Skip to main content
SpringerLink
Log in

Contribution of Pseudogenes to Sequence Diversity

  • Protocol
  • First Online:
Pseudogenes

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

Abstract

Pseudogenes are very common in the genomes of a wide range of organisms and, although they were originally considered as genetic junk, now several functions have been attributed to them. One important function of pseudogenes, as discussed in this chapter, is to provide material for genetic diversity. This is most prominent in the case of immunological recognition molecules such as immunoglobulins and B- and T-cell receptors, as well as in the case of antigenic variation in intracellular pathogens. Other examples discussed are olfactory receptors, ribosomal proteins, cytochrome P450s, and pseudokinases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (Canada)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (Canada)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (Canada)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (Canada)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

') var buybox = document.querySelector("[data-id=id_"+ timestamp +"]").parentNode var buyingOptions = buybox.querySelectorAll(".buying-option") ;[].slice.call(buyingOptions).forEach(initCollapsibles) var buyboxMaxSingleColumnWidth = 480 function initCollapsibles(subscription, index) { var toggle = subscription.querySelector(".buying-option-price") subscription.classList.remove("expanded") var form = subscription.querySelector(".buying-option-form") var priceInfo = subscription.querySelector(".price-info") var buyingOption = toggle.parentElement if (toggle && form && priceInfo) { toggle.setAttribute("role", "button") toggle.setAttribute("tabindex", "0") toggle.addEventListener("click", function (event) { var expandedBuyingOptions = buybox.querySelectorAll(".buying-option.expanded") var buyboxWidth = buybox.offsetWidth ;[].slice.call(expandedBuyingOptions).forEach(function(option) { if (buyboxWidth <= buyboxMaxSingleColumnWidth && option != buyingOption) { hideBuyingOption(option) } }) var expanded = toggle.getAttribute("aria-expanded") === "true" || false toggle.setAttribute("aria-expanded", !expanded) form.hidden = expanded if (!expanded) { buyingOption.classList.add("expanded") } else { buyingOption.classList.remove("expanded") } priceInfo.hidden = expanded }, false) } } function hideBuyingOption(buyingOption) { var toggle = buyingOption.querySelector(".buying-option-price") var form = buyingOption.querySelector(".buying-option-form") var priceInfo = buyingOption.querySelector(".price-info") toggle.setAttribute("aria-expanded", false) form.hidden = true buyingOption.classList.remove("expanded") priceInfo.hidden = true } function initKeyControls() { document.addEventListener("keydown", function (event) { if (document.activeElement.classList.contains("buying-option-price") && (event.code === "Space" || event.code === "Enter")) { if (document.activeElement) { event.preventDefault() document.activeElement.click() } } }, false) } function initialStateOpen() { var buyboxWidth = buybox.offsetWidth ;[].slice.call(buybox.querySelectorAll(".buying-option")).forEach(function (option, index) { var toggle = option.querySelector(".buying-option-price") var form = option.querySelector(".buying-option-form") var priceInfo = option.querySelector(".price-info") if (buyboxWidth > buyboxMaxSingleColumnWidth) { toggle.click() } else { if (index === 0) { toggle.click() } else { toggle.setAttribute("aria-expanded", "false") form.hidden = "hidden" priceInfo.hidden = "hidden" } } }) } initialStateOpen() if (window.buyboxInitialised) return window.buyboxInitialised = true initKeyControls() })()

Institutional subscriptions

Similar content being viewed by others

References

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Balakirev E, Ayala FJ (2003) Pseudogenes: are they “junk” or functional DNA? Annu Rev Genet 37:123–151

    Article  CAS  PubMed  Google Scholar 

  4. Pink RC, Wicks K, Caley DP et al (2011) Pseudogenes: pseudo-functional or key regulators in health and disease. RNA 17:792–798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Wen Y-Z, Zheng L-L, Hu L-H et al (2012) Pseudogenes are not pseudo any more. RNA Biol 9:27–32

    Article  PubMed  Google Scholar 

  6. Balasubramaniam S, Zheng D, Liu Y-J et al (2009) Comparative analysis of processed ribosomal pseudogenes for four mammalian genomes. Genome Biol 10:R2

    Article  Google Scholar 

  7. Tonner P, Srinivasasainagendra V, Zhang S et al (2012) Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data. BMC Genomics 13:412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Niimura Y (2009) Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents. Hum Genomics 4:107–118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Olender T, Lancet D, Nebert DW (2008) Update on the olfactory receptor (OR) gene superfamily. Hum Genomics 3:87–97

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  11. Mombaerts P (2001) The human repertoire of odorant receptor genes and pseudogenes. Annu Rev Genomics Hum Genet 2:493–510

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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 dicot1[w]. Plant Physiol 135:756–772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lam HY, Khurana E, Fang G et al (2009) Pseudofam: the pseudogene families database. Nucleic Acids Res 37:D738–D743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Svensson Ö, Arvestad L, Lagergren J (2006) Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol 2(5):e46

    Article  PubMed  PubMed Central  Google Scholar 

  16. Ortutay C, Siermala M, Vihinen M (2007) Molecular characterization of the immune system: emergence of proteins, processes and domains. Immunogenetics 59:333–348

    Article  PubMed  Google Scholar 

  17. Samarghitean C, Väliaho J, Vihinen M (2007) IDR knowledgebase for primary immunodeficiencies. Immunome Res 3:6

    Article  PubMed  PubMed Central  Google Scholar 

  18. Piirilä H, Väliaho J, Vihinen M (2006) Immuno deficiency mutation databases (IDbases). Hum Mutat 27:1200–1208

    Google Scholar 

  19. Ortutay C, Vihinen M (2009) Immunome Knowledge Base (IKB): an integrated service for immunome research. BMC Immunol 10:3

    Article  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  21. Ollila J, Vihinen M (2005) B cells. Int J Biochem Cell Biol 37:518–523

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Tang ES, Martin A (2007) Immunoglobulin gene conversion: synthesizing antibody diversification and DNA repair. DNA Repair 6: 1557–1571

    Article  CAS  PubMed  Google Scholar 

  24. Li H, Cui X, Pramanik S et al (2002) Genetic diversity of the human immunoglobulin heavy chain VH region. Immunol Rev 190:53–68

    Article  CAS  PubMed  Google Scholar 

  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

    Google Scholar 

  26. Schmucker D, Clemns JC, Shu H (2000) Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101:671–684

    Article  CAS  PubMed  Google Scholar 

  27. Cahoon LA, Seifert HS (2011) Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria. Mol Microbiol 81:1136–1143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Smith GP (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228:1315–1317

    Article  CAS  PubMed  Google Scholar 

  29. Göringer HU (2012) ‘Gestalt’, composition and function of the Trypanosoma brucei editosome. Annu Rev Microbiol 66:65–82

    Article  PubMed  Google Scholar 

  30. Cahoon LA, Seifert HS (2009) An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoaeae. Science 325:764–767

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Singh P, Cole ST (2011) Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol 6:57–71

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ndung’u T, Weiss RA (2012) On HIV diversity. AIDS 26:1255–1260

    Article  PubMed  Google Scholar 

  33. Manning G, Whyte DB, Martinez R et al (2002) The protein kinase complement of the human genome. Science 298:1912–1934

    Article  CAS  PubMed  Google Scholar 

  34. Zeqiraj E, van Aalten DMF (2010) Pseudokinases-remnants of evolution or key allosteric regulators? Curr Opin Struct Biol 20:772–781

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Boudeau J, Miranda-Saavedra D, Barton GF et al (2006) Emerging roles of pseudokinases. Trends Cell Biol 16:443–452

    Article  CAS  PubMed  Google Scholar 

  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 U S A 101:11707–11712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Experimental Medical Science, Lund University, Sölvegatan 19, BMC D10, SE-221 84, Lund, Sweden

    Mauno Vihinen

Authors
  1. Mauno Vihinen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mauno Vihinen .

Editor information

Editors and Affiliations

  1. Istituto Toscano Tumori, Pisa, Italy

    Laura Poliseno

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Vihinen, M. (2014). Contribution of Pseudogenes to Sequence Diversity. 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_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-0835-6_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0834-9

  • Online ISBN: 978-1-4939-0835-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation

-