In and out of the rRNA genes: Characterization of Pokey elements in the sequenced Daphnia genome

Mobile DNA

Volumn 4, Issue 1, 2013, Pages

  Elliott, Tyler A ^a   Stage, Deborah E ^b,c   Crease, Teresa J ^a   Eickbush, Thomas H ^b  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF ROCHESTER   (United States)

^c Butler County Community College   (United States)

Author keywords

Daphnia; Insertion specificity; Pokey; Ribosomal DNA; Transposons

Indexed keywords

DNA; RIBOSOME DNA; RIBOSOME RNA; RNA 28S; SPACER DNA; TRANSPOSASE;

ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DAPHNIA; DAPHNIA PULEX; GENE DELETION; GENE DOSAGE; GENE INSERTION; GENE SEQUENCE; GENE TRANSFER; GENETIC ASSOCIATION; GENOME; INVERTED REPEAT; LONG TERM SURVIVAL; MINIATURE INVERTED REPEAT TRANSPOSABLE ELEMENT; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; POKEY GENE; PRIORITY JOURNAL; TRANSPOSON;

ACARI; DAPHNIA; DAPHNIA PULEX;

EID: 84884389970     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-4-20     Document Type: Article

References (65)

1. Dynamic interactions between transposable elements and their hosts. Levin HL, Moran JV, Nat Rev Genet 2011 12 615 627 21850042
2. Finely orchestrated movements: evolution of the ribosomal RNA genes. Eickbush TH, Eickbush DG, Genetics 2007 175 477 485 10.1534/genetics.107.071399 17322354 (Pubitemid 46798252)
3. Pokey, a new DNA transposon in Daphnia (Cladocera: Crustacea). Penton EH, Sullender BW, Crease TJ, J Mol Evol 2002 55 664 673 10.1007/s00239-002-2362-9 12486525 (Pubitemid 35387399)
4. Role of recombination in the long-term retention of transposable elements in rRNA gene loci. Zhang X, Eickbush MT, Eickbush TH, Genetics 2008 180 1617 1626 10.1534/genetics.108.093716 18791229
5. A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci. Zhou J, Eickbush MT, Eickbush TH, PLoS Genet 2013 9 1003179 10.1371/journal.pgen.1003179 23326244
6. High-efficiency transformation of Plasmodium falciparum by the lepidopteran transposable element piggyBac. Balu B, Shoue DA, Fraser MJ Jr, Adams JH, Proc Natl Acad Sci U S A 2005 102 16391 16396 10.1073/pnas.0504679102 16260745 (Pubitemid 41688924)
7. Evolution of the transposable element Pokey in the ribosomal DNA of species in the subgenus Daphnia (Crustacea: Cladocera). Penton EH, Crease TJ, Mol Biol Evol 2004 21 1727 1739 10.1093/molbev/msh189 15201395 (Pubitemid 39096889)
8. Identification and characterization of piggyBac-like elements in the genome of domesticated silkworm, Bombyx mori. Xu H-F, Xia Q-Y, Liu C, Cheng T-C, Zhao P, Duan J, Zha X-F, Liu S-P, Mol Genet Genomics 2006 276 31 40 10.1007/s00438-006-0124-x 16685528 (Pubitemid 43946092)
9. Repbase update: a database and an electronic journal of repetitive elements. Jurka J, Trends Genet 2000 9 418 420 (Pubitemid 30665376)
10. Massive horizontal gene transfer in Bdelloid rotifers. Gladyshev EA, Meselson M, Arkhipova IR, Science 2008 320 1210 1213 10.1126/science.1156407 18511688 (Pubitemid 351929508)
11. The association between breeding system and transposable element dynamics in Daphnia pulex. Valizadeh P, Crease TJ, J Mol Evol 2008 66 643 654 10.1007/s00239-008-9118-0 18491025
12. Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex. Ambrose C, Crease T, BMC Genet 2011 12 13 21261945
13. Sequence variation within the rRNA gene loci of 12 Drosophila species. Stage DE, Eickbush TH, Genome Res 2007 17 1888 1897 10.1101/gr.6376807 17989256 (Pubitemid 351360011)
14. Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia. Stage DE, Eickbush TH, Insect Mol Biol 2010 19 37 48 20167016
15. The ecoresponsive genome of Daphnia pulex. Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, et al. Science 2011 331 555 561 10.1126/science.1197761 21292972
16. The effect of transposon Pokey insertions on sequence variation in the 28S rRNA gene of Daphnia pulex. Glass SK, Moszczynska A, Crease TJ, Genome 2008 51 988 1000 10.1139/G08-092 19088812
17. Rates of recombination in the ribosomal DNA of apomictically propagated Daphnia obtusa lines. McTaggart SJ, Dudycha JL, Omilian A, Crease TJ, Genetics 2007 175 311 320 17110499 (Pubitemid 46168575)
18. The minimum internal and external sequence requirements for transposition of the eukaryotic transformation vector piggyBac. Li X, Lobo N, Bauser CA, Fraser MJ, Mol Genet Genomics 2001 266 190 198 10.1007/s004380100525 11683259 (Pubitemid 32938412)
19. Evolution of a transposon in Daphnia hybrid genomes. Vergilino R, Elliott TA, Desjardins Proulx P, Crease TJ, Dufresne F, Mobile DNA 2013 4 7 10.1186/1759-8753-4-7 23384095
20. Mutational analysis of highly conserved aspartate residues essential to the catalytic core of the piggyBac transposase. Keith JH, Schaeper CA, Fraser TS, Fraser MJ, BMC Mol Biol 2008 9 73 10.1186/1471-2199-9-73 18694512
21. PiggyBac transposon-mediated gene transfer in human cells. Wilson MH, Coates CJ, George AL, Mol Ther 2007 15 139 145 10.1038/sj.mt.6300028 17164785 (Pubitemid 46043659)
22. Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum. Wang J, Dua Y, Wang S, Brown SJ, Park Y, Insect Biochem Mol Biol 2008 38 490 498 10.1016/j.ibmb.2007.04.012 18342253
23. piggyBac-like elements in the pink bollworm, Pectinophora gossypiella. Wang J, Miller ED, Simmons GS, Miller TA, Tabashnik BE, Park Y, Insect Mol Biol 2010 19 177 184 10.1111/j.1365-2583.2009.00964.x 20017756
24. piggyBac can bypass DNA synthesis during cut and paste transposition. Mitra R, Fain-Thornton J, Craig NL, EMBO J 2008 27 1097 1109 10.1038/emboj.2008.41 18354502 (Pubitemid 351508151)
25. A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. Li X, Ewis H, Hice RH, Malani N, Parker N, Zhou L, Feschotte C, Bushman FD, Atkinson PW, Craig NL, Proc Natl Acad Sci U S A 2012 109 22 27 10.1073/pnas.1109202108 22190489
26. Loss of transposase-DNA interaction may underlie the divergence of mariner family transposable elements and the ability of more than one mariner to occupy the same genome. Lampe DJ, Walden KKO, Robertson HM, Mol Biol Evol 2001 18 954 961 10.1093/oxfordjournals.molbev.a003896 11371583 (Pubitemid 32520467)
27. DNA transposons and the evolution of eukaryotic genomes. Feschotte C, Pritham EJ, Annu Rev Genet 2007 41 331 368 10.1146/annurev.genet.40.110405. 090448 18076328
28. Physical properties of DNA components affecting the transposition efficiency of the mariner Mos1 element. Casteret S, Chbab N, Cambefort J, Auge-Gouillou C, Bigot Y, Rouleux-Bonnin F, Mol Genet Gen 2009 282 531 546 10.1007/s00438-009-0484-0
29. Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Bureau TE, Wessler SR, Plant Cell 1992 4 1283 1294 1332797
30. Miniature inverted-repeat transposable elements: discovery, distribution, and activity. Fattash I, Rebecca Rooke R, Amy Wong A, Caleb Hui C, Luu T, Bhardwaj P, Yang G, Genome 2013 56 1 12 10.1139/gen-2012-0097 23379333
31. Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. Feschotte C, Zhang X, Wessler SR, Edited by Craig NL, Craigie R, Gellert M, Lambowitz AM Washington DC: American Society for Microbiology Press, Mobile DNAII, 2002 1147 1158
32. Mar, a MITE family of hAT transposons in Drosophila. Deprá M, Ludwig A, Valente VLS, Loreto ELS, Mobile DNA 2012 3 13 10.1186/1759-8753-3-13 22935191
33. Transposon excision from an atypical site: a mechanism of evolution of novel transposable elements. Langer M, Sniderhan LF, Grossniklaus U, Ray A, PLoS One 2007 10 965
34. A component of Drosophila RNA polymerase I promoter lies within the rRNA transcription unit. Kohorn BD, Rae PMM, Nature 1983 304 179 181 10.1038/304179a0 6306476 (Pubitemid 13079149)
35. Virtually the entire Xenopus laevis rDNA mulikilobase intergenic spacer serves to stimulate polymerase I transcription. Mougey EB, Pape LK, Soliner-Webb B, J Biol Chem 1996 271 27138 27145 10.1074/jbc.271.43.27138 8900206 (Pubitemid 26359135)
36. Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster. Ye J, Eickbush TH, Mol Cell Biol 2006 26 8781 8790 10.1128/MCB.01409-06 17000772 (Pubitemid 44851938)
37. Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Yang J, Malik HS, Eickbush TH, Proc Natl Acad Sci U S A 1999 96 7847 7852 10.1073/pnas.96.14.7847 10393910 (Pubitemid 29328370)
38. R5 retrotransposons insert into a family of infrequently transcribed 28S rRNA genes of planaria. Burke WD, Singh D, Eickbush TH, Mol Biol Evol 2003 20 1260 1270 10.1093/molbev/msg141 12777502 (Pubitemid 36961244)
39. Functional expression of a sequence-specific endonuclease encoded by the retrotransposon R2Bm. Xiong YE, Eickbush TH, Cell 1988 55 235 246 10.1016/0092-8674(88)90046-3 2844414
40. Downstream 28S gene sequences on the RNA template affect the choice of primer and the accuracy of initiation by the R2 reverse transcriptase. Luan DD, Eickbush TH, Mol Cell Biol 1996 16 4726 4734 8756630 (Pubitemid 26272126)
41. Retrotransposon R1Bm endonuclease cleaves the target sequence. Feng Q, Schumann G, Boeke JD, Proc Natl Acad Sci U S A 1998 95 2083 2088 10.1073/pnas.95.5.2083 9482842 (Pubitemid 28145898)
42. Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies. Maita N, Aoyagi H, Osanai M, Shirakawa M, Fujiwara H, Nucl Acids Res 2007 35 3918 3927 10.1093/nar/gkm397 17537809 (Pubitemid 47244615)
43. Ribosomal DNA insertion elements R1Bm and R2Bm can transpose in a sequence specific manner to locations outside the 28S genes. Xiong Y, Burke WD, Jakubczak JL, Eickbush TH, Nucl Acids Res 1988 16 10561 10573 10.1093/nar/16.22.10561 2849750
44. In vitro position-specific integration of a retrovirus-like element requires Pol III transcription factors. Kirchner J, Connolly CM, Sandmeyer SB, Science 1995 267 1488 1491 10.1126/science.7878467 7878467
45. Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes. Bachman N, Eby Y, Boeke JD, Genome Res 2004 14 1232 1247 10.1101/gr.2052904 15197163 (Pubitemid 39029220)
46. Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin. Dai J, Xie W, Brady TL, Gao J, Voytas DF, Mol Cell 2007 27 289 299 10.1016/j.molcel.2007.06.010 17643377 (Pubitemid 47058305)
47. High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe. Guo Y, Levin HL, Genome Res 2010 20 239 248 10.1101/gr.099648.109 20040583
48. Transposable elements in clonal lineages: lethal hangover from sex. Nuzhdin SV, Petrov DA, Biol J Linn Soc 2003 79 33 41 10.1046/j.1095-8312.2003. 00188.x (Pubitemid 36590297)
49. Epigenetic regulation of retrotransposons within the nucleolus of Drosophila. Eickbush DG, Ye J, Zhang X, Burke WD, Eickbush TH, Mol Cell Biol 2008 28 6452 6461 10.1128/MCB.01015-08 18678644
50. The behavior of a Daphnia pulex transposable element in cyclically and obligately parthenogenetic populations. Sullender BW, Crease TJ, J Mol Evol 2001 53 63 69 11683324 (Pubitemid 32523329)
51. DNA transposon dynamics in populations of Daphnia pulex with and without sex. Schaack S, Pritham EJ, Wolf A, Lynch M, Proc R Soc B 2010 277 2381 2387 10.1098/rspb.2009.2253 20356890
52. Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia. Eagle SHC, Crease TJ, Mobile DNA 2012 3 4 10.1186/1759-8753-3-4 22390386
53. Basic local alignment search tool. Altschul S, Gish W, Miller W, Myers E, Lipman D, J Mol Biol 1990 215 403 410 2231712
54. BLAST [ http://blast.ncbi.nlm.nih.gov/Blast.cgi ]
55. GenBank trace files [ http://www.ncbi.nlm.nih.gov/Traces/trace.cgi ]
56. WFleaBase [ http://wfleabase.org ]
57. Origin of nascent lineages and the mechanisms used to prime second-strand synthesis in the R1 and R2 retrotransposons of Drosophila. Stage DE, Eickbush TH, Genome Biol 2009 10 49 10.1186/gb-2009-10-5-r49 19416522
58. PSORT II [ http://psort.hgc.jp/form2.html ]
59. EMBL-EBI alignment tools [ http://www.ebi.ac.uk/Tools/sequence.html ]
60. BioEdit [ http://www.mbio.ncsu.edu/BioEdit/page2.html ]
61. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Kimura M, J Mol Evol 1980 16 111 120 10.1007/BF01731581 7463489 (Pubitemid 11166431)
62. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
63. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
64. Confidence limits on phylogenies: an approach using the bootstrap. Felsenstein J, Evolution 1985 39 783 791 10.2307/2408678
65. WebLogo [ http://weblogo.threeplusone.com ]