Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons

Nucleic Acids Research

Volumn 34, Issue 19, 2006, Pages 5498-5507

  Maxwell, Patrick H ^a   Belote, John M ^a   Levis, Robert W ^a  

^a SYRACUSE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAG; GENE AMPLIFICATION; GENE EXPRESSION REGULATION; GENE MAPPING; INTRON; LONG TERMINAL REPEAT; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; RELIABILITY; RETROPOSON; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TELOMERE; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; UNINDEXED SEQUENCE;

5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; DNA; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAGS; INTRONS; MOLECULAR SEQUENCE DATA; POLYADENYLATION; POLYMERASE CHAIN REACTION; PROMOTER REGIONS (GENETICS); REPRODUCIBILITY OF RESULTS; RETROELEMENTS; RNA SPLICE SITES; SEQUENCE ALIGNMENT; TELOMERE; TRANSCRIPTION INITIATION SITE;

DROSOPHILA MELANOGASTER;

EID: 33751008398     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl709     Document Type: Article

References (45)

1. Biessmann,H. and Mason,J.M. (1995) The unusual telomeres of Drosophila. Trends Genet., 11, 58-62.
2. Pardue,M.L. and DeBaryshe,P.G. (2003) Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres. Annu. Rev. Genet., 37, 485-511.
3. Levis,R.W., Ganesan,R., Houtchens,K., Tolar,L.A. and Sheen,F.M. (1993) Transposons in place of telomeric repeats at a Drosophila telomere. Cell, 75, 1083-1093.
4. McEachern,M.J., Krauskopf,A. and Blackburn,E.H. (2000) Telomeres and their control. Annu. Rev. Genet., 34, 331-358.
5. Abad,J.P., De Pablos,B., Osoegawa,K., De Jong,P.J., Martin-Gallardo,A. and Villasante,A. (2004) TAHRE, a novel telomeric retrotransposon from Drosophila melanogaster, reveals the origin of Drosophila telomeres. Mol. Biol. Evol., 21, 1620-1624.
6. Sheen,F.M. and Levis,R.W. (1994) Transposition of the LINE-like retrotransposon TART to Drosophila chromosome termini. Proc. Natl Acad. Sci. USA., 91, 12510-12514.
7. Malik,H.S., Burke,W.D. and Eickbush,T.H. (1999) The age and evolution of non-LTR retrotransposable elements. Mol. Biol. Evol., 16, 793-805.
8. Mizrokhi,L.J., Georgieva,S.G. and Ilyin,Y.V. (1988) Jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II. Cell, 54, 685-691.
9. Swergold,G.D. (1990) Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol. Cell. Biol., 10, 6718-6729.
10. Minchiotti,G. and Di Nocera,P.P. (1991) Convergent transcription initiates from oppositely oriented promoters within the 5′ end regions of Drosophila melanogaster F elements. Mol. Cell. Biol., 11, 5171-5180.
11. McLean,C., Bucheton,A. and Finnegan,D.J. (1993) The 50 untranslated region of the I factor, a long interspersed nuclear element-like retrotransposon of Drosophila melanogaster, contains an internal promoter and sequences that regulate expression. Mol. Cell. Biol., 13, 1042-1050.
12. Schumann,G., Zundorf,I., Hofmann,J., Marschalek,R. and Dingermann,T. (1994) Internally located and oppositely oriented polymerase II promoters direct convergent transcription of a LINE-like retroelement, the Dictyostelium repetitive element, from Dictyostelium discoideum. Mol. Cell. Biol., 14, 3074-3084.
13. Contursi,C., Minchiotti,G. and Di Nocera,P.P. (1995) Identification of sequences which regulate the expression of Drosophila melanogaster Doc elements. J. Biol. Chem., 270, 26570-26576.
14. Sewell,E. and Kinsey,J.A. (1996) Tad, a Neurospora LINE-like retrotransposon exhibits a complex pattern of transcription. Mol. Gen. Genet., 252, 137-145.
15. DeBerardinis,R.J. and Kazazian,H.H., Jr (1999) Analysis of the promoter from an expanding mouse retrotransposon subfamily. Genomics, 56, 317-323.
16. Takahashi,H. and Fujiwara,H. (1999) Transcription analysis of the telomeric repeat-specific retrotransposons TRAS1 and SART1 of the silkworm Bombyx mori. Nucleic Acids Res., 27, 2015-2021.
17. Kutach,A.K. and Kadonaga,J.T. (2000) The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol., 20, 4754-4764.
18. Danilevskaya,O.N., Arkhipova,I.R., Traverse,K.L. and Pardue,M.L. (1997) Promoting in tandem: The promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs. Cell, 88, 647-655.
19. Danilevskaya,O.N., Traverse,K.L., Hogan,N.C., DeBaryshe,P.G. and Pardue,M.L. (1999) The two Drosophila telomeric transposable elements have very different patterns of transcription. Mol. Cell. Biol., 19, 873-881.
20. Beaudoing,E., Freier,S., Wyatt,J.R., Claverie,J.M. and Gautheret,D. (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res., 10, 1001-1010.
21. Tian,B., Hu,J., Zhang,H. and Lutz,C.S. (2005) A large-scale analysis of mRNA poyladenylation of human and mouse genes. Nucleic Acids Res., 33, 201-212.
22. Graber,J.H., Cantor,C.R., Mohr,S.C. and Smith,T.F. (1999) In silico detection of control signals: MRNA 3′-end-processing sequences in diverse species. Proc. Natl Acad. Sci. USA, 96, 14055-14060.
23. Currie,P.D. and Sullivan,D.T. (1994) Structure and expression of the gene encoding phosphofructokinase (PFK) in Drosophila melanogaster. J. Biol. Chem., 269, 24679-24687.
24. Benoit,B., Nemeth,A., Aulner,N., Kuhn,U., Simonelig,M., Wahle,E. and Bourbon,H.M. (1999) The Drosophila poly(A)-binding protein II is ubiquitous throughout Drosophila development and has the same function in mRNA polyadenylation as its bovine homolog in vitro. Nucleic Acids Res., 27, 3771-3778.
25. Talamillo,A., Fernandez-Moreno,M.A., Martinez-Azorin,F., Bornstein,B., Ochoa,P. and Garesse,R. (2004) Expression of the Drosophila melanogaster ATP synthase α subunit gene is regulated by a transcriptional element containing GAF and Adf-1 binding sites. Eur. J. Biochem., 271, 4003-4013.
26. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
27. Arkhipova,I.R. (1995) Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics, 139, 1359-1369.
28. Ohler,U., Liao,G.C., Niemann,H. and Rubin,G.M. (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol., 3, research 0087.1-87.12.
29. Boeke,J.D. and Stoye,J.P. (1997) Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In Coffin,J.M., Hughes,S.H. and Varmus,H.E. (eds), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 343-435.
30. Arkhipova,I.R. and Ilyin,Y.V. (1991) Properties of promoter regions of mdg1 Drosophila retrotransposon indicate that it belongs to a specific class of promoters. EMBO J., 10, 1169-1177.
31. Brierley,C. and Flavell,A.J. (1990) The retrotransposon copia controls the relative levels of its gene products post-transcriptionally by differential expression from its two major mRNAs. Nucleic Acids Res., 18, 2947-2951.
32. Pelisson,A., Song,S.U., Prud'homme,N., Smith,P.A., Bucheton,A. and Corces,V.G. (1994) Gypsy transposition correlates with the production of a retroviral envelope-like protein under the tissue-specific control of the Drosophila flamenco gene. EMBO J., 13, 4401-4411.
33. Perepelitsa-Belancio,V. and Deininger,P. (2003) RNA truncation by premature polyadenylation attenuates human mobile element activity. Nature Genet., 35, 363-366.
34. Han,J.S., Szak,S.T. and Boeke,J.D. (2004) Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature, 429, 268-274.
35. Aravin,A.A., Lagos-Quintana,M., Yalcin,A., Zavolan,M., Marks,D., Snyder,B., Gaasterland,T., Meyer,J. and Tuschl,T. (2003) The small RNA profile during Drosophila melanogaster development. Dev. Cell, 5, 337-350.
36. Savitsky,M., Dmitry,K., Georgiev,P., Kalmykova,A. and Gvozdev,V. (2006) Telomere elongation is under the control of the RNAi-based mechanism in the Drosophila germline. Genes Dev., 20, 345-354.
37. Nigumann,P., Redik,K., Matlik,K. and Speek,M. (2002) Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics, 79, 628-634.
38. Duncan,L., Bouckaert,K., Yeh,F. and Kirk,D.L. (2002) Kangaroo, a mobile element from Volvox carteri, is a member of a newly recognized third class of retrotransposons. Genetics, 162, 1617-1630.
39. Arkhipova,I.R., Pyatkov,K.I., Meselson,M. and Evgen'ev,M.B. (2003) Retroelements containing introns in diverse invertebrate taxa. Nature Genet., 33, 123-124.
40. Arkhipova,I.R., Mazo,A.M., Cherkasova,V.A., Gorelova,T.V., Schuppe,N.G. and Ilyin,Y.V. (1986) The steps of reverse transcription of Drosophila mobile dispersed genetic elements and U3-R-U5 structure of their LTRs. Cell, 44, 555-563.
41. Ziarczyk,P., Fourcade-Peronnet,F., Simonart,S., Maisonhaute,C. and Best-Belpomme,M. (1989) Functional analysis of the long terminal repeats of Drosophila 1731 retrotransposon: Promoter function and steroid regulation. Nucleic Acids Res., 17, 8631-8644.
42. Inouye,S., Hattori,K., Yuki,S. and Saigo,K. (1986) Structural variations in the Drosophila retrotransposon, 17.6. Nucleic Acids Res., 14, 4765-4778.
43. Yuki,S., Inouye,S., Ishimaru,S. and Saigo,K. (1986) Nucleotide sequence characterization of a Drosophila retrotransposon, 412. Eur. J. Biochem., 158, 403-410.
44. Burke,T.W. and Kadonaga,J.T. (1996) Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev., 10, 711-724.
45. Di Nocera,P.P. (1988) Close relationship between non-viral retroposons in Drosophila melanogaster. Nucleic Acids Res., 16, 4041-4052.