Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

Nucleic Acids Research

Volumn 40, Issue 7, 2012, Pages

  Zhuang, Fanglei ^a   Fuchs, Ryan T ^a   Sun, Zhiyi ^a   Zheng, Yu ^a   Robb, G Brett ^a  

^a NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA ADAPTER; MICRORNA; NUCLEOTIDE; RNA; RNA LIGASE; T4 RNA LIGASE; UNCLASSIFIED DRUG;

3' ADAPTER LIGATION; ARTICLE; CHEMICAL REACTION; HIGH THROUGHPUT SEQUENCING; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE;

ANIMALS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICE; MICRORNAS; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA; RNA FOLDING; RNA LIGASE (ATP); SEQUENCE ANALYSIS, RNA; VIRAL PROTEINS;

EID: 84860198538     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1263     Document Type: Article

References (46)

1. Silber, R., Malathi, V.G. and Hurwitz, J. (1972) Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl Acad. Sci. USA, 69, 3009-3013.
2. Ho, C.K. and Shuman, S. (2002) Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc. Natl Acad. Sci. USA, 99, 12709-12714.
3. Cranston, J.W., Silber, R., Malathi, V.G. and Hurwitz, J. (1974) Studies on ribonucleic acid ligase. Characterization of an adenosine triphosphate-inorganic pyrophosphate exchange reaction and demonstration of an enzyme-adenylate complex with T4 bacteriophage-induced enzyme. J. Biol. Chem., 249, 7447-7456.
4. Sugino, A., Snoper, T.J. and Cozzarelli, N.R. (1977) Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates. J. Biol. Chem., 252, 1732-1738.
5. Amitsur, M., Levitz, R. and Kaufmann, G. (1987) Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J., 6, 2499-2503.
6. Levitz, R., Chapman, D., Amitsur, M., Green, R., Snyder, L. and Kaufmann, G. (1990) The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. EMBO J., 9, 1383-1389.
7. Shuman, S. and Lima, C.D. (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr. Opin. Struct. Biol., 14, 757-764. (Pubitemid 39592587)
8. Liu, X. and Gorovsky, M.A. (1993) Mapping the 50 and 30 ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Nucleic Acids Res., 21, 4954-4960. (Pubitemid 23330173)
9. Maruyama, K. and Sugano, S. (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene, 138, 171-174. (Pubitemid 24087571)
10. Zhang, X.H. and Chiang, V.L. (1996) Single-stranded DNA ligation by T4 RNA ligase for PCR cloning of 50-noncoding fragments and coding sequence of a specific gene. Nucleic Acids Res., 24, 990-991.
11. Tessier, D.C., Brousseau, R. and Vernet, T. (1986) Ligation of single-stranded oligodeoxyribonucleotides by T4 RNA ligase. Anal. Biochem., 158, 171-178. (Pubitemid 17184474)
12. Kinoshita, Y., Nishigaki, K. and Husimi, Y. (1997) Fluorescence-, isotope-or biotin-labeling of the 50-end of single-stranded DNA/RNA using T4 RNA ligase. Nucleic Acids Res., 25, 3747-3748. (Pubitemid 27390199)
13. Lau, N.C., Lim, L.P., Weinstein, E.G. and Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862. (Pubitemid 33032104)
14. Du, T. and Zamore, P.D. (2005) microPrimer: the biogenesis and function of microRNA. Development, 132, 4645-4652. (Pubitemid 41685275)
15. van den Berg, A., Mols, J. and Han, J. (2008) RISC-target interaction: cleavage and translational suppression. Biochim. Biophys. Acta, 1779, 668-677.
16. Matranga, C. and Zamore, P.D. (2007) Small silencing RNAs. Curr. Biol., 17, R789-793. (Pubitemid 47380389)
17. Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
18. Chang, T.C. and Mendell, J.T. (2007) microRNAs in vertebrate physiology and human disease. Annu. Rev. Genomics Hum. Genet., 8, 215-239.
19. Berezikov, E., Thuemmler, F., van Laake, L.W., Kondova, I., Bontrop, R., Cuppen, E. and Plasterk, R.H. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat. Genet., 38, 1375-1377. (Pubitemid 44837558)
20. Ruby, J.G., Jan, C., Player, C., Axtell, M.J., Lee, W., Nusbaum, C., Ge, H. and Bartel, D.P. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127, 1193-1207. (Pubitemid 44894525)
21. Morin, R.D., O'Connor, M.D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.L., Zhao, Y., McDonald, H., Zeng, T., Hirst, M. et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res., 18, 610-621. (Pubitemid 351482785)
22. Berezikov, E., Robine, N., Samsonova, A., Westholm, J.O., Naqvi, A., Hung, J.H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R. et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res., 21, 203-215.
23. Stoeckius, M., Maaskola, J., Colombo, T., Rahn, H.P., Friedlander, M.R., Li, N., Chen, W., Piano, F. and Rajewsky, N. (2009) Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat. Methods, 6, 745-751.
24. Linsen, S.E., de Wit, E., Janssens, G., Heater, S., Chapman, L., Parkin, R.K., Fritz, B., Wyman, S.K., de Bruijn, E., Voest, E.E. et al. (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat. Methods, 6, 474-476.
25. Hafner, M., Renwick, N., Brown, M., Mihailovic, A., Holoch, D., Lin, C., Pena, J.T., Nusbaum, J.D., Morozov, P., Ludwig, J. et al. (2011) RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA, 17, 1697-1712.
26. Jayaprakash, A.D., Jabado, O., Brown, B.D. and Sachidanandam, R. (2011) Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res., September 21 (doi:10.1093/nar/ gkr693; epub ahead of print).
27. Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F.A., van Dyk, L.F., Ho, C.K., Shuman, S., Chien, M. et al. (2005) Identification of microRNAs of the herpesvirus family. Nat. Methods, 2, 269-276. (Pubitemid 41131008)
28. Viollet, S., Fuchs, R.T., Munafo, D.B., Zhuang, F. and Robb, G.B. (2011) T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis. BMC Biotechnol., 11, 72.
29. Rothberg, J.M., Hinz, W., Rearick, T.M., Schultz, J., Mileski, W., Davey, M., Leamon, J.H., Johnson, K., Milgrew, M.J., Edwards, M. et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475, 348-352.
30. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-158. (Pubitemid 351149713)
31. Bindereif, A., Schon, A. and Westhof, E. (2009) Handbook of RNA Biochemistry: Stduent Edition. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
32. Zhelkovsky, A.M. and McReynolds, L.A. (2011) Simple and efficient synthesis of 5' pre-adenylated DNA using thermostable RNA ligase. Nucleic Acids Res., 39, e117.
33. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
34. Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., Chapter 19, Unit 19 10 11-21.
35. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455. (Pubitemid 41400913)
36. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, S., Tacker, M. and Schuster. (1994) Fast folding and comparison of RNA secondary sStructures. Monatshefte f. Chemie, 125, 22.
37. Bernhart, S.H., Tafer, H., Muckstein, U., Flamm, C., Stadler, P.F. and Hofacker, I.L. (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol., 1, 3.
38. Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940. (Pubitemid 29248642)
39. Munafo, D.B. and Robb, G.B. (2010) Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA. RNA, 16, 2537-2552.
40. Workman, C.T., Yin, Y., Corcoran, D.L., Ideker, T., Stormo, G.D. and Benos, P.V. (2005) enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res., 33, W389-392. (Pubitemid 44529949)
41. Zhuang, F., Karberg, M., Perutka, J. and Lambowitz, A.M. (2009) EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting. RNA, 15, 432-449.
42. Do, C.B., Woods, D.A. and Batzoglou, S. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-e98. (Pubitemid 44288277)
43. Tuma, R.S., Beaudet, M.P., Jin, X., Jones, L.J., Cheung, C.Y., Yue, S. and Singer, V.L. (1999) Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators. Anal. Biochem., 268, 278-288. (Pubitemid 29147143)
44. Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L., Mahuvakar, V.R., Andersen, M.R. et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res., 33, e179.
45. Smith, A.M., Heisler, L.E., St Onge, R.P., Farias-Hesson, E., Wallace, I.M., Bodeau, J., Harris, A.N., Perry, K.M., Giaever, G., Pourmand, N. et al. (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res., 38, e142.
46. Alon, S., Vigneault, F., Eminaga, S., Christodoulou, D.C., Seidman, J.G., Church, G.M. and Eisenberg, E. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res., 21, 1506-1511.