Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts

Genomics, Proteomics and Bioinformatics

Volumn 14, Issue 4, 2016, Pages 216-223

  Jakobi, Tobias ^a,b   Czaja Hasse, Lisa F ^c   Reinhardt, Richard ^c   Dieterich, Christoph ^a,b  

^a UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^b DZHK GERMAN CENTRE FOR CARDIOVASCULAR RESEARCH   (Germany)

^c Max Planck Genome Centre Cologne   (Germany)

Author keywords

Cardiomyopathy; Cardiovascular disease; circSeq; Circular RNA; Computational cardiology

Indexed keywords

CIRCULAR RNA; HECT DOMAIN CONTAINING E3 UBIQUITIN PROTEIN LIGASE 1; PHOSPHOPROTEIN PHOSPHATASE 2; PROTEIN PHOSPHATASE 2 REGULATORY SUBUNIT B PROTEIN; RIBONUCLEASE; RIBONUCLEASE R; RNA; RYANODINE RECEPTOR 2; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG; EXORIBONUCLEASE; RNA, CIRCULAR;

ADULT; ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; CONGESTIVE CARDIOMYOPATHY; CONTROLLED STUDY; EXON; GENE EXPRESSION; GENE LOCUS; HEART; HEART RIGHT VENTRICLE DYSPLASIA; HYPERTROPHIC CARDIOMYOPATHY; INTRON; LETTER; MOUSE; NONHUMAN; RNA SEQUENCE; RNA STRUCTURE; ANIMAL; CARDIAC MUSCLE; CARDIOVASCULAR DISEASE; CHEMISTRY; COMPUTER INTERFACE; GENETICS; INTERNET; METABOLISM; PATHOLOGY; RNA SPLICING; SEQUENCE ANALYSIS;

ANIMALS; CARDIOVASCULAR DISEASES; EXORIBONUCLEASES; INTERNET; MICE; MYOCARDIUM; RNA; RNA SPLICING; SEQUENCE ANALYSIS, RNA; USER-COMPUTER INTERFACE;

EID: 84973652333     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2016.02.003     Document Type: Letter

References (24)

1. [1] Nigro, J.M., Cho, K.R., Fearon, E.R., Kern, S.E., Ruppert, J.M., Oliner, J.D., et al. Scrambled exons. Cell 64 (1991), 607–613.
2. [2] Hansen, T.B., Jensen, T.I., Clausen, B.H., Bramsen, J.B., Finsen, B., Damgaard, C.K., et al. Natural RNA circles function as efficient microRNA sponges. Nature 495 (2013), 384–388.
3. [3] Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495 (2013), 333–338.
4. [4] Li, Z., Huang, C., Bao, C., Chen, L., Lin, M., Wang, X., et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 22 (2015), 256–264.
5. [5] Jeck, W.R., Sharpless, N.E., Detecting and characterizing circular RNAs. Nat Biotechnol 32 (2014), 453–461.
6. [6] Lasda, E., Parker, R., Circular RNAs: diversity of form and function. RNA, 2014, 1829–1842.
7. [7] Jeck, W.R., Sorrentino, J.A., Wang, K., Slevin, M.K., Burd, C.E., Liu, J., et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19 (2013), 141–157.
8. [8] Chen, I., Chen, C.Y., Chuang, T.J., Biogenesis, identification, and function of exonic circular RNAs. Wiley Interdiscip Rev RNA 6 (2015), 563–579.
9. [9] Ivanov, A., Memczak, S., Wyler, E., Torti, F., Porath, H.T., Orejuela, M.R., et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Rep 10 (2015), 170–177.
10. [10] Cheng, J., Metge, F., Dieterich, C., Specific identification and quantification of circular RNAs from sequencing data. Bioinformatics 32 (2016), 1094–1096.
11. [11] Boeckel, J.N., Jaé, N., Heumüller, A.W., Chen, W., Boon, R.A., Stellos, K., et al. Identification and characterization of hypoxia-regulated endothelial circular RNA. Circ Res 117 (2015), 884–890.
12. [12] Salzman, J., Chen, R.E., Olsen, M.N., Wang, P.L., Brown, P.O., Cell-type specific features of circular RNA expression. PLoS Genet, 9, 2013, e1003777.
13. [13] Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., et al. The human genome browser at UCSC. Genome Res 12 (2002), 996–1006.
14. [14] Wellcome Trust Case Control Consortium, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447 (2007), 661–678.
15. [15] Anderson E, Khvorova A, Seto AG, Baskerville S, Leinwand L, Sullivan KG. Identification of miRNA profiles that are diagnostic of hypertrophic cardiomyopathy. 2010; US Patent US20110160285 A1.
16. [16] Zhou X, Song G, Gan X, Li C, Yang N, Zheng F. Human PPP2R3A genetic mutation and application thereof. 2012; China Patent CN102443630A.
17. [17] Domarkiene, I., Pranculis, A., Germanas, Š., Jakaitiene, A., Vitkus, D., Dženkevičiute, V., et al. Rtn4 and Fbxl17 genes are associated with coronary heart disease in genome-wide association analysis of Lithuanian families. Balk J Med Genet 16 (2013), 17–22.
18. [18] Willer, C.J., Schmidt, E.M., Sengupta, S., Peloso, G.M., Gustafsson, S., Kanoni, S., et al. Discovery and refinement of loci associated with lipid levels. Nat Genet 45 (2013), 1274–1283.
19. [19] Deng, X., Sabino, E.C., Cunha-Neto, E., Ribeiro, A.L., Ianni, B., Mady, C., et al. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. PLoS One, 8, 2013, e79629.
20. [20] Muntoni, F., Torelli, S., Ferlini, A., Dystrophin and mutations: one gene, several proteins, multiple phenotypes. Lancet Neurol 2 (2003), 731–740.
21. [21] Herman, D.S., Lam, L., Taylor, M.R., Wang, L., Teekakirikul, P., Christodoulou, D., et al. Truncations of titin causing dilated cardiomyopathy. N Engl J Med 366 (2012), 619–628.
22. [22] Kanehisa, M., Goto, S., KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28 (2000), 27–30.
23. [23] Dodt, M., Roehr, J.T., Ahmed, R., Dieterich, C., FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms. Biology (Basel) 1 (2012), 895–905.
24. [24] Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29 (2013), 15–21.