Intronic hammerhead ribozymes in mRNA biogenesis

Biological Chemistry

Volumn 393, Issue 11, 2012, Pages 1317-1326

  Garcia Robles, Inmaculada ^a   Sanchez Navarro, Jesus ^a   Pena, Marcos De La ^a  

^a Ciudad Politécnica de la Innovación   (Spain)

Author keywords

Alternative splicing; Amniotes; Retrotransposon; RNA self cleavage

Indexed keywords

HAMMERHEAD RIBOZYME; MESSENGER RNA;

BIOGENESIS; BIOINFORMATICS; BIOSYNTHESIS; FISH; GENOME; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVIEW; RNA SPLICING; TURTLE; VERTEBRATE;

ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; RNA SPLICING; RNA, CATALYTIC; RNA, MESSENGER;

AMNIOTA; AVES; COELACANTHIDAE; EUKARYOTA; MAMMALIA; REPTILIA; TESTUDINES; VERTEBRATA;

EID: 84869406789     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/hsz-2012-0223     Document Type: Review

References (43)

1. Bejerano, G., Lowe, C.B., Ahituv, N., King, B., Siepel, A., Salama, S.R., Rubin, E.M., Kent, W.J., and Haussler, D. (2006). A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441, 87-90.
2. Canny, M.D., Jucker, F.M., and Pardi, A. (2007). Efficient ligation of the Schistosoma hammerhead ribozyme. Biochemistry 46, 3826-3834.
3. Chadalavada, D.M., Gratton, E.A., and Bevilacqua, P.C. (2010). The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry 49, 5321-5330.
4. Chi, Y.I., Martick, M., Lares, M., Kim, R., Scott, W.G., and Kim, S.H. (2008). Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol. 6, e234.
5. Daros, J.A. and Flores, R. (1995). Identification of a retroviroid-like element from plants. Proc. Natl. Acad. Sci. USA 92, 6856-6860. De la Pena, M. and Garcia-Robles, I. (2010a). Intronic hammerhead ribozymes are ultraconserved in the human genome. EMBO Rep. 11, 711-716.
6. De la Pena, M. and Garcia-Robles, I. (2010b). Ubiquitous presence of the hammerhead ribozyme motif along the tree of life. RNA 16, 1943-1950.
7. De la Pena, M., Gago, S., and Flores, R. (2003). Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J. 22, 5561-5570.
8. Eickbush, D.G. and Eickbush, T.H. (2010). R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript. Mol. Cell. Biol. 30, 3142-3150.
9. Epstein, L.M. and Coats, S.R. (1991). Tissue-specific permutations of self-cleaving newt satellite-2 transcripts. Gene 107, 213-218.
10. Epstein, L.M. and Gall, J.G. (1987). Self-cleaving transcripts of satellite DNA from the newt. Cell 48, 535-543.
11. Ferbeyre, G., Smith, J.M., and Cedergren, R. (1998). Schistosome satellite DNA encodes active hammerhead ribozymes. Mol. Cell. Biol. 18, 3880-3888.
12. Ferre-D' Amare, A.R. and Scott, W.G. (2010). Small self-cleaving ribozymes. Cold Spring Harb. Perspect. Biol. 2, a003574.
13. Flores, R., Delgado, S., Gas, M.E., Carbonell, A., Molina, D., Gago, S., and De la Pena, M. (2004). Viroids: the minimal non-coding RNAs with autonomous replication. FEBS Lett. 567, 42-48.
14. Forster, A.C., Davies, C., Sheldon, C.C., Jeffries, A.C., and Symons, R.H. (1988). Self-cleaving viroid and newt RNAs may only be active as dimers. Nature 334, 265-267.
15. Garrett, T.A., Pabon-Pena, L.M., Gokaldas, N., and Epstein, L.M. (1996). Novel requirements in peripheral structures of the extended satellite 2 hammerhead. RNA 2, 699-706.
16. Gould, S.J. and Vrba, E.S. (1982). Exaptation; a missing term in the science of form. Paleobiology 8, 4-15.
17. Gromak, N., Talotti, G., Proudfoot, N.J., and Pagani, F. (2008). Modulating alternative splicing by cotranscriptional cleavage of nascent intronic RNA. RNA 14, 359-366.
18. Hammann, C., Luptak, A., Perreault, J., and de la Pena, M. (2012). The ubiquitous hammerhead ribozyme. RNA 18, 871-885.
19. Jimenez, R.M., Delwart, E., and Luptak, A. (2011). Structurebased search reveals hammerhead ribozymes in the human microbiome. J. Biol. Chem. 286, 7737-7743.
20. Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S.D. (2003). Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10, 708-712.
21. Le Hir, H., Nott, A., and Moore, M.J. (2003). How introns influence and enhance eukaryotic gene expression. Trends Biochem. Sci. 28, 215-220.
22. Leipzig, J., Pevzner, P., and Heber, S. (2004). The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 32, 3977-3983.
23. Luzi, E., Eckstein, F., and Barsacchi, G. (1997). The newt ribozyme is part of a riboprotein complex. Proc. Natl. Acad. Sci. USA 94, 9711-9716.
24. Martick, M. and Scott, W.G. (2006). Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309-320.
25. Martick, M., Horan, L.H., Noller, H.F., and Scott, W.G. (2008). A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. Nature 454, 899-902.
26. Oh, J., Takahashi, R., Kondo, S., Mizoguchi, A., Adachi, E., Sasahara, R.M., Nishimura, S., Imamura, Y., Kitayama, H., Alexander, D.B., et al. (2001). The membrane-anchored MMP inhibitor RECK is a key regulator of extracellular matrix integrity and angiogenesis. Cell 107, 789-800.
27. Okada, N., Sasaki, T., Shimogori, T., and Nishihara, H. (2010). Emergence of mammals by emergency: exaptation. Genes Cells 15, 801-812.
28. Pan, Q., Shai, O., Lee, L.J., Frey, B.J., and Blencowe, B.J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415.
29. Pastor, T., Dal Mas, A., Talotti, G., Bussani, E., and Pagani, F. (2011). Intron cleavage affects processing of alternatively spliced transcripts. RNA 17, 1604-1613.
30. Perreault, J., Weinberg, Z., Roth, A., Popescu, O., Chartrand, P., Ferbeyre, G., and Breaker, R.R. (2011). Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput. Biol. 7, e1002031.
31. Prody, G.A., Bakos, J.T., Buzayan, J.M., Schneider, I.R., and Bruening, G. (1986). Autolytic processing of dimeric plant virus satellite RNA. Science 231, 1577-1580.
32. Rojas, A.A., Vazquez-Tello, A., Ferbeyre, G., Venanzetti, F., Bachmann, L., Paquin, B., Sbordoni, V., and Cedergren, R. (2000). Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets. Nucleic Acids Res. 28, 4037-4043.
33. Ruminski, D.J., Webb, C.H., Riccitelli, N.J., and Luptak, A. (2011). Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes. J. Biol. Chem. 286, 41286-41295.
34. Salehi-Ashtiani, K., Luptak, A., Litovchick, A., and Szostak, J.W. (2006). A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 313, 1788-1792.
35. Scott, W.G., Martick, M., and Chi, Y.I. (2009). Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. Biochim. Biophys. Acta 1789, 634-641.
36. Seehafer, C., Kalweit, A., Steger, G., Graf, S., and Hammann, C. (2011). From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA 17, 21-26.
37. Shepotinovskaya, I. and Uhlenbeck, O.C. (2010). Enhanced product stability in the hammerhead ribozyme. Biochemistry 49, 4494-4500.
38. Takahashi, C., Sheng, Z., Horan, T.P., Kitayama, H., Maki, M., Hitomi, K., Kitaura, Y., Takai, S., Sasahara, R.M., Horimoto, A., et al. (1998). Regulation of matrix metalloproteinase-9 and inhibition of tumor invasion by the membrane-anchored glycoprotein RECK. Proc. Natl. Acad. Sci. USA 95, 13221-13226.
39. Vogler, C., Spalek, K., Aerni, A., Demougin, P., Muller, A., Huynh, K.D., Papassotiropoulos, A., and de Quervain, D.J. (2009). CPEB3 is associated with human episodic memory. Front. Behav. Neurosci. 3, 4.
40. Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., and Burge, C.B. (2008). Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476.
41. Webb, C.H. and Luptak, A. (2011). HDV-like self-cleaving ribozymes. RNA Biol. 8, 719-727.
42. Webb, C.H., Riccitelli, N.J., Ruminski, D.J., and Luptak, A. (2009). Widespread occurrence of self-cleaving ribozymes. Science 326, 953.
43. Zardoya, R. and Meyer, A. (1997). The complete DNA sequence of the mitochondrial genome of a'living fossil', the coelacanth ( Latimeria chalumnae ). Genetics 146, 995-1010.