Using Alu elements as polyadenylation sites: A case of retroposon exaptation

Molecular Biology and Evolution

Volumn 26, Issue 2, 2009, Pages 327-334

  Chen, Chongjian ^a,b   Ara, Takeshi ^c   Gautheret, Daniel ^a  

^a UNIVERSITÉ PARIS SACLAY   (France)

^b SUN YAT SEN UNIVERSITY   (China)

^c KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

Alu; Polyadenylation; Retroposons; SINE

Indexed keywords

EID: 58449095204     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn249     Document Type: Article

References (33)

1. An HJ, Lee D, Lee KH, Bhak J. 2004. The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3′ untranslated regions. BMC Genomics. 5:97.
2. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet. 3:370-379.
3. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. 2000. Patterns of variant polyadenylation signal usage in human genes. Genome Res. 10:1001-1010.
4. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. 2006. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441:87-90.
5. Carninci P, Waki K, Shiraki T, et al. (47 co-authors). 2003. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res. 13:1273-1289.
6. Colgan DF, Manley JL. 1997. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11:2755-2766.
7. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
8. Gould SJ, Vrba ES. 1982. Exaptation: a missing term in the science of form. Paleobiology. 8:4-15.
9. Graber JH, Cantor CR, Mohr SC, Smith TF. 1999. In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc Natl Acad Sci USA. 96:14055-14060.
10. Han JS, Szak ST, Boeke JD. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature. 429:268-274.
11. Imanishi T, Itoh T, Suzuki Y, et al. (158 co-authors). 2004. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2:e162.
12. Jurka J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci USA. 94:1872-1877.
13. Kapitonov V, Jurka J. 1996. The age of Alu subfamilies. J Mol Evol. 42:59-65.
14. Karolchik D, Baertsch R, Diekhans M, et al. (13 co-authors). 2003. The UCSC Genome Browser Database. Nucleic Acids Res. 31:51-54.
15. Kreahling J, Graveley BR. 2004. The origins and implications of Aluternative splicing. Trends Genet. 20:1-4.
16. Lander ES, Linton LM, Birren B, et al. (255 co-authors). 2001. Initial sequencing and analysis of the human genome. Nature. 409:860-921.
17. Lee JY, Ji Z, Tian B. 2008. Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes. Nucleic Acids Res. 36:5581-5590.
18. Legendre M, Gautheret D. 2003. Sequence determinants in human polyadenylation site selection. BMC Genomics. 4:7.
19. Lev-Maor G, Sorek R, Shomron N, Ast G. 2003. The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science. 300:1288-1291.
20. Li WH, Gu Z, Wang H, Nekrutenko A. 2001. Evolutionary analyses of the human genome. Nature. 409:847-849.
21. Lopez F, Granjeaud S, Ara T, Ghattas B, Gautheret D. 2006. The disparate nature of "intergenic" polyadenylation sites. RNA. 12:1794-1801.
22. Lowe CB, Bejerano G, Haussler D. 2007. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA. 104:8005-8010.
23. Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G. 2005. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 33:D141-D146.
24. Mills RE, Bennett EA, Iskow RC, Devine SE. 2007. Which transposable elements are active in the human genome? Trends Genet. 23:183-191.
25. Polak P, Domany E. 2006. Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics. 7:133.
26. Proudfoot N. 1991. Poly(A) signals. Cell. 64:671-674.
27. Roy-Engel AM, El-Sawy M, Farooq L, Odom GL, Perepelitsa-Belancio V, Bruch H, Oyeniran OO, Deininger PL. 2005. Human retroelements may introduce intragenic polyadenylation signals. Cytogenet Genome Res. 110:365-371.
28. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. 2008. Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science. 320:1643-1647.
29. Smit A, Hubley R, Green P. 1996-2008. RepeatMasker Open-3.0. [Internet]. Available from http://www.repeatmasker.org.
30. Sorek R, Ast G, Graur D. 2002. Alu-containing exons are alternatively spliced. Genome Res. 12:1060-1067.
31. Wheelan SJ, Aizawa Y, Han JS, Boeke JD. 2005. Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Res. 15:1073-1078.
32. Xing J, Hedges DJ, Han K, Wang H, Cordaux R, Batzer MA. 2004. Alu element mutation spectra: molecular clocks and the effect of DNA methylation. J Mol Biol. 344:675-682.
33. Zhang H, Lee JY, Tian B. 2005. Biased alternative polyadenylation in human tissues. Genome Biol. 6:R100.