Contribution of pseudogenes to sequence diversity

Methods in Molecular Biology

Volumn 1167, Issue , 2014, Pages 15-24

  Vihinen, Mauno ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Antigen variation; B cell receptor; Gene conversion; Genetic diversity; Immunoglobulin; Immunome; Pseudogene; T cell receptor

Indexed keywords

B LYMPHOCYTE RECEPTOR; CYTOCHROME P450; CYTOKINE; IMMUNOGLOBULIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; PROTEIN KINASE; RIBOSOME PROTEIN; T LYMPHOCYTE RECEPTOR; ANTIGEN; IMMUNOGLOBULIN RECEPTOR;

ANTIGENIC VARIATION; ARTICLE; CYTOKINE RELEASE; GENE CONVERSION; GENE SEQUENCE; GENETIC VARIABILITY; MAJOR HISTOCOMPATIBILITY COMPLEX; OLFACTORY RECEPTOR; PRIORITY JOURNAL; PSEUDOGENE; VDJ RECOMBINATION; ANIMAL; GENETICS; HUMAN; IMMUNITY;

ANIMALS; ANTIGENS; GENETIC VARIATION; HUMANS; IMMUNITY; PROTEIN KINASES; PSEUDOGENES; RECEPTORS, IMMUNOLOGIC;

EID: 84922280585     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0835-6_2     Document Type: Article

References (38)

1. Karro JE, Yan Y, Zheng D et al (2007) Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 35:D55–D60
2. Zhang Z, Harrison PM, Liu Y et al (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseu-dogenes in human genome. Genome Res 13: 2541–2558
3. Balakirev E, Ayala FJ (2003) Pseudogenes: are they “junk” or functional DNA? Annu Rev Genet 37:123–151
4. Pink RC, Wicks K, Caley DP et al (2011) Pseudogenes: pseudo-functional or key regulators in health and disease. RNA 17:792–798
5. Wen Y-Z, Zheng L-L, Hu L-H et al (2012) Pseudogenes are not pseudo any more. RNA Biol 9:27–32
6. Balasubramaniam S, Zheng D, Liu Y-J et al (2009) Comparative analysis of processed ribo-somal pseudogenes for four mammalian genomes. Genome Biol 10:R2
7. Tonner P, Srinivasasainagendra V, Zhang S et al (2012) Detecting transcription of ribo-somal protein pseudogenes in diverse human tissues from RNA-seq data. BMC Genomics 13:412
8. Niimura Y (2009) Evolutionary dynamics of olfactory receptor genes in chordates: interactionbetween environments and genomic contents. Hum Genomics 4:107–118
9. Olender T, Lancet D, Nebert DW (2008) Update on the olfactory receptor (OR) gene superfamily. Hum Genomics 3:87–97
10. Glusman G, Sosinksy A, Ben-Asher E et al (2000) Sequence, structure, and evolution of a complete human olfactory receptor gene cluster. Genomics 63:227–245
11. Mombaerts P (2001) The human repertoire of odorant receptor genes and pseudogenes. Annu Rev Genomics Hum Genet 2:493–510
12. Nelson DR, Zeldin DC, Hoffman SMG et al (2004) Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. Pharmacogenetics 14:1–18
13. Nelson DR, Schuler MA, Paquette SM (2004) Comparative genomics of rice and arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from monocot and dicot 1[w]. Plant Physiol 135:756–772
14. Lam HY, Khurana E, Fang G et al (2009) Pseudofam: the pseudogene families database. Nucleic Acids Res 37:D738–D743
15. Svensson Ö, Arvestad L, Lagergren J (2006) Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol 2(5):e46
16. Or tutay C, Siermala M, Vihinen M (2007) Molecular characterization of the immune system: emergence of proteins, processes and domains. Immunogenetics 59:333–348
17. Samarghitean C, Väliaho J, Vihinen M (2007) IDR knowledgebase for primary immunodefi -ciencies. Immunome Res 3:6
18. Piirilä H, Väliaho J, Vihinen M (2006) Immuno deficiency mutation databases (IDbases). Hum Mutat 27:1200–1208
19. Or tutay C, Vihinen M (2009) Immunome Knowledge Base (IKB): an integrated service for immunome research. BMC Immunol 10:3
20. Or tutay C, Vihinen M (2008) PseudoGene Quest: identification of different pseudogene types in the human genome. BMC Bioinfor-matics 9:299
21. Ollila J, Vihinen M (2005) B cells. Int J Biochem Cell Biol 37:518–523
22. Pramanik S, Cui X, Wang H-Y et al (2011) Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region. BMC Genomics 12:78
23. Tang ES, Martin A (2007) Immunoglobulin gene conversion: synthesizing antibody diversi-fication and DNA repair. DNA Repair 6: 1557–1571
24. Li H, Cui X, Pramanik S et al (2002) Genetic diversity of the human immunoglobulin heavy chain V H region. Immunol Rev 190:53–68
25. Sun Y, Liu Z, Ren L et al (2012) Immuno globulin genes and diversity: what we have learned from domestic animals. J Anim Sci Biotechnol 3:18
26. Schmucker D, Clemns JC, Shu H (2000) Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101:671–684
27. Cahoon LA, Seifert HS (2011) Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria. Mol Microbiol 81:1136–1143
28. Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–1317
29. Göringer HU (2012) ‘Gestalt’, composition and function of the Trypanosoma brucei edito-some. Annu Rev Microbiol 66:65–82
30. Cahoon LA, Seifert HS (2009) An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoaeae. Science 325:764–767
31. Singh P, Cole ST (2011) Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol 6:57–71
32. Ndung’u T, Weiss RA (2012) On HIV diversity. AIDS 26:1255–1260
33. Manning G, Whyte DB, Martinez R et al (2002) The protein kinase complement of the human genome. Science 298:1912–1934
34. Zeqiraj E, van Aalten DMF (2010) Pseudokinases- remnants of evolution or key allosteric regulators? Curr Opin Struct Biol 20:772–781
35. Boudeau J, Miranda-Saavedra D, Barton GF et al (2006) Emerging roles of pseudokinases. Trends Cell Biol 16:443–452
36. Caenepeel S, Charydczak G, Sudarsanam S et al (2004) The mouse kinome: discovery and comparative genomics of all mouse protein kinases. Proc Natl Acad Sci USA 101:11707–11712
37. Han YJ, Ma SF, Yourek G, Park YD et al (2011) A transcribed pseudogene of MYLK promotes cell proliferation. FASEB J 25: 2305–2312
38. Andersen JN, Jansen PG, Echwald SM (2004) A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and antigenic disease linkage. FASEB J 18: 8–30