Transcriptome-wide discovery of circular RNAs in Archaea

Nucleic Acids Research

Volumn 40, Issue 7, 2012, Pages 3131-3142

  Danan, Miri ^a   Schwartz, Schraga ^a   Edelheit, Sarit ^a   Sorek, Rotem ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR RIBONUCLEIC ACID; RIBOSOME RNA; RNA; TRANSCRIPTOME; TRANSFER RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; BACTERIAL GENOME; CONTROLLED STUDY; HALOBACTERIUM SALINARUM; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA PROCESSING; SULFOLOBUS ACIDOCALDARIUS; SULFOLOBUS SOLFATARICUS;

GENE EXPRESSION PROFILING; INTRONS; RNA; RNA, ARCHAEAL; RNA, RIBOSOMAL; RNA, TRANSFER; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SULFOLOBUS ACIDOCALDARIUS; SULFOLOBUS SOLFATARICUS; TRANSCRIPTOME;

EID: 84860171056     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1009     Document Type: Article

References (51)

1. Kos, A., Dijkema, R., Arnberg, A.C., van der Meide, P.H. and Schellekens, H. (1986) The hepatitis delta (delta) virus possesses a circular RNA. Nature, 323, 558-560. (Pubitemid 16025382)
2. Flores, R., Hernandez, C., Martinez de Alba, A.E., Daros, J.A. and Di Serio, F. (2005) Viroids and viroid-host interactions. Annu. Rev. Phytopathol., 43, 117-139. (Pubitemid 41318867)
3. Sanger, H.L., Klotz, G., Riesner, D., Gross, H.J. and Kleinschmidt, A.K. (1976) Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl Acad. Sci. USA, 73, 3852-3856.
4. Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F. and Sekine, Y. (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science, 318, 450-453. (Pubitemid 47614530)
5. Nielsen, H., Fiskaa, T., Birgisdottir, A.B., Haugen, P., Einvik, C. and Johansen, S. (2003) The ability to form full-length intron RNA circles is a general property of nuclear group I introns. RNA, 9, 1464-1475. (Pubitemid 37463473)
6. Nielsen, H. and Johansen, S.D. (2009) Group I introns: moving in new directions. RNA Biol., 6, 375-383.
7. Vicens, Q. and Cech, T.R. (2009) A natural ribozyme with 30, 50 RNA ligase activity. Nat. Chem. Biol., 5, 97-99.
8. Hensgens, L.A., Arnberg, A.C., Roosendaal, E., van der Horst, G., van der Veen, R., van Ommen, G.J. and Grivell, L.A. (1983) Variation, transcription and circular RNAs of the mitochondrial gene for subunit I of cytochrome c oxidase. J. Mol. Biol., 164, 35-58. (Pubitemid 13123246)
9. Burd, C.E., Jeck, W.R., Liu, Y., Sanoff, H.K., Wang, Z. and Sharpless, N.E. (2010) Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet., 6, e1001233.
10. Capel, B., Swain, A., Nicolis, S., Hacker, A., Walter, M., Koopman, P., Goodfellow, P. and Lovell-Badge, R. (1993) Circular transcripts of the testis-determining gene Sry in adult mouse testis. Cell, 73, 1019-1030. (Pubitemid 23165616)
11. Cocquerelle, C., Mascrez, B., Hetuin, D. and Bailleul, B. (1993) Mis-splicing yields circular RNA molecules. FASEB J., 7, 155-160. (Pubitemid 23034027)
12. Halbreich, A., Pajot, P., Foucher, M., Grandchamp, C. and Slonimski, P. (1980) A pathway of cytochrome b mRNA processing in yeast mitochondria: specific splicing steps and an intron-derived circular DNA. Cell, 19, 321-329. (Pubitemid 10152879)
13. Lykke-Andersen, J., Aagaard, C., Semionenkov, M. and Garrett, R.A. (1997) Archaeal introns: splicing, intercellular mobility and evolution. Trends Biochem. Sci., 22, 326-331. (Pubitemid 27376265)
14. Salgia, S.R., Singh, S.K., Gurha, P. and Gupta, R. (2003) Two reactions of Haloferax volcanii RNA splicing enzymes: joining of exons and circularization of introns. RNA, 9, 319-330. (Pubitemid 36246171)
15. Kjems, J. and Garrett, R.A. (1991) Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing. Proc. Natl Acad. Sci. USA, 88, 439-443. (Pubitemid 21915480)
16. Singh, S.K., Gurha, P., Tran, E.J., Maxwell, E.S. and Gupta, R. (2004) Sequential 20-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J. Biol. Chem., 279, 47661-47671. (Pubitemid 39540912)
17. Clouet d'Orval, B., Bortolin, M.L., Gaspin, C. and Bachellerie, J.P. (2001) Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res., 29, 4518-4529. (Pubitemid 33095012)
18. Kjems, J. and Garrett, R.A. (1988) Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desulfurococcus mobilis. Cell, 54, 693-703.
19. Burggraf, S., Larsen, N., Woese, C.R. and Stetter, K.O. (1993) An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum. Proc. Natl Acad. Sci. USA, 90, 2547-2550. (Pubitemid 23078665)
20. Dalgaard, J.Z. and Garrett, R.A. (1992) Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum. Gene, 121, 103-110.
21. Tang, T.H., Rozhdestvensky, T.S., d'Orval, B.C., Bortolin, M.L., Huber, H., Charpentier, B., Branlant, C., Bachellerie, J.P., Brosius, J. and Huttenhofer, A. (2002) RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res., 30, 921-930. (Pubitemid 34679660)
22. Starostina, N.G., Marshburn, S., Johnson, L.S., Eddy, S.R., Terns, R.M. and Terns, M.P. (2004) Circular box C/D RNAs in Pyrococcus furiosus. Proc. Natl Acad. Sci. USA, 101, 14097-14101. (Pubitemid 39305036)
23. Clouet-d'Orval, B., Gaspin, C. and Mougin, A. (2005) Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. Biochimie, 87, 889-895. (Pubitemid 41297815)
24. Sorek, R. and Cossart, P. (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat. Rev. Genet., 11, 9-16.
25. Wurtzel, O., Sapra, R., Chen, F., Zhu, Y., Simmons, B.A. and Sorek, R. (2010) A single-base resolution map of an archaeal transcriptome. Genome Res., 20, 133-141.
26. Brock, T.D., Brock, K.M., Belly, R.T. and Weiss, R.L. (1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch. Mikrobiol., 84, 54-68.
27. Suzuki, H., Zuo, Y., Wang, J., Zhang, M.Q., Malhotra, A. and Mayeda, A. (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.
28. Cocquet, J., Chong, A., Zhang, G. and Veitia, R.A. (2006) Reverse transcriptase template switching and false alternative transcripts. Genomics, 88, 127-131. (Pubitemid 44183763)
29. Gilboa, E., Mitra, S.W., Goff, S. and Baltimore, D. (1979) A detailed model of reverse transcription and tests of crucial aspects. Cell, 18, 93-100. (Pubitemid 10228240)
30. Roy, S.W. and Irimia, M. (2008) When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis. Bioessays, 30, 601-605. (Pubitemid 351859416)
31. Haas, B.J., Gevers, D., Earl, A., Feldgarden, M., Ward, D.V., Giannokous, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E. et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res., 21, 494-504.
32. Vincent, H.A. and Deutscher, M.P. (2009) Insights into how RNase R degrades structured RNA: analysis of the nuclease domain. J. Mol. Biol., 387, 570-583.
33. Cheng, Z.F. and Deutscher, M.P. (2002) Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II. J. Biol. Chem., 277, 21624-21629. (Pubitemid 34952311)
34. Zago, M.A., Dennis, P.P. and Omer, A.D. (2005) The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Microbiol., 55, 1812-1828. (Pubitemid 40445215)
35. Sugahara, J., Kikuta, K., Fujishima, K., Yachie, N., Tomita, M. and Kanai, A. (2008) Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol. Biol. Evol., 25, 2709-2716.
36. Tang, T.H., Polacek, N., Zywicki, M., Huber, H., Brugger, K., Garrett, R., Bachellerie, J.P. and Huttenhofer, A. (2005) Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus. Mol. Microbiol., 55, 469-481. (Pubitemid 40179381)
37. Watanabe, Y., Yokobori, S., Inaba, T., Yamagishi, A., Oshima, T., Kawarabayasi, Y., Kikuchi, H. and Kita, K. (2002) Introns in protein-coding genes in Archaea. FEBS Lett., 510, 27-30. (Pubitemid 34084878)
38. Kiss, T. (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J., 20, 3617-3622. (Pubitemid 32691772)
39. Mackie, G.A. (1998) Ribonuclease E is a 50-end-dependent endonuclease. Nature, 395, 720-723.
40. Mackie, G.A. (2000) Stabilization of circular rpsT mRNA demonstrates the 50-end dependence of RNase E action in vivo. J. Biol. Chem., 275, 25069-25072.
41. Puttaraju, M. and Been, M.D. (1995) Generation of nuclease resistant circular RNA decoys for HIV-Tat and HIV-Rev by autocatalytic splicing. Nucleic Acids Symp. Ser., 33, 152-155.
42. Andersson, A.F., Lundgren, M., Eriksson, S., Rosenlund, M., Bernander, R. and Nilsson, P. (2006) Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol., 7, R99.
43. Arn, E.A. and Abelson, J.N. (1996) The 20-50 RNA ligase of Escherichia coli. Purification, cloning, and genomic disruption. J. Biol. Chem., 271, 31145-31153.
44. Kato, M., Shirouzu, M., Terada, T., Yamaguchi, H., Murayama, K., Sakai, H., Kuramitsu, S. and Yokoyama, S. (2003) Crystal structure of the 20-50 RNA ligase from Thermus thermophilus HB8. J. Mol. Biol., 329, 903-911. (Pubitemid 36683148)
45. Brooks, M.A., Meslet-Cladiere, L., Graille, M., Kuhn, J., Blondeau, K., Myllykallio, H. and van Tilbeurgh, H. (2008) The structure of an archaeal homodimeric ligase which has RNA circularization activity. Protein Sci., 17, 1336-1345.
46. Englert, M., Sheppard, K., Aslanian, A., Yates, J.R. III and Soll, D. (2011) Archaeal 30-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. Proc. Natl Acad. Sci. USA, 108, 1290-1295.
47. Berquist, B.R., Mü ller, J.A. and DasSarma, S. (2006) 27 Genetic Systems for Halophilic Archaea. In: Rainey, F.A. and Aharon, O. (eds), Methods Microbiology. Academic Press, Jerusalem, pp. 649-680.
48. Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R. and Hannon, G.J. (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat. Methods., 5, 679-682.
49. Omer, A.D., Lowe, T.M., Russell, A.G., Ebhardt, H., Eddy, S.R. and Dennis, P.P. (2000) Homologs of small nucleolar RNAs in Archaea. Science, 288, 517-522. (Pubitemid 30236034)
50. Pearson, W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.
51. She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M.J., Chan-Weiher, C.C., Clausen, I.G., Curtis, B.A., De Moors, A. et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl Acad. Sci. USA, 98, 7835-7840. (Pubitemid 32642647)