Highly efficient ligation of small RNA molecules for MicroRNA quantitation by high-throughput sequencing

Journal of Visualized Experiments

Volumn , Issue 93, 2014, Pages

  Lee, Jerome E ^a   Yi, Rui ^a,b  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

High throughput sequencing; Issue 93; Ligation; Linker; miR Seq; miRNA; Molecular Biology; Oligonucleotide; RNA

Indexed keywords

EID: 84911412034     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/52095     Document Type: Article

References (13)

1. Hafner, M., et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA. 17, (9), 1697-1712 (2011).
2. Zhang, Z., Lee, J. E., Riemondy, K., Anderson, E. M., Yi, R. High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing. Genome Biology. 14, (10), 109(2013).
3. Consortium, T. E. P. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 306, (5696), 636-640 (2004).
4. Consortium, T. E. P. An integrated encyclopedia of DNA elements in the human genome. Nature. 489, (7414), 57-74 (2012).
5. Linsen, S. E. V., et al. Limitations and possibilities of small RNA digital gene expression profiling. Nature Methods. 6, (7), 474-476 (2009).
6. Jayaprakash, A. D., Jabado, O., Brown, B. D., Sachidanandam, R. Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Research. 39, (21), 141(2011).
7. McLaughlin, L. W., Romaniuk, E., Romaniuk, P. J., Neilson, T. The Effect of Acceptor Oligoribonucleotide Sequence on the T4 RNA Ligase Reaction. European Journal of Biochemistry. 125, (3), 639-643 (1982).
8. Zhuang, F., Fuchs, R. T., Sun, Z., Zheng, Y., Robb, G. B. Structural bias in T4 RNA ligase-mediated 3′-adapter ligation. Nucleic Acids Research. 40, (7), 54(2012).
9. Harrison, B., Zimmerman, S. B. Polymer-stimulated ligation: enhanced ligation of oligo- and polynucleotides by T4 RNA ligase in polymer solutions. Nucleic Acids Research. 12, (21), 8235-8251 (1984).
10. Torchia, C., Takagi, Y., Ho, C. K. Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA. Nucleic Acids Research. 36, (19), 6218-6227 (2008).
11. Lau, N. C., Lim, L. P., Weinstein, E. G., Bartel, D. P. An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans. Science. 294, (5543), 858-862 (2001).
12. Yi, R., et al. DGCR8-dependent microRNA biogenesis is essential for skin development. Proceedings of the National Academy of Sciences. 106, (2), 498-502 (2009).
13. Leung, A. K. L., et al. Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nature Structural & Molecular Biology. 18, (2), 237-244 (2011).