ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Hayward, Alexander ^a   Ghazal, Awaisa ^b   Andersson, Göran ^b   Andersson, Leif ^a,b   Jern, Patric ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE ACETYLTRANSFERASE; PROTEIN C7ORF29; PROTEIN ZBED1; PROTEIN ZBED2; PROTEIN ZBED3; PROTEIN ZBED4; PROTEIN ZBED5; PROTEIN ZBED6; PROTEIN ZBEDX; UNCLASSIFIED DRUG;

ARTICLE; C7ORF29 GENE; CHROMOSOME ANALYSIS; CLADISTICS; DOMESTICATION; GENE; GENE FUNCTION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HOST; HUMAN; MOLECULAR EVOLUTION; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TRANSPOSON; VERTEBRATE; ZBED GENE; ZBED1 GENE; ZBED2 GENE; ZBED3 GENE; ZBED4 GENE; ZBED5 GENE; ZBED6 GENE; ZBEDX GENE;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; MEMBRANE PROTEINS; TRANSCRIPTION FACTORS;

EID: 84875303118     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059940     Document Type: Article

References (36)

1. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-482.
2. Markljung E, Jiang L, Jaffe JD, Mikkelsen TS, Wallerman O, et al. (2009) ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 7: e1000256.
3. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, et al. (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425: 832-836.
4. Arensburger P, Hice RH, Zhou L, Smith RC, Tom AC, et al. (2011) Phylogenetic and functional characterization of the hAT transposon superfamily. Genetics 188: 45-57.
5. Deininger PL, Batzer MA, (2002) Mammalian retroelements. Genome Res 12: 1455-1465.
6. Sinzelle L, Izsvak Z, Ivics Z, (2009) Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol Life Sci 66: 1073-1093.
7. 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.
8. 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.
9. Kashkush K, Feldman M, Levy AA, (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33: 102-106.
10. Lowe CB, Haussler D, (2012) 29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome. PLoS ONE 7: e43128.
11. Feschotte C, Pritham EJ, (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41: 331-368.
12. Volff JN, (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28: 913-922.
13. Aravind L, (2000) The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases. Trends Biochem Sci 25: 421-423.
14. Matsukage A, Hirose F, Yoo MA, Yamaguchi M, (2008) The DRE/DREF transcriptional regulatory system: a master key for cell proliferation. Biochim Biophys Acta 1779: 81-89.
15. Chen T, Li M, Ding Y, Zhang LS, Xi Y, et al. (2009) Identification of zinc-finger BED domain-containing 3 (Zbed3) as a novel Axin-interacting protein that activates Wnt/beta-catenin signaling. J Biol Chem 284: 6683-6689.
16. Saghizadeh M, Gribanova Y, Akhmedov NB, Farber DB, (2011) ZBED4, a cone and Muller cell protein in human retina, has a different cellular expression in mouse. Mol Vis 17: 2011-2018.
17. Kapitonov VV, Jurka J, (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3: e181.
18. Babu MM, Iyer LM, Balaji S, Aravind L, (2006) The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res 34: 6505-6520.
19. Emerson RO, Thomas JH, (2011) Gypsy and the birth of the SCAN domain. J Virol 85: 12043-12052.
20. Casola C, Hucks D, Feschotte C, (2008) Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol 25: 29-41.
21. Kojima KK, Jurka J, (2011) Crypton transposons: identification of new diverse families and ancient domestication events. Mob DNA 2: 12.
22. Feschotte C, (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405.
23. Curcio MJ, Derbyshire KM, (2003) The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol 4: 865-877.
24. Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, et al. (2005) Molecular architecture of a eukaryotic DNA transposase. Nat Struct Mol Biol 12: 715-721.
25. Yuan YW, Wessler SR, (2011) The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci U S A 108: 7884-7889.
26. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
27. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
28. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ, (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191.
29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
30. Drummond AJ, Suchard MA, Xie D, Rambaut A, (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29 (8) (): 1969-1973.
31. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
32. Shapiro B, Rambaut A, Drummond AJ, (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23: 7-9.
33. Hasegawa M, Kishino H, Yano T, (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
34. Kumar S, Subramanian S, (2002) Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A 99: 803-808.
35. Yang Z, (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
36. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.