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Computational Methods for Pseudogene Annotation Based on Sequence Homology

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Pseudogenes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1167))

Abstract

The number of complete genome sequences explodes more and more with each passing year. Thus, methods for genome annotation need to be honed constantly to handle the deluge of information. Annotation of pseudogenes (i.e., gene copies that appear not to make a functional protein) in genomes is a persistent problem; here, we overview pseudogene annotation methods that are based on the detection of sequence homology in genomic DNA.

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References

  1. Harrison PM, Gerstein M (2002) Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol 318:1155–1174

    Article  CAS  PubMed  Google Scholar 

  2. Harrison PM, Carriero N, Liu Y, Gerstein M (2003) A “polyORFomic” analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs. J Mol Biol 333:885–892

    Article  CAS  PubMed  Google Scholar 

  3. Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M (2005) Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res 33:2374–2383

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Torrents D, Suyama M, Zdobnov E, Bork P (2003) A genome-wide survey of human pseudogenes. Genome Res 13:2559–2567

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Yu Z, Morais D, Ivanga M, Harrison PM (2007) Analysis of the role of retrotransposition in gene evolution in vertebrates. BMC Bioinformatics 8:308

    Article  PubMed Central  PubMed  Google Scholar 

  6. Zhang Z, Harrison PM, Liu Y, Gerstein M (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13:2541–2558

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Yang L, Takuno S, Waters ER, Gaut BS (2011) Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation. Mol Biol Evol 28:1193–1203

    Article  CAS  PubMed  Google Scholar 

  8. Harrison PM, Sternberg MJE (1996) The disulphide beta-cross: from cystine geometry and clustering to classification of small disulphide-rich protein folds. J Mol Biol 264:603–623

    Article  CAS  PubMed  Google Scholar 

  9. Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M (2002) Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res 12:272–280

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M (2002) A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res 30:1083–1090

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. van Baren MJ, Brent MR (2006) Iterative gene prediction and pseudogene removal improves genome annotation. Genome Res 16:678–685

    Article  PubMed Central  PubMed  Google Scholar 

  12. Zhang Z, Harrison P, Gerstein M (2002) Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 12:1466–1482

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Harrison PM, Khachane A, Kumar M (2010) Genomic assessment of the evolution of the prion protein gene family in vertebrates. Genomics 95:268–277

    Article  CAS  PubMed  Google Scholar 

  14. Khachane AN, Harrison PM (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 10:435

    Article  PubMed Central  PubMed  Google Scholar 

  15. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigo R, Harrow J, Gerstein MB (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 17:839–851

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Zheng D, Gerstein MB (2006) A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol 7(Suppl 1):S13.1–S13.10

    Article  Google Scholar 

  17. Harrison PM, Kumar A, Lan N, Echols N, Snyder M, Gerstein M (2002) A small reservoir of disabled ORFs in the sequenced yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol 316:409–419

    Article  CAS  PubMed  Google Scholar 

  18. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG (2001) Massive gene decay in the leprosy bacillus. Nature 409:1007–1011

    Article  CAS  PubMed  Google Scholar 

  19. Gilad Y, Man O, Paabo S, Lancet D (2003) Human specific loss of olfactory receptor genes. Proc Natl Acad Sci U S A 100:3324–3327

    Google Scholar 

  20. Kim HL, Igawa T, Kawashima A, Satta Y, Takahata N (2010) Divergence, demography and gene loss along the human lineage. Philos Trans R Soc Lond B Biol Sci 365:2451–2457

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Wang X, Grus WE, Zhang J (2006) Gene losses during human origins. PLoS Biol 4:e52

    Article  PubMed Central  PubMed  Google Scholar 

  22. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132:185–219

    CAS  PubMed  Google Scholar 

  24. Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22:1437–1439

    Article  CAS  PubMed  Google Scholar 

  25. Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M (2007) Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 35:D55–D60

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Khelifi A, Duret L, Mouchiroud D (2005) HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res 33:D59–D66

    Article  PubMed  Google Scholar 

  27. Huang X, Miller W (1991) A time-efficient linear-space local similarity algorithm. Adv Appl Math 12:337–357

    Article  Google Scholar 

  28. Suyama M, Torrents D, Bork P (2004) BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinformatics 20:1968–1970

    Article  CAS  PubMed  Google Scholar 

  29. Birney E, Clamp M, Durbin R (2004) Genewise and genomewise. Genome Res 14:988–995

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  31. Thibaud-Nissen F, Ouyang S, Buell CR (2009) Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics 10:317

    Article  PubMed Central  PubMed  Google Scholar 

  32. Lafontaine I, Dujon B (2010) Origin and fate of pseudogenes in hemiascomycetes: a comparative analysis. BMC Genomics 11:260

    Article  PubMed Central  PubMed  Google Scholar 

  33. Liu Y, Harrison PM, Kunin V, Gerstein M (2004) Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol 5:R64

    Article  PubMed Central  PubMed  Google Scholar 

  34. Lerat E, Ochman H (2004) Psi-Phi: exploring the outer limits of bacterial pseudogenes. Genome Res 14:2273–2278

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  35. Lerat E, Ochman H (2005) Recognizing the pseudogenes in bacterial genomes. Nucleic Acids Res 33:3125–3132

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Yao A, Charlab R, Li P (2006) Systematic identification of pseudogenes through whole genome expression evidence profiling. Nucleic Acids Res 34:4477–4485

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  37. Florea L, di Francesco V, Miller J, Turner R, Yao A, Harris M, Walenz B, Mobarry C, Merkulov GV, Charlab R, Dew I, Deng Z, Istrail S, Li P, Sutton G (2005) Gene and alternative splicing annotation with AIR. Genome Res 15:54–66

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  38. Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA (2006) Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum Mutat 27:545–552

    Article  CAS  PubMed  Google Scholar 

  39. Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7(Suppl 1):S10.1–S10.12

    Article  Google Scholar 

  40. de Lima Morais DA, Harrison PM (2010) Large-scale evidence for conservation of NMD candidature across mammals. PLoS One 5:e11695

    Article  PubMed Central  PubMed  Google Scholar 

  41. Morais DD, Harrison PM (2009) Genomic evidence for non-random endemic populations of decaying exons from mammalian genes. BMC Genomics 10:309

    Article  PubMed Central  PubMed  Google Scholar 

  42. Terai G, Yoshizawa A, Okida H, Asai K, Mituyama T (2010) Discovery of short pseudogenes derived from messenger RNAs. Nucleic Acids Res 38:1163–1171

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Molineris I, Sales G, Bianchi F, di Cunto F, Caselle M (2010) A new approach for the identification of processed pseudogenes. J Comput Biol 17:755–765

    Article  CAS  PubMed  Google Scholar 

  44. Ortutay C, Vihinen M (2008) PseudoGene-Quest: service for identification of different pseudogene types in the human genome. BMC Bioinformatics 9:299

    Google Scholar 

  45. Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB (2010) Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res 38:6997–7007

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  46. Suyama M, Harrington E, Bork P, Torrents D (2006) Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PLoS Comput Biol 2:e76

    Article  PubMed Central  PubMed  Google Scholar 

  47. Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:W609–W612

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  48. Ranwez V, Harispe S, Delsuc F, Douzery EJ (2011) MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 6:e22594

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biology, McGill University, Stewart Biology Building, 1205 Doctor Penfield Avenue, Montreal, QC, Canada, H3A 1B1

    Paul M. Harrison Ph.D.

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  1. Paul M. Harrison Ph.D.
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Correspondence to Paul M. Harrison Ph.D. .

Editor information

Editors and Affiliations

  1. Istituto Toscano Tumori, Pisa, Italy

    Laura Poliseno

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Harrison, P.M. (2014). Computational Methods for Pseudogene Annotation Based on Sequence Homology. In: Poliseno, L. (eds) Pseudogenes. Methods in Molecular Biology, vol 1167. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0835-6_3

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  • DOI: https://doi.org/10.1007/978-1-4939-0835-6_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0834-9

  • Online ISBN: 978-1-4939-0835-6

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