2010, 10.
28. Brookfield J. Evolutionary genetics: can genes be truly redundant?. Curr. Biol. 1992, 2:553-554.
29. Zhang J.Z. Evolution by gene duplication: an update. Trends Ecol. Evol. 2003, 18:292-298.
30. Clark A.G. Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. USA 1994, 91:2950-2954.
31. Janga S.C., Babu M.M. Transcript stability in the protein interaction network of Escherichia coli. Mol. BioSyst. 2009, 5:154-162.
32. Nadeau J.H., Sankoff D. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 1997, 147:1259-1266.
33. Chen J.M., Cooper D.N., Chuzhanova N., Ferec C., Patrinos G.P. Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet. 2007, 8:762-775.
34. Wagner A. Robustness against mutations in genetic networks of yeast. Nat. Genet. 2000, 24:355-361.
35. Nowak M.A., Boerlijst M.C., Cooke J., Smith J.M. Evolution of genetic redundancy. Nature 1997, 388:167-171.
36. Papp B., Pal C., Hurst L.D. Dosage sensitivity and the evolution of gene families in yeast. Nature 2003, 424:194-197.
37. Jensen-Seaman M.I., et al. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 2004, 14:528-538.