Common evolutionary trends for SINE RNA structures

Trends in Genetics

Volumn 23, Issue 1, 2007, Pages 26-33

  Sun, Feng Jie ^a   Fleurdépine, Sophie ^b   Bousquet Antonelli, Cécile ^b   Caetano Anollés, Gustavo ^a   Deragon, Jean Marc ^b,c  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITÉ CLERMONT AUVERGNE   (France)

^c UNIVERSITÉ DE PERPIGNAN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ARTICLE; CLADISTICS; CONSENSUS SEQUENCE; EUKARYOTE; EVOLUTION; GENE EXPRESSION; GENOME; LONG INTERSPERSED REPEAT; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RNA GENE; RNA STRUCTURE; SHORT INTERSPERSED REPEAT;

EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; MODELS, GENETIC; PHYLOGENY; RNA, TRANSFER; SELECTION (GENETICS); SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EUKARYOTA; MAMMALIA; PISCES;

EID: 33845637289     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2006.11.005     Document Type: Article

References (52)

1. Kramerov D.A., and Vassetzky N.S. Short retroposons in eukaryotic genomes. Int. Rev. Cytol. 247 (2005) 165-221
2. Perepelitsa-Belancio V., and Deininger P. RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat. Genet. 35 (2003) 363-366
3. Han J.S., et al. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429 (2004) 268-274
4. Muotri A.R., et al. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435 (2005) 903-910
5. Jurka J. Origin and evolution of Alu repetitive elements. In: Maraia R. (Ed). The Impact of Short Interspersed Elements (SINEs) on the Host Genome (1995), R.G. Landes, Springer 25-41
6. Okada N., and Ohshima K. Evolution of tRNA-derived SINEs. In: Maraia R. (Ed). The Impact of Short Interspersed Elements (SINEs) on the Host Genome (1995), R.G. Landes, Springer 61-80
7. Dewannieux M., et al. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35 (2003) 41-48
8. Kajikawa M., and Okada N. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111 (2002) 433-444
9. Kapitonov V.V., and Jurka J. A novel class of SINE elements derived from 5S rRNA. Mol. Biol. Evol. 20 (2003) 694-702
10. Piskurek O., et al. Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources. Mol. Biol. Evol. 20 (2003) 1659-1668
11. Arnaud P., et al. Analysis of the SINE S1 pol III promoter from Brassica; impact of methylation and influence of external sequences. Plant J. 26 (2001) 295-305
12. Gilbert N., and Labuda D. Evolutionary inventions and continuity of CORE-SINEs in mammals. J. Mol. Biol. 298 (2000) 365-377
13. Ogiwara I., et al. V-SINEs: A new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res. 12 (2002) 316-324
14. Nishihara H., et al. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16 (2006) 864-874
15. Labuda D., and Zietkiewicz E. Evolution of secondary structure in the family of 7SL-like RNAs. J. Mol. Evol. 39 (1994) 506-518
16. Sinnett D., et al. Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units. J. Biol. Chem. 266 (1991) 8675-8678
17. Rozhdestvensky T.S., et al. Neuronal BC1 RNA structure: evolutionary conversion of a tRNA(Ala) domain into an extended stem-loop structure. RNA 7 (2001) 722-730
18. Kawagoe-Takaki H., et al. Probing the secondary structure of salmon SmaI SINE RNA. Gene 365 (2006) 67-73
19. Matsumoto K., et al. Gene for lysine tRNA1 may be a progenitor of the highly repetitive and transcribable sequences present in the salmon genome. Proc. Natl. Acad. Sci. U. S. A. 83 (1986) 3156-3160
20. Deragon, J.M. and Zhang, X. Short interspersed elements (sines) in plants: origin, classification and use as phylogenetic markers. Syst. Biol. (in press)
21. Gardner P.P., and Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5 (2004) 140. http://www.biomedcentral.com 10.1186/1471-2105-5-140
22. Reeder J., et al. Beyond Mfold: recent advances in RNA bioinformatics. J. Biotechnol. 124 (2006) 41-55
23. Jurka J. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8 (1998) 333-337
24. Churakov G., et al. A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus). Mol. Biol. Evol. 22 (2005) 886-893
25. Schmitz J., and Zischler H. A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates. Mol. Phylogenet. Evol. 28 (2003) 341-349
26. Lin Z., et al. Characterization of a SINE species from vicuna and its distribution in animal species including the family Camelidae. Mamm. Genome 12 (2001) 305-308
27. Caetano-Anollés G. Evolved RNA secondary structure and the rooting of the universal tree of life. J. Mol. Evol. 54 (2002) 333-345
28. Caetano-Anollés G. Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res. 30 (2002) 2575-2587
29. Maraia R., and Sarrowa J. Alu-family SINE RNA: interacting proteins and pathways of expression. In: Maraia R. (Ed). The Impact of Short Interspersed Elements (SINEs) on the Host Genome (1995), R.G. Landes, Springer 163-196
30. Morl M., and Marchfelder A. The final cut: the importance of tRNA 3′-end processing. EMBO Rep. 2 (2001) 17-20
31. Muddashetty R.S., et al. Poly(A)-binding protein is associated with neural BC1 and BC200 ribonucleoprotein particles. J. Mol. Biol. 321 (2002) 433-445
32. West N., et al. Shared protein components of SINE RNPs. J. Mol. Biol. 321 (2002) 423-432
33. Moran J., and Gilbert N. Mammalian LINE-1 retrotransposons and related elements. In: Craig N., et al. (Ed). Mobile DNA II (2002), ASM Press 836-869
34. Maran A., and Mathews M.B. Characterization of the double-stranded RNA implicated in the inhibition of protein synthesis in cells infected with a mutant adenovirus defective for VA RNA. Virology 164 (1988) 106-113
35. - RNA supports Burkitt's lymphoma growth through interleukin-10 induction. EMBO J. 19 (2000) 6742-6750
36. Doudna J.A., and Batey R.T. Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73 (2004) 539-557
37. Michels A.A., et al. Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/cyclin T) inhibitor. EMBO J. 23 (2004) 2608-2619
38. Kondrashov A.V., et al. Inhibitory effect of naked neural BC1 RNA or BC200 RNA on eukaryotic in vitro translation systems is reversed by poly(A)-binding protein (PABP). J. Mol. Biol. 353 (2005) 88-103
39. Wang H., et al. Dendritic BC1 RNA in translational control mechanisms. J. Cell Biol. 171 (2005) 811-821
40. Zalfa F., et al. Fragile X mental retardation protein (FMRP) binds specifically to the brain cytoplasmic RNAs BC1/BC200 via a novel RNA-binding motif. J. Biol. Chem. 280 (2005) 33403-33410
41. Zalfa F., et al. The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses. Cell 112 (2003) 317-327
42. van Zon A., et al. Multiple human vault RNAs. Expression and association with the vault complex. J. Biol. Chem. 276 (2001) 37715-37721
43. Allen T.A., et al. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11 (2004) 816-821
44. Espinoza C., et al. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 11 (2004) 822-829
45. Rubin C.M., et al. Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res. 30 (2002) 3253-3261
46. Schmid C.W. Does SINE evolution preclude Alu function?. Nucleic Acids Res. 26 (1998) 4541-4550
47. Williams B.R. PKR; a sentinel kinase for cellular stress. Oncogene 18 (1999) 6112-6120
48. Hasler J., and Strub K. Alu RNP and Alu RNA regulate translation initiation in vitro. Nucleic Acids Res. 34 (2006) 2374-2385
49. Pelissier T., et al. Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res. 32 (2004) 3957-3966
50. Ohshima K., and Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet. Genome Res. 110 (2005) 475-490
51. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 244 (1989) 48-52
52. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415