Transposable Element‐driven Duplications during Hominoid Genome Evolution

Bud Mishra, New York University, New York, USA

Published online: May 2008

DOI: 10.1002/9780470015902.a0020756

Hominoid genomes exhibit a significant number of large segmental duplications; these and other similar duplications in mammalian genomes are hypothesized to be mediated by transposable elements such as Alus or L1s in hominoids and rodents, respectively. The true evolutionary mechanisms that sculpted these duplications are emerging to be much more subtle and complex.

Keywords: segmental duplications (SD); low-copy repeats (LCR); copy number variations (CNV); transposable elements; rearrangement hotspots

Figure 1. Zhou–Mishra model. The model formulates the changes in the distribution of flanking region pairs over different states as a Markov process over evolution time. At a particular evolution time, t, the flanking region pairs are distributed over different states (circles) defined by the configuration of the repeats in the flanking region (–/–, +/– or +/+) and the age group of the duplicated segments (k). During evolution, in each time interval t, the flanking region pairs may change its state through many possible transitions (arrows). The change in the distribution of the flanking region pairs in a particular state at time t+t from time t depends on how much has entered into this state from other states, as well as how much has exited out of this state into other states in interval t since time t. At the same time, the flanking region pairs in other states can change into state A2,k(dashed arrows). The difference between A2,k(t) and A2,k(t+t) can be calculated by taking the difference between the sum of the outflows (grey arrows) and inflows (dashed arrows). Reproduced from Zhou and Mishra (2005).
close
 References
    Armengol L, Marquès-Bonet T, Cheung J et al. (2003) Murine segmental duplications are hot spots for chromosome and gene evolution. Genomics 86(6): 692–700.
    Armengol L, Pujana MA, Cheung J, Scherer SW and Estivill X (2003) Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Human Molecular Genetics 12: 2201–2208.
    Bailey JA, Church DM, Ventura M, Rocchi M and Eichler EE (2004) Analysis of segmental duplications and genome assembly in the mouse. Genome Research 14: 789–801.
    Bailey JA and Eichler EE (2006) Primate segmental duplications: crucibles of evolution, diversity and disease. Nature Reviews. Genetics 7(7): 552–564.
    Bailey JA, Gu Z, Clark RA et al. (2002) Recent segmental duplications in the human genome. Science 297: 1003–1007.
    Bailey JA, Liu G and Eichler EE (2003) An Alu transposition model for the origin and expansion of human segmental duplications. American Journal of Human Genetics 73: 823–834.
    Cheng Z, Ventura M, She X et al. (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437(7055): 88–93.
    Difilippantonio MJ, Petersen S, Chen HT et al. (2002) Evidence for replicative repair of DNA double-strand breaks leading to oncogenic translocation and gene amplification. The Journal of Experimental Medicine 196: 469–480.
    Dunham MJ, Badrane H, Ferea T et al. (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the USA 99: 16144–16149.
    Emanuel BS and Shaikh TH (2001) Segmental duplications: an ‘expanding’ role in genomic instability and disease. Nature Reviews. Genetics 2: 791.
    Fiston-Lavier AS, Anxolabehere D and Quesneville H (2007) A model of segmental duplication formation in Drosophila melanogaster. Genome Research 17: 1458–1470.
    Fitch DH, Bailey WJ, Tagle DA et al. (1991) Duplication of the gamma-globin gene mediated by L1 long interspersed repetitive elements in an early ancestor of simian primates. Proceedings of the National Academy of Sciences of the USA 88: 7396–7400.
    Force A, Lynch M, Pickett KB et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531–1545.
    Fraser JA, Huang JC, Pukkila-Worley R et al. (2005) Chromosomal translocation and segmental duplication in Cryptococcus neoformans. Eukaryotic Cell 4(2): 401–406.
    Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proceedings. Biological Sciences 256: 119–124.
    Iafrate AJ, Feuk L, Rivera MN et al. (2004) Detection of large-scale variation in the human genome. Nature Genetics 36(9): 949–951.
    International HapMap Consortium (2005) A haplotype map of the human genome. Nature 27: 1299–1320.
    Kellis M, Birren BW and Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617–624.
    Kolomietz E, Meyn MS, Pandita A and Squire JA (2002) The role of Alu repeat clusters as mediators of recurrent chromosomal aberrations in tumors. Genes, Chromosomes & Cancer 35: 97–112.
    Koszul R, Caburet S, Dujon B and Fischer G (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. The EMBO Journal 23: 234–243.
    Linardopoulou EV, Williams EM, Fan Y et al. (2005) Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437(7055): 94–100.
    Locke DP, Sharp AJ, McCarroll SA et al. (2006) Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. American Journal of Human Genetics 79(2): 275–290.
    Lucito R, West J, Reiner A et al. (2000) Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations. Genome Research 10(11): 1726–1736.
    Lynch M and Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151.
    Mishra B (2002) Comparing genomes. Computing in Science and Engineering 4(1): 42–49.
    Nadeau JH and Sankoff D (1997) Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 147: 1259.
    book Ohno S (1970) Evolution by Gene Duplication. Berlin: Springer.
    Paxia S, Rudra A, Zhou Y and Mishra B (2002) A random walk down the genomes: DNA evolution in VALIS. Computer 35(7): 73–79.
    Prince VE and Pickett FB (2002) Splitting pairs: the diverging fates of duplicated genes. Nature Reviews. Genetics 3: 827–837.
    Redon R, Ishikawa S, Fitch KR et al. (2006) Global variation in copy number in the human genome. Nature 444(7118): 444–454.
    Riehle MM, Bennett AF and Long AD (2001) Genetic architecture of thermal adaptation in Escherichia coli. Proceedings of the National Academy of Sciences of the USA 98: 525–530.
    Samonte RV and Eichler EE (2002) Segmental duplications and the evolution of the primate genome. Nature Reviews 3: 65–72.
    Sebat J (2007) Major changes in our DNA lead to major changes in our thinking. Nature Genetics 39: S3.
    Sebat J, Lakshmi B, Troge J et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305(5683): 525–528.
    Shaikh TH, Kurahashi H, Saitta SC et al. (2000) Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis. Human Molecular Genetics 9(4): 489–501.
    Sharp AJ, Hansen S, Selzer RR et al. (2006) Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature Genetics 38(9): 1038–1042.
    Sharp AJ, Locke DP, McGrath SD et al. (2005) Segmental duplications and copy-number variation in the human genome. American Journal of Human Genetics 77(1): 78–88.
    Smith PD and Moss SE (1994) Z-DNA-forming sequences at a putative duplication site in the human annexin VI-encoding gene. Gene 138: 239–242.
    Thomas EE, Srebro N, Sebat J et al. (2004) Distribution of short paired duplications in mammalian genomes. Proceedings of the National Academy of Sciences of the USA 101(28): 10349–10354.
    Thorisson GA and Stein LD (2003) The SNP consortium website: past, present and future. Nucleic Acids Research 31(1): 124–127.
    Tuzun E, Bailey JA and Eichler EE (2004) Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Research 14: 493–506.
    Van de Peer Y, Taylor JS, Braasch I and Meyer A (2001) The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. Journal of Molecular Evolution 53: 436.
    Walsh B (2003) Population-genetic models of the fates of duplicate genes. Genetica 118: 279–294.
    Zhang L, Lu HHS, Chung W-Y, Yang J and Li W-H (2005) Patterns of segmental duplication in the human genome. Molecular Biology and Evolution 22: 135–141.
    other Zhou Y (2005) Statistical Analyses and Markov Modeling of Duplication in Genome Evolution. PhD thesis, Department of Biology, New York University.
    other Zhou Y and Mishra B (2004) Models of genome evolution. Modeling in Molecular Biology, Natural Computing Series, pp. 287–304, Lecture Notes in Computer Science.
    Zhou Y and Mishra B (2005) Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. Proceedings of the National Academy of Sciences of the USA 102(11): 4051–4056.
 Further Reading
    Durand D and Hoberman R (2006) Diagnosing duplications – can it be done? Trends in Genetics 22(3): 156–164.
 Web Links
    ePath Chimpanzee Segmental Duplication Database, Genome Sciences, University of Washington; URL Link: http://chimpparalogy.gs.washington.edu.
    ePath Ensembl Genome Browsers; URL Link: http://www.ensembl.org.
    ePath Human Genome Segmental Duplication Database, Hospital for Sick Children, University of Toronto; URL Link: http://projects.tcag.ca/humandup.
    ePath Human Segmental Duplication Database, Genome Sciences, University of Washington; URL Link: http://humanparalogy.gs.washington.edu.
    ePath UCSC Genome Bioinformatics; URL Link: http://genome.ucsc.edu.

Related Sub-Topics:

Evolutionary Genomics | Molecular Evolution | Human Evolution | Evolution of Coding and Functional Modules
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Transposable Element‐driven Duplications during Hominoid Genome Evolution
 
How to Cite close
Mishra, Bud(May 2008) Transposable Element‐driven Duplications during Hominoid Genome Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020756]