The effect of transposable element insertions on gene expression evolution in Rodents

PLoS ONE

Volumn 4, Issue 2, 2009, Pages

  Pereira, Vini ^a,b   Enard, David ^a,c   Eyre Walker, Adam ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^c ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE FUNCTION; GENE INSERTION; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; QUANTITATIVE ANALYSIS; RAT; REGULATORY SEQUENCE; SEQUENCE HOMOLOGY; SPECIES COMPARISON; SPECIES DIVERSITY; TRANSPOSON;

RATTUS; RODENTIA;

EID: 84887212541     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004321     Document Type: Article

References (35)

1. IHGSC (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405.
3. Makalowski W (2000) Genomic scrap yard: how genomes utilize all that junk. Gene 259: 61-67.
4. Nekrutenko A, Li W-H (2001) Transposable elements are found in a large number of protein-coding gene. Trends Genet 17: 619-621.
5. Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 19: 68-72.
6. Britten RJ (1996) DNA sequence insertion and evolutionary variation in gene regulation. Proc Natl Acad Sci U S A 93: 9374-9377.
7. Brosius J (1999) Genomes were forged by massice bombardments with retroelements and retrosequences. Genetica 107: 209-238.
8. van de Lagemaat LN, Landry JR, Mager DL, Medstrand P (2003) Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19: 530-536.
9. McClintock B (1946) Maize Genetics. Carnegie Inst Washington Year Book 45: 176-186.
10. Britten RJ, Davidson EH (1971) Repetitive and non-repetitive DNA sequences and a specualtion on the origins of genetic novelty. Q Rev Biol 46: 111-138.
11. Silva JC, Shabalina SA, Harris DG, Spouge JL, Kondrashov AS (2003) Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genet Res 82: 1-18.
12. Kamal M, Xie X, Lander ES (2006) A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci U S A 103: 2740-2745.
13. Lowe CB, Bejerano G, Haussler D (2007) Thousands of human mobile element fragments undergo strong pruifying selection near developmental genes. Proc Natl Acad Sci USA 19: 8005-8010.
14. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177.
15. Xie X, Kamal M, Lander ES (2006) A family of conserved noncoding elements derived from an ancient transposable element. Proc Natl Acad Sci U S A 103: 11659-11664.
16. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502.
17. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, et al. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87-90.
18. Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK (2005) Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet Genome Res 110: 333-341.
19. Medstrand P, van de Lagemaat LN, Dunn CA, Landry JR, Svenback D, et al. (2005) Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 110: 342-352.
20. Urrutia AO, Ocana LB, Hurst LD (2008) Do Alu repeats drive the evolution of the primate transcriptome? Genome Biol 9: R25.
21. Mouse_Genome↘quencing_Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
22. Liao B-Y, Zhang J (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23: 530-540.
23. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
24. Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, et al. (2004) A neutral model of transcriptome evolution. PLoS Biol 2: E132.
25. Han JS, Szak ST, Boeke JD (2004) Transcriptional disruption by the LI retrotransposon and implications for mammalian transcriptomes. Nature 429: 268-274.
26. Han JS, Boeke JD (2005) LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? Bioessays 27: 775-784.
27. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein coding transcriptomes. Proc Natl Acad Sci USA 101: 6062-6067.
28. Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, et al. (2004) Applications of a rat multiple tissue gene expression data set. Genome Res 14: 742-749.
29. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
30. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
31. Smit A (1999) Interspersed repeats and the other mementos of transposable elements in the mammalian genomes. Curr Op Genet Dev 9: 657-663.
32. Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, et al. (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res 35: D668-673.
33. Pereira V (2008) Automated paleontology of repetitive DNA with REannotate. BMC Genomics 9: 614.
34. Keightley PD, Gaffney DJ (2003) Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci U S A 100: 13402-13406.
35. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, et al. (2007) Ensembl 2007. Nucleic Acids Res 35: D610-617.