A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Gao, Dongying ^a   Chen, Jinfeng ^b   Chen, Mingsheng ^b   Meyers, Blake C ^c   Jackson, Scott ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^c UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; GENE INSERTION SEQUENCE; GENE LOCATION; GENE TARGETING; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GRASS; LONG TERMINAL REPEAT; MAIZE; MOLECULAR EVOLUTION; NONHUMAN; ORYZA BRACHYANTHA; PHYLOGENETIC TREE; PLANT GENOME; RETROPOSON; RICE; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENE; POACEAE;

BIOLOGICAL EVOLUTION; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; GENES, PLANT; GENOME, PLANT; POACEAE; RETROELEMENTS; TERMINAL REPEAT SEQUENCES;

EID: 84863183645     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032010     Document Type: Article

References (71)

1. Kumar A, Bennetzen JL, (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
2. Feschotte C, Jiang N, Wessler SR, (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3: 329-341.
3. Cordaux R, Batzer MA, (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691-703.
4. Wendel JF, Wessler SR, (2000) Retrotransposon-mediated genome evolution on a local ecological scale. Proc Natl Acad Sci U S A 97: 6250-6252.
5. Kazazian HH Jr, (2004) Mobile elements: drivers of genome evolution. Science 303: 1626-32.
6. Wessler SR, (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci U S A 103: 17600-1761.
7. Lippman Z, Martienssen R, (2004) The role of RNA interference in heterochromatic silencing. Nature 431: 364-370.
8. Maxwell PH, Belote JM, Levis RW, (2006) Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons. Nucleic Acids Res 34: 5498-507.
9. Grewal SI, Jia S, (2007) Heterochromatin revisited. Nat Rev Genet 8: 35-46.
10. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982.
11. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
12. Witte CP, Le QH, Bureau T, Kumar A, (2001) Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci USA 98: 13778-13783.
13. Havecker ER, Gao X, Voytas DF, (2004) The diversity of LTR retrotransposons. Genome Biol 5: 225.
14. Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, et al. (2004) Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics 166: 1437-1450.
15. Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, et al. (2008) Cassandra retrotransposons carry independently transcribed 5S RNA. Proc Natl Acad Sci USA 105: 5833-5838.
16. Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, et al. (2002) Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161: 1293-1305.
17. Soleimani VD, Baum BR, Johnson DA, (2006) Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome. Genome 49: 389-396.
18. Pélissier T, Tutois S, Tourmente S, Deragon JM, Picard G, (1996) DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97: 141-151.
19. Presting GG, Malysheva L, Fuchs J, Schubert I, (1998) A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16: 721-728.
20. Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, et al. (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14: 1691-1704.
21. Devos KM, Brown JK, Bennetzen JL, (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079.
22. Ammiraju JS, Zuccolo A, Yu Y, Song X, Piegu B, et al. (2007) Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 52: 342-351.
23. Gao D, Gill N, Kim HR, Walling JG, Zhang W, et al. (2009) A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J 60: 820-831.
24. Neumann P, Pozárková D, Macas J, (2003) Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced. Plant Mol Biol 53: 399-410.
25. Vitte C, Panaud O, Quesneville H, (2007) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8: 218.
26. Wessler SR, (2001) Plant transposable elements. A hard act to follow. Plant Physiol 125: 149-151.
27. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, et al. (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16: 1262-1269.
28. Ding Y, Wang X, Su L, Zhai J, Cao S, et al. (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 19: 9-22.
29. Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, et al. (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461: 427-430.
30. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P, (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10: 908-915.
31. Vitte C, Panaud O, (2003) Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol 20: 528-540.
32. Xu Z, Wang H, (2007) LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: W265-268.
33. Gaut BS, (2002) Evolutionary dynamics of grass genomes. New Phytol 154: 15-28.
34. Charles M, Tang H, Belcram H, Paterson A, Gornicki P, et al. (2009) Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae. Mol Biol Evol 26: 1651-1661.
35. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL, (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45.
36. Ma J, Bennetzen JL, (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101: 12404-12410.
37. Sang T, Ge S, (2007) Genetics and phylogenetics of rice domestication. Curr Opin Genet Dev 17: 533-538.
38. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
39. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Research 35: D883-D887.
40. Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, et al. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res pp. D1028-1033.
41. Ito H, Gaubert H, Bucher E, Mirouze M, Vaillant I, et al. (2011) An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472: 115-119.
42. German MA, Luo S, Schroth G, Meyers BC, Green PJ, (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 4: 356-362.
43. Xiong Y, Eickbush TH, (1990) Origin and evolution of retroelements based upon their reverse-transcriptase sequences. EMBO J 9: 3353-3362.
44. Malik HS, Eickbush TH, (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11: 1187-1197.
45. Marín I, Lloréns C, (2000) Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol Biol Evol 17: 1040-1049.
46. Diao X, Freeling M, Lisch D, (2006) Horizontal transfer of a plant transposon. PLoS Biol 4: e5.
47. Roulin A, Piegu B, Wing RA, Panaud O, (2008) Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J 53: 950-959.
48. Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, et al. (2010) Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J 63: 353-365.
49. Bedell JA, Budinman MA, Nunberg A, Citek RM, Robbins D, et al. (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3: e13.
50. Feschotte C, Wessler SR, (2002) Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci U S A 99: 280-285.
51. Mouse genome sequencing consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
52. Bureau TE, Wessler SR, (1992) Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4: 1283-1294.
53. Bureau TE, Wessler SR, (1994) Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6: 907-916.
54. Naito K, Cho E, Yang G, Campbell MA, Yano K, et al. (2006) Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci U S A 103: 17620-17625.
55. Yang G, Dong J, Chandrasekharan MB, Hall TC, (2001) Kiddo, a new transposable element family closely associated with rice genes. Mol Genet Genomics 266: 417-424.
56. Berget SM, Moore C, Sharp PA, (1977) Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci U S A 74: 3171-3175.
57. Li W, Tucker AE, Sung W, Thomas WK, Lynch M, (2009) Extensive, recent intron gains in Daphnia populations. Science 326 (5957): 1260-1262.
58. Girard A, Hannon GJ, (2008) Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 18: 136-148.
59. Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, et al. (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461: 423-426.
60. Liu J, He Y, Amasino R, Chen X, (2004) siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev 18: 2873-2878.
61. Ying SY, Chang CP, Lin SL, (2010) Intron-mediated RNA interference, intronic microRNAs, and applications. Methods Mol Biol 629: 205-237.
62. Ehrlich SD, (1989) Illegitimate recombination in bacteria. In: Berg DE, Howe MM, editors. Mobile DNA Washington, D.C. American Society for Microbiology pp. 799-832.
63. Sugawara N, Haber JE, (1992) Characterization of double-strand break-induced recombination: Homology requirements and single-stranded DNA formation. Mol Cell Biol 12: 563-575.
64. Fernandes J, Dong Q, Schneider B, Morrow DJ, Nan GL, et al. (2004) Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biol 5: R82.
65. Bai L, Brutnell TP, (2011) The activator/dissociation transposable elements comprise a two-component gene regulatory switch that controls endogenous gene expression in maize. Genetics 187: 749-759.
66. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M, (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93: 7783-7788.
67. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
68. Higgins DG, Thompson JD, Gibson TJ, (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266: 383-402.
69. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
70. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 25 (4): 402-408.
71. Zhang C, Mallery EL, Schlueter J, Huang S, Fan Y, et al. (2008) Arabidopsis SCARs function interchangeably to meet actin-related protein 2/3 activation thresholds during morphogenesis. Plant Cell 20: 995-1011.