Large-scale analysis of pseudogenes in the human genome

Current Opinion in Genetics and Development

Volumn 14, Issue 4, 2004, Pages 328-335

  Zhang, Zhaolei ^a   Gerstein, Mark ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

CDS; coding sequence; cyc; cytochrome c; Ka; Ks; LINEs; long interspersed nuclear elements; nitric oxide synthase; nNOS; non synonymous rate of substitution; short interspersed nuclear elements; SINEs; synonymous rate of substitution; untranslated region; UTR

Indexed keywords

CALCULATION; DNA SEQUENCE; EUKARYOTE; EVOLUTION; FOSSIL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE NUMBER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC STABILITY; GENETIC TRANSCRIPTION; GENOME; GENOME SIZE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PSEUDOGENE; RETROPOSON; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE DATA; PSEUDOGENES; RETROELEMENTS;

EUKARYOTA;

EID: 3142594265     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2004.06.003     Document Type: Review

References (57)

1. Mighell A.J., Smith N.R., Robinson P.A., Markham A.F. Vertebrate pseudogenes. FEBS Lett. 468:2000;109-114
2. Balakirev E.S., Ayala F.J. Pseudogenes: are they "junk" or functional DNA? Annu Rev Genet. 37:2003;123-151 This is a more detailed and up-to-date review on pseudogenes than [1]. The authors also discuss pseudogenes in an evolutionary perspective.
3. Maestre J., Tchenio T., Dhellin O., Heidmann T. mRNA retroposition in human cells: processed pseudogene formation. EMBO J. 14:1995;6333-6338
4. Esnault C., Maestre J., Heidmann T. Human LINE retrotransposons generate processed pseudogenes. Nat Genet. 24:2000;363-367
5. Deininger P.L., Moran J.V., Batzer M.A., Kazazian H.H. Jr. Mobile elements and mammalian genome evolution. Curr Opin Genet Dev. 13:2003;651-658 This is a comprehensive review on mobile elements in the mammalian genome.
6. Harrison P.M., Hegyi H., Balasubramanian S., Luscombe N.M., Bertone P., Echols N., Johnson T., Gerstein M. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12:2002;272-280 In this pilot study before the whole-genome survey, we developed a computational search algorithm that is based on sequence similarity. We searched for pseudogenes in the human chromosome 21 and 22 and identified 189 processed pseudogenes and 195 non-processed ones. This is the first report that demonstrated the great prevalence of pseudogenes in the human genome.
7. Zhang Z., Harrison P., Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res. 12:2002;1466-1482 Building upon the work from [1], we searched for retrotransposed pseudogenes of the ribosomal proteins (RPs) in the entire human genome. There are 79 functional RP genes in the human genome but >2000 retrotransposed pseudogenes. Some global properties of these pseudogenes such as chromosomal location, sequence decay, were discussed in this paper.
8. Glusman G., Yanai I., Rubin I., Lancet D. The complete human olfactory subgenome. Genome Res. 11:2001;685-702
9. Tourmen Y., Baris O., Dessen P., Jacques C., Malthiery Y., Reynier P. Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics. 80:2002;71-77
10. Woischnik M., Moraes C.T. Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res. 12:2002;885-893
11. Ohshima K., Hattori M., Yada T., Gojobori T., Sakaki Y., Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol. 4:2003;R74 These authors reported the retrotransposed pseudogenes in the human genome that are >90% of the complete cDNA length. They also devised a more rigorous approach in calculating the ages of the pseudogenes.
12. Zhang Z., Harrison P.M., Liu Y., Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 13:2003;2541-2558 This is a continuation of our work on ribosomal protein pseudogenes. We describe the overall properties of the human pseudogenes, such as genomic distribution, functional categories, and synteny in the mouse genome.
13. Torrents D., Suyama M., Zdobnov E., Bork P. A genome-wide survey of human pseudogenes. Genome Res. 13:2003;2559-2567 These authors designed a functionality test, by calculating Ka/Ks ratios, to identify ∼19, 000 pseudogene candidates in the human genome. Retrotransposed pseudogenes were separated from duplicated pseudogenes on the basis of mouse synteny information.
14. Hirotsune S., Yoshida N., Chen A., Garrett L., Sugiyama F., Takahashi S., Yagami K., Wynshaw-Boris A., Yoshiki A. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature. 423:2003;91-96
15. Hurst L.D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18:2002;486
16. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
17. Harrison P.M., Echols N., Gerstein M.B. Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Res. 29:2001;818-830
18. Harrison P., Kumar A., Lan N., Echols N., Snyder M., Gerstein M. A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol. 316:2002;409-419
19. Dasilva C., Hadji H., Ozouf-Costaz C., Nicaud S., Jaillon O., Weissenbach J., Crollius H.R. Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome. Proc Natl Acad Sci USA. 99:2002;13636-13641
20. Harrison P.M., Milburn D., Zhang Z., Bertone P., Gerstein M. Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res. 31:2003;1033-1037
21. Ogata H., Audic S., Renesto-Audiffren P., Fournier P.E., Barbe V., Samson D., Roux V., Cossart P., Weissenbach J., Claverie J.M., et al. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science. 293:2001;2093-2098
22. Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R., Wheeler P.R., Honore N., Garnier T., Churcher C., Harris D., et al. Massive gene decay in the leprosy bacillus. Nature. 409:2001;1007-1011
23. Homma K., Fukuchi S., Kawabata T., Ota M., Nishikawa K. A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene. 294:2002;25-33
24. Lawrence J.G., Hendrix R.W., Casjens S. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9:2001;535-540
25. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., Agarwala R., Ainscough R., Alexandersson M., An P., et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:2002;520-562
26. Zhang Z., Carriero N., Gerstein M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet. 20:2004;62-67 Using the same approach as for human pseudogenes, we identified ∼5000 retrotransposed pseudogenes in the mouse genome. On the basis of age profile and the synteny information, we estimate that ∼60% of the pseudogenes are lineage specific.
27. Graur D., Shuali Y., Li W.H. Deletions in processed pseudogenes accumulate faster in rodents than in humans. J Mol Evol. 28:1989;279-285
28. Pavlicek A., Jabbari K., Paces J., Paces V., Hejnar J.V., Bernardi G. Similar integration but different stability of Alus and LINEs in the human genome. Gene. 276:2001;39-45
29. Fleishman S.J., Dagan T., Graur D. pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes. Mol Biol Evol. 20:2003;1876-1880
30. Goncalves I., Duret L., Mouchiroud D. Nature and structure of human genes that generate retropseudogenes. Genome Res. 10:2000;672-678
31. Zhang Z., Gerstein M. The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse. Gene. 312:2003;61-72 We have found that cytochrome c gene has 49 pseudogenes in the human genome. An evolutionary history of this gene was revealed from analysis of the pseudogenes. This gene, which has very important roles in cellular respiration and apoptosis, had undergone accelerated sequence changes during the last 20-30 million years.
32. Winter H., Langbein L., Krawczak M., Cooper D.N., Jave-Suarez L.F., Rogers M.A., Praetzel S., Heidt P.J., Schweizer J. Human type I hair keratin pseudogene phihHaA has functional orthologs in the chimpanzee and gorilla: evidence for recent inactivation of the human gene after the Pan-Homo divergence. Hum Genet. 108:2001;37-42
33. Petrov D.A., Sangster T.A., Johnston J.S., Hartl D.L., Shaw K.L. Evidence for DNA loss as a determinant of genome size. Science. 287:2000;1060-1062
34. Zhang Z., Gerstein M. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31:2003;5338-5348
35. Long M., Langley C.H. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science. 260:1993;91-95
36. Brosius J. Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet. 15:1999;304-305
37. Long M., Deutsch M., Wang W., Betran E., Brunet F.G., Zhang J. Origin of new genes: evidence from experimental and computational analyses. Genetica. 118:2003;171-182
38. Brosius J. Genomes were forged by massive bombardments with retroelements and retrosequences. Genetica. 107:1999;209-238
39. Brosius J. The contribution of RNAs and retroposition to evolutionary novelties. Genetica. 118:2003;99-116
40. Harper L.V., Hilton A.C., Jones A.F. RT-PCR for the pseudogene-free amplification of the glyceraldehyde-3-phosphate dehydrogenase gene (gapd). Mol Cell Probes. 17:2003;261-265
41. Ruud P., Fodstad O., Hovig E. Identification of a novel cytokeratin 19 pseudogene that may interfere with reverse transcriptase-polymerase chain reaction assays used to detect micrometastatic tumor cells. Int J Cancer. 80:1999;119-125
42. Heyworth P.G., Noack D., Cross A.R. Identification of a novel NCF-1 (p47-phox) pseudogene not containing the signature GT deletion: significance for A47 degrees chronic granulomatous disease carrier detection. Blood. 100:2002;1845-1851
43. Harbord M., Hankin A., Bloom S., Mitchison H. Association between p47phox pseudogenes and inflammatory bowel disease. Blood. 101:2003;3337
44. Fujii G.H., Morimoto A.M., Berson A.E., Bolen J.B. Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN. Oncogene. 18:1999;1765-1769
45. Zhang J., Pontoppidan B., Xue J., Rask L., Meijer J. The third myrosinase gene TGG3 in Arabidopsis thaliana is a pseudogene specifically expressed in stamen and petal. Physiol Plant. 115:2002;25-34
46. McCarrey J.R., Riggs A.D. Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. Proc Natl Acad Sci USA. 83:1986;679-683
47. Korneev S.A., Park J.H., O'Shea M. Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J Neurosci. 19:1999;7711-7720
48. Lee J.T. Molecular biology: complicity of gene and pseudogene. Nature. 423:2003;26-28
49. Vargas-Madrazo E., Almagro J.C., Lara-Ochoa F. Structural repertoire in VH pseudogenes of immunoglobulins: comparison with human germline genes and human amino acid sequences. J Mol Biol. 246:1995;74-81
50. S test is useful in the identification of long exons and single exon genes, and has lower false-positive and false-negative rates than almost all current gene-prediction methods.
51. Echols N., Harrison P., Balasubramanian S., Luscombe N.M., Bertone P., Zhang Z., Gerstein M. Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res. 30:2002;2515-2523
52. Mounsey A., Bauer P., Hope I.A. Evidence Suggesting That a Fifth of Annotated Caenorhabditis elegans Genes May Be Pseudogenes. Genome Res. 12:2002;770-775
53. Rinn J.L., Euskirchen G., Bertone P., Martone R., Luscombe N.M., Hartman S., Harrison P.M., Nelson F.K., Miller P., Gerstein M., et al. The transcriptional activity of human Chromosome 22. Genes Dev. 17:2003;529-540
54. Balasubramanian S., Harrison P., Hegyi H., Bertone P., Luscombe N., Echols N., McGarvey P., Zhang Z., Gerstein M. SNPs on human chromosomes 21 and 22-analysis in terms of protein features and pseudogenes. Pharmacogenomics. 3:2002;393-402
55. Strichman-Almashanu L.Z., Bustin M., Landsman D. Retroposed copies of the HMG genes: a window to genome dynamics. Genome Res. 13:2003;800-812
56. Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T., Prentice M.B., Sebaihia M., James K.D., Churcher C., Mungall K.L., et al. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 413:2001;523-527
57. Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.