Atypical RNAs in the coelacanth transcriptome

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 322, Issue 6, 2014, Pages 342-351

  Nitsche, Anne ^a   Doose, Gero ^a   Tafer, Hakim ^b   Robinson, Mark ^c   Saha, Nil Ratan ^c   Gerdol, Marco ^d   Canapa, Adriana ^e   Hoffmann, Steve ^a   Amemiya, Chris T ^c,f   Stadler, Peter F ^a,b,g,h,i,j  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

^c BENAROYA RESEARCH INSTITUTE   (United States)

^d UNIVERSITY OF TRIESTE   (Italy)

^e UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

^f UNIVERSITY OF WASHINGTON   (United States)

^g MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^h FRAUNHOFER INSTITUTE FOR CELL THERAPY AND IMMUNOLOGY   (Germany)

ⁱ UNIVERSITY OF COPENHAGEN   (Denmark)

^j SANTA FE INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COELACANTHIDAE; MAMMALIA;

LONG UNTRANSLATED RNA; RNA; TRANSCRIPTOME;

ANIMAL; FISH; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA SPLICING; SEQUENCE ANALYSIS;

ANIMALS; BASE SEQUENCE; FISHES; MOLECULAR SEQUENCE DATA; RNA; RNA SPLICING; RNA, LONG NONCODING; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84905565502     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.22542     Document Type: Article

References (48)

1. Al-Balool HH, Weber D, Liu Y, et al. 2011. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Res 21:1788-1799.
2. Altschul SF, Madden TL, Schäffer AA, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
3. Amemiya CT, Alföldi J, Lee AP, et al. 2013. The african coelacanth genome provides insights into tetrapod evolution. Nature 496:311-316.
4. Bailey TL, Elkan C. 1995. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach Learn 21:51-80.
5. Burd CE, Jeck WR, Liu Y, et al. 2010. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 6:e1001233.
6. Caldas C, So CW, MacGregor A, et al. 1998. Exon scrambling of MLL transcripts occur commonly and mimic partial genomic duplication of the gene. Gene 208:167-176.
7. Caudevilla C, Serra D, Miliar A, et al. 1998. Natural trans-splicing in carnitine octanoyltransferase pre-mRNAs in rat liver. Proc Natl Acad Sci USA 95:12185-12190.
8. Cocquet J, Chong A, Zhang G, Veitia RA. 2006. Reverse transcriptase template switching and false alternative transcripts. Genomics 88:127-131.
9. De Pristo MA, Banks E, Poplin R, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498.
10. Dixon RJ, Eperon IC, Hall L, Samani NJ. 2005. A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species. Nucleic Acids Res 33:5904-5913.
11. Djebali S, Lagarde J, Kapranov P, et al. 2012. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS ONE 7:e28213.
12. Dorn R, Reuter G, Loewendorf A. 2001. Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in drosophila. Proc Natl Acad Sci USA 98:9724-9729.
13. Frantz SA, Thiara AS, Lodwick D, et al. 1999. Exon repetition in mRNA. Proc Natl Acad Sci USA 96:5400-5405.
14. Frenkel-Morgenstern M, Valencia A. 2012. Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics 28:i67-i74.
15. Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, et al. 2012. Chimeras taking shape: potential functions of proteins encoded by chimeric rna transcripts. Genome Res 22:1231-1242.
16. Frenkel-Morgenstern M, Gorohovski A, Lacroix V, et al. 2013. ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res 41:D142-D151.
17. Gingeras TR. 2011. Implications of chimaeric non-co-linear transcripts. Nature 461:206-211.
18. Guttman M, Amit I, Garber M, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227.
19. Hansen TB, Jensen TI, Clausen BH, et al. 2013. Natural RNA circles function as efficient microRNA sponges. Nature 495:384-388.
20. Hoffmann S, Otto C, Kurtz S, et al. 2009. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 5:e1000502.
21. Houseley J, Tollervey D. 2010. Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS ONE 5:e12271.
22. Jeck WR, Sorrentino JA, Wang K, et al. 2013. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19:141-157.
23. Lab H. 2011. FASTX Toolkit. Available online at: http://hannonlab.cshl.edu/fastx_toolkit/ [accessed 01/02/2013].
24. Labrador M, Corces VG. 2003. Extensive exon reshuffling over evolutionary time coupled to trans-splicing in Drosophila. Genome Res 13:2220-2228.
25. Li BL, Li XL, Duan ZJ, et al. 1999. Human acyl-CoA:cholesterol acyltransferase-1 (ACAT-1) gene organization and evidence that the 4.3-kilobase ACAT-1 mRNA is produced from two different chromosomes. J Biol Chem 274:11060-11071.
26. Li X, Zhao L, Jiang H, Wang W. 2009. Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. J Mol Evol 68:56-65.
27. Ma L, Yang S, Zhao W, et al. 2012. Identification and analysis of pig chimeric mRNAs using RNA sequencing data. BMC Genomics 13:429.
28. Marques AC, Ponting CP. 2009. Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol 10:R124.
29. Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 17(1). Available online at: http://journal.embnet.org/index.php/embnetjournal/article/view/200
30. McManus CJ, Duff MO, Eipper-Mains J, Graveley BR. 2010. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci USA 107:12975-12979.
31. Memczak S, Jens M, Elefsinioti A, et al. 2013. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333-338.
32. Pallavicini A, Canapa A, Barucca M, et al. 2013. Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. BMC Genomics 14:538.
33. Pang KC, Frith MC, Mattick JS. 2006. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22:1-5.
34. Ponjavic J, Ponting CP, Lunter G. 2007. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17:556-565.
35. Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England) 26:841-842.
36. Rigatti R, Jia JH, Samani NJ, Eperon IC. 2004. Exon repetition: a major pathway for processing mRNA of some genes is allele-specific. Nucleic Acids Res 32:441-446.
37. Roberts A, Pimentel H, Trapnell C, Pachter L. 2011. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (Oxford, England) 27:2325-2329.
38. Roy SW, Irimia M. 2008. When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis. Bioessays 30:601-605.
39. Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. 2012. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7:e30733.
40. Surono A, Takeshima Y, Wibawa T, et al. 1999. Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing. Hum Mol Genet 8:493-500.
41. Suzuki H, Zuo Y, Wang J, et al. 2006. Characterization of rnase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res 34:e63.
42. Trapnell C, Roberts A, Goff L, Pertea G, Kim D. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562-578.
43. Viles KD, Sullenger BA. 2008. Proximity-dependent and proximity-independent trans-splicing in mammalian cells. RNA 14:1081-1094.
44. Washietl S, Findeiss S, Müller SA, et al. 2011. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA 17:578-594.
45. Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11:377-394.
46. Young RS, Marques AC, Tibbit C, et al. 2012. Identification and properties of 1, 119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol 4:427-442.
47. Zaphiropoulos PG. 1996. Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. Proc Natl Acad Sci USA 93:6536-6541.
48. Zaphiropoulos PG. 2011. Trans-splicing in higher eukaryotes: implications for cancer development? Front Genet 2:92.