The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs

RNA

Volumn 22, Issue 2, 2016, Pages 254-264

  Kim, Eugene Z ^a   Wespiser, Adam R ^a   Caffrey, Daniel R ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Alu; LincRNA; LncRNA; Noncoding; RNA

Indexed keywords

COMPLEMENTARY RNA; LONG UNTRANSLATED RNA; MESSENGER RNA; UNTRANSLATED RNA; 3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION;

ALU SEQUENCE; ARTICLE; CHROMOSOME; CHROMOSOME 17; CHROMOSOME 19; CONSENSUS SEQUENCE; EXON; GENE DUPLICATION; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; 3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BIOLOGY; CHEMISTRY; GENETICS; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; PROCEDURES;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ALU ELEMENTS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; EXONS; GENOME, HUMAN; HUMANS; RNA, LONG NONCODING;

EID: 84956823188     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.048280.114     Document Type: Article

References (47)

1. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. 2011. lncRNAdb: A reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-D151.
2. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet 3: 370-379.
3. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Series B Methodol 57: 289-300.
4. Berger A, Strub K. 2010. Multiple roles of Alu-related noncoding RNAs. In Long non-coding RNAs of progress in molecular and subcellular biology (ed. Ugarkovic D), Vol. 51, pp. 119-146. Springer, Berlin, Heidelberg.
5. Bracken AP, Helin K. 2009. Polycomb group proteins: Navigators of lineage pathways led astray in cancer. Nat Rev Cancer 9: 773-784.
6. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, et al. 2013. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341: 789-792.
7. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, et al. 2012. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491: 1-6.
8. Chang DY, Hsu K, Maraia RJ. 1996. Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells. Nucleic Acids Res 24: 4165-4170.
9. Chen C, Ara T, Gautheret D. 2009. Using Alu elements as polyadenylation sites: A case of retroposon exaptation. Mol Biol Evol 26: 327-334.
10. de Souza FSJ, Franchini LF, Rubinstein M. 2013. Exaptation of transposable elements into novel cis-regulatory elements: Is the evidence always strong? Mol Biol Evol 30: 1239-1251.
11. Deininger P. 2011. Alu elements: Know the SINEs. Genome Biol 12: 236.
12. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22: 1775-1789.
13. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. 2012. Landscape of transcription in human cells. Nature 489: 101-108.
14. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, et al. 2011. Ensembl 2012. Nucleic Acids Res 40(Database issue): D84-D90.
15. Gong C, Maquat LE. 2011. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature 470: 284-288.
16. Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, et al. 2004. The DNA sequence and biology of human chromosome 19. Nature 428: 529-535.
17. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
18. Han SP, Tang YH, Smith R. 2010. Functional diversity of the hnRNPs: Past, present and perspectives. Biochem J 430: 379-392.
19. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al. 2012. GENCODE: The reference human genome annotation for the ENCODE project. Genome Res 22: 1760-1774.
20. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419.
21. Ihaka R, Gentleman R. 1996. R: A language for data analysis and graphics. J Comput Graph Stat 5: 299-314.
22. Johnson R, Guigo R. 2014. The RIDL hypothesis: Transposable elements as functional domains of long noncoding RNAs. RNA 20: 959-976.
23. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
24. Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. 2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 9: E1003470.
25. Kelley D, Rinn J. 2012. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 13: R107.
26. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci 106: 11667-11672.
27. Kouzarides T. 2007. Chromatin modifications and their function. Cell 128: 693-705.
28. Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Võsa U, et al. 2013. Human disease-Associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 9: E1003201.
29. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
30. 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.
31. Li TH, SchmidCW. 2004. Alu's dimeric consensus sequence destabilizes its transcripts. Gene 324: 191-200.
32. Lin L, Jiang P, Shen S, Sato S, Davidson BL, Xing Y. 2009. Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes. Hum Mol Genet 18: 2204-2214.
33. MakalowskiW, Mitchell GA, Labuda D. 1994. Alu sequences in the coding regions of mRNA: A source of protein variability. Trends Genet 10: 188-193.
34. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. 2008. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci 105: 716-721.
35. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. 2014. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640.
36. Ricci EP, Kucukural A, Cenik C, Mercier BC, Singh G, Heyer EE, Ashar-Patel A, Peng L, Moore MJ. 2000. Staufen1 senses overall transcript secondary structure to regulate translation. Nat Struct Mol Biol 21: 26-35.
37. Rinn JL, Chang HY. 2012. Genome regulation by long noncoding RNAs. Annu Rev Biochem 81: 145-166.
38. Sarrowa J, Chang DY, Maraia RJ. 1997. The decline in human Alu retroposition was accompanied by an asymmetric decrease in SRP9/14 binding to dimeric Alu RNA and increased expression of small cytoplasmic Alu RNA. Mol Cell Biol 17: 1144-1151.
39. Sinnett D, Richer C, Deragon JM, Labuda D. 1991. Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units. J Biol Chem 266: 8675-8678.
40. Smit AFA. RepeatMasker. http://www.repeatmasker.org/
41. Sorek R, Ast G, Graur D. 2002. Alu-containing exons are alternatively spliced. Genome Res 12: 1060-1067.
42. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, et al. 2010. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39: 925-938.
43. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. 2009. EnsemblCompara GeneTrees: Complete, duplication-Aware phylogenetic trees in vertebrates. Genome Res 19: 327-335.
44. Ward LD, Kellis M. 2012. Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol 30: 1095-1106.
45. Washietl S, Kellis M, Garber M. 2014. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res 24: 616-628.
46. Yang Y, Zhou X, Jin Y. 2013. ADAR-mediated RNA editing in non-coding RNA sequences. Sci China Life Sci 56: 944-952.
47. Yulug IG, Yulug A, Fisher EM. 1995. The frequency and position of Alu repeats in cDNAs, as determined by database searching. Genomics 27: 544-548.