BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters

Plant Journal

Volumn 56, Issue 1, 2008, Pages 40-50

  Chang, Wei ^a   Schulman, Alan H ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Barley; mRNA; Polyadenylation; Promoter; Retrotransposon life cycle; Transcriptional regulation

Indexed keywords

BARE 1 PROTEIN, HORDEUM VULGARE; BARE-1 PROTEIN, HORDEUM VULGARE; PLANT DNA; TATA BINDING PROTEIN; VEGETABLE PROTEIN;

ARTICLE; BARLEY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; LONG TERMINAL REPEAT; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PROMOTER REGION; RETROPOSON; SEQUENCE ALIGNMENT; TRANSCRIPTION INITIATION SITE;

BASE SEQUENCE; DNA, PLANT; GENE EXPRESSION REGULATION, PLANT; HORDEUM; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; POLYADENYLATION; PROMOTER REGIONS (GENETICS); RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TATA-BOX BINDING PROTEIN; TERMINAL REPEAT SEQUENCES; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

HORDEUM; HORDEUM VULGARE; MIRIDAE; POACEAE;

EID: 52649115360     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2008.03572.x     Document Type: Article

References (39)

1. Alexandrov, N.N., Troukhan, M.E., Brover, V.V., Tatarinova, T., Flavell, R.B. Feldmann, K.A. (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol. Biol. 60, 69 85.
2. Beelman, C.A. Parker, R. (1995) Degradation of mRNA in eukaryotes. Cell, 81, 179 183.
3. Böhmdorfer, G., Hofacker, I.L., Garber, K., Jelenic, S., Nizhynska, V., Hirochika, H., Stadler, P.F. Bachmair, A. (2005) Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate. RNA, 11, 1181 1191.
4. Cullen, B.R. (2003) Nuclear RNA export. J. Cell Sci. 116, 587 597.
5. Don, R.H., Cox, P.T., Wainwright, B.J., Baker, K. Mattick, J.S. (1991) 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucl. Acids Res. 19, 4008.
6. Dreher, T.W. Miller, W.A. (2006) Translational control in positive strand RNA plant viruses. Virology, 344, 185 197.
7. Erkmann, J.A., Sànchez, R., Treichel, N., Marzluff, W.F. Kutay, U. (2005) Nuclear export of metazoan replication-dependent histone mRNAs is dependent on RNA length and is mediated by TAP. RNA, 11, 45 58.
8. Feldbrügge, M., Arizti, P., Sullivan, M.L., Zamore, P.D., Belasco, J.G. Green, P.J. (2001) Comparative analysis of the plant mRNA-destabilizing element, DST, in mammalian and tobacco cells. Plant Mol. Biol. 49, 215 223.
9. Feschotte, C., Jiang, N. Wessler, S. (2002) Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3, 329 341.
10. Fuke, H. Ohno, M. (2008) Role of poly (A) tail as an identity element for mRNA nuclear export. Nucl. Acids Res. 36, 1037 1049.
11. Gallie, D.R. Walbot, V. (1990) RNA pseudoknot domain of tobacco mosaic virus can functionally substitute for a poly(A) tail in plant and animal cells. Genes Dev. 4, 1149 1157.
12. Grandbastien, M.A., Audeon, C., Bonnivard, E., Casacuberta, J.M., Chalhoub, B., Costa, A.P., Le, Q.H., Melayah, D., Petit, M., Poncet, C., Tam, S.M., Van Sluys, M.A. Mhiri, C. (2005) Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110, 229 241.
13. Jääskeläinen, M., Mykkänen, A.-H., Arna, T., Vicient, C., Suoniemi, A., Kalendar, R., Savilahti, H. Schulman, A.H. (1999) Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J. 20, 413 422.
14. Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E. Schulman, A.H. (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. USA 97, 6603 6607.
15. Kawaguchi, R. Bailey-Serres, J. (2002) Regulation of translational initiation in plants. Curr. Opin. Plant Biol. 5, 460 465.
16. Kumar, A. Bennetzen, J. (1999) Plant retrotransposons. Annu. Rev. Genet. 33, 479 532.
17. LeBlanc, J.J., Uddowla, S., Abraham, B., Clatterbuck, S. Beemon, K.L. (2007) Tap and Dbp5, but not Gag, are involved in DR-mediated nuclear export of unspliced Rous sarcoma virus RNA. Virology, 363, 376 386.
18. Liu, Z.L., Han, F.P., Tan, M., Shan, X.H., Dong, Y.Z., Wang, X.Z., Fedak, G., Hao, S. Liu, B. (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor. Appl. Genet. 109, 200 2009.
19. Manninen, I. Schulman, A.H. (1993a) BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol. Biol. 22, 829 846.
20. Melton, D.A., Krieg, P.A., Rebagliati, M.R., Maniatis, T., Zinn, K. Green, M.R. (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucl. Acids Res. 12, 7035 7056.
21. Nikolaitchik, O., Rhodes, T.D., Ott, D. Hu, W.S. (2006) Effects of mutations in the human immunodeficiency virus type 1 Gag gene on RNA packaging and recombination. J. Virol. 80, 4691 4697.
22. Ratnasabapathy, R., Sheldon, M., Johal, L. Hernandez, N. (1990) The HIV-1 long terminal repeat contains an unusual element that induces the synthesis of short RNAs from various mRNA and snRNA promoters. Genes Dev. 4, 2061 2074.
23. Sabot, F. Schulman, A. (2007) Template switching can create complex LTR retrotransposon insertions in Triticeae genomes. BMC Genomics, 8, 247.
24. Sabot, F. Schulman, A.H. (2006) Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity, 97, 381 388.
25. Schulman, A.H. Kalendar, R. (2005) A movable feast: diverse retrotransposons and their contribution to barley genome dynamics. Cytogenet. Genome Res. 110, 598 605.
26. Shirasu, K., Schulman, A.H., Lahaye, T. Schulze-Lefert, P. (2000) A contiguous 66 kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10, 908 915.
27. Suoniemi, A., Anamthawat-Jónsson, K., Arna, T. Schulman, A.H. (1996a) Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol. Biol. 30, 1321 1329.
28. Suoniemi, A., Narvanto, A. Schulman, A.H. (1996b) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol. Biol. 31, 295 306.
29. Suoniemi, A., Tanskanen, J., Pentikäinen, O., Johnson, M.S. Schulman, A.H. (1998) The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution. Mol. Biol. Evol. 15, 1135 1144.
30. Takeda, S., Sugimoto, K., Otsuki, H. Hirochika, H. (1998) Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Mol. Biol. 36, 365 376.
31. Tanskanen, J.A., Sabot, F., Vicient, C. Schulman, A.H. (2007) Life without GAG: the BARE-2 retrotransposon as a parasite′s parasite. Gene, 390, 166 174.
32. Vicient, C.M., Jääskeläinen, M., Kalendar, R. Schulman, A.H. (2001a) Active retrotransposons are a common feature of grass genomes. Plant Physiol. 125, 1283 1292.
33. Vicient, C.M., Kalendar, R. Schulman, A.H. (2001b) Envelope-containing retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Res. 11, 2041 2049.
34. Vicient, C.M. Schulman, A.H. (2002) Copia-like retrotransposons in the rice genome: few and assorted. Genome Lett. 1, 35 47.
35. Vicient, C.M. Schulman, A.H. (2005) Variability, recombination, and mosaic evolution of the barley BARE-1 retrotransposon. Mol. Biol. Evol. 61, 275 291.
36. Vicient, C.M., Suoniemi, A., Anamthawat-Jónsson, K., Tanskanen, J., Beharav, A., Nevo, E. Schulman, A.H. (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell, 11, 1769 1784.
37. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J., Capy, P., Chalhoub, B., Flavell, A.J., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P. Schulman, A.H. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973 982.
38. Wright, D.A. Voytas, D.F. (2002) Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res. 12, 122 131.
39. Zeenko, V. Gallie, D.R. (2005) Cap-independent translation of tobacco etch virus is conferred by an RNA pseudoknot in the 5′-leader. J. Biol. Chem. 280, 26813 26824.