Addressing bias in small RNA library preparation for sequencing: A new protocol recovers microRNAs that evade capture by current methods

Frontiers in Genetics

Volumn 6, Issue DEC, 2015, Pages

  Baran Gale, Jeanette ^a   Lisa Kurtz, C ^a   Erdos, Michael R ^b   Sison, Christina ^c   Young, Alice ^c   Fannin, Emily E ^a   Chines, Peter S ^b   Sethupathy, Praveen ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Adapter dimers; Adapter ligation bias; MicroRNA; Sequencing; Small RNA library preparation

Indexed keywords

MICRORNA; MICRORNA 200C 3P; MICRORNA 24 3P; MICRORNA 26A 5P; MICRORNA 29B 3P; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; FEMALE; MOLECULAR LIBRARY; MOUSE; NONHUMAN; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SMALL RNA LIBRARY;

EID: 84954467693     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2015.00352     Document Type: Article

References (29)

1. Alon, S., Vigneault, F., Eminaga, S., Christodoulou, D. C., Seidman, J. G., Church, G. M., et al. (2011). Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 21, 1506-1511. doi: 10.1101/gr.121715.111
2. Baker, M. (2010). MicroRNA profiling: separating signal from noise. Nat. Methods 7, 687-692. doi: 10.1038/nmeth0910-687
3. Bandiera, S., Pfeffer, S., Baumert, T. F., and Zeisel, M. B. (2015). miR-122-a key factor and therapeutic target in liver disease. J. Hepatol. 62, 448-457. doi: 10.1016/j.jhep.2014.10.004
4. Baran-Gale, J., Fannin, E. E., Kurtz, C. L., and Sethupathy, P. (2013). Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS ONE 8:e73240. doi: 10.1371/journal.pone.0073240
5. Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233. doi: 10.1016/j.cell.2009.01.002
6. Couzin, J. (2008). MicroRNAs make big impression in disease after disease. Science 319, 1782-1784. doi: 10.1126/science.319.5871.1782
7. Frost, R. J. A., and Olson, E. N. (2011). Control of glucose homeostasis and insulin sensitivity by the Let-7 family of microRNAs. Proc. Natl. Acad. Sci. U.S.A. 108, 21075-21080. doi: 10.1073/pnas.1118922109
8. Fuchs, R. T., Sun, Z., Zhuang, F., and Robb, G. B. (2015). Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure. PLoS ONE 10:e0126049. doi: 10.1371/journal.pone.0126049
9. Gunaratne, P. H., Coarfa, C., Soibam, B., and Tandon, A. (2012). "miRNA data analysis: next-gen sequencing, " in Methods in Molecular Biology, ed. J.-B. Fan (New York City, NY: Humana Press), 273-288. doi: 10.1007/978-1-61779-427-8_19
10. Hafner, M., Renwick, N., Brown, M., Mihailovic, A., Holoch, D., Lin, C., et al. (2011). RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17, 1697-1712. doi: 10.1261/rna.2799511
11. 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. 39, e141-e141. doi: 10.1093/nar/gkr693
12. Kawano, M., Kawazu, C., Lizio, M., Kawaji, H., Carninci, P., Suzuki, H., et al. (2010). Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing. Biotechniques 49, 751-755. doi: 10.2144/000113516
13. Latreille, M., Hausser, J., Stützer, I., Zhang, Q., Hastoy, B., Gargani, S., et al. (2014). MicroRNA-7a regulates pancreatic β cell function. J. Clin. Invest. 124, 2722-2735. doi: 10.1172/JCI73066
14. Liao, X., Xue, H., Wang, Y.-C., Nazor, K. L., Guo, S., Trivedi, N., et al. (2013). Matched miRNA and mRNA signatures from an hESC-based in vitro model of pancreatic differentiation reveal novel regulatory interactions. J. Cell Sci. 126, 3848-3861. doi: 10.1242/jcs.123570
15. Linsen, S. E. V., and Cuppen, E. (2012). Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing. Methods Mol. Biol. 822, 205-217. doi: 10.1007/978-1-61779-427-8_14
16. Linsen, S. E. V., de Wit, E., Janssens, G., Heater, S., Chapman, L., Parkin, R. K., et al. (2009). Limitations and possibilities of small RNA digital gene expression profiling. Nat. Methods 6, 474-476. doi: 10.1038/nmeth0709-474
17. Melkman-Zehavi, T., Oren, R., Kredo-Russo, S., Shapira, T., Mandelbaum, A. D., Rivkin, N., et al. (2011). miRNAs control insulin content in pancreatic β-cells via downregulation of transcriptional repressors. EMBO J. 30, 835-845. doi: 10.1038/emboj.2010.361
18. Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., MacDonald, P. E., et al. (2004). A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226-230. doi: 10.1038/nature03076
19. Poy, M. N., Hausser, J., Trajkovski, M., Braun, M., Collins, S., Rorsman, P., et al. (2009). miR-375 maintains normal pancreatic alpha-and beta-cell mass. Proc. Natl. Acad. Sci. U.S.A. 106, 5813-5818. doi: 10.1073/pnas.0810550106
20. Pritchard, C. C., Cheng, H. H., and Tewari, M. (2012). MicroRNA profiling: approaches and considerations. Nat. Rev. Genet. 13, 358-369. doi: 10.1038/nrg3198
21. Pullen, T. J., da Silva Xavier, G., Kelsey, G., and Rutter, G. A. (2011). miR-29a and miR-29b contribute to pancreatic beta-cell-specific silencing of monocarboxylate transporter 1 (Mct1). Mol. Cell. Biol. 31, 3182-3194. doi: 10.1128/MCB.01433-10
22. Roggli, E., Gattesco, S., Caille, D., Briet, C., Boitard, C., Meda, P., et al. (2012). Changes in microRNA expression contribute to pancreatic β-cell dysfunction in prediabetic NOD mice. Diabetes Metab. Res. Rev. 61, 1742-1751. doi: 10.2337/db11-1086
23. Sorefan, K., Pais, H., Hall, A. E., Kozomara, A., Griffiths-Jones, S., Moulton, V., et al. (2012). Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence 3, 4. doi: 10.1186/1758-907X-3-4
24. Tian, G., Yin, X., Luo, H., Xu, X., Bolund, L., Zhang, X., et al. (2010). Sequencing bias: comparison of different protocols of microRNA library construction. BMC Biotechnol. 10:64. doi: 10.1186/1472-6750-10-64
25. Tsai, W.-C., Hsu, S.-D., Hsu, C.-S., Lai, T.-C., Chen, S.-J., Shen, R., et al. (2012). MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. J. Clin. Invest. 122, 2884-2897. doi: 10.1172/JCI63455
26. Van Nieuwerburgh, F., Soetaert, S., Podshivalova, K., Ay-Lin Wang, E., Schaffer, L., Deforce, D., et al. (2011). Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS ONE 6:e26969. doi: 10.1371/journal.pone.0026969
27. Willenbrock, H., Salomon, J., Sokilde, R., Barken, K. B., Hansen, T. N., Nielsen, F. C., et al. (2009). Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA 15, 2028-2034. doi: 10.1261/rna.1699809
28. Zhu, Y., You, W., Wang, H., Li, Y., Qiao, N., Shi, Y., et al. (2013). MicroRNA-24/MODY gene regulatory pathway mediates pancreatic β-cell dysfunction. Diabetes Metab. Res. Rev. 62, 3194-3206. doi: 10.2337/db13-0151
29. Zhuang, F., Fuchs, R. T., Sun, Z., Zheng, Y., and Robb, G. B. (2012). Structural bias in T4 RNA ligase-mediated 3'-adapter ligation. Nucleic Acids Res. 40: e54. doi: 10.1093/nar/gkr1263