Abstract
Next Generation Sequencing (NGS) is becoming a routine experimental technology. It has been a great success in recent years to profile small-RNA species using NGS. Indeed, a large quantity of small-RNA profiling data has been generated from NGS, and computational methods have been developed to process and analyze NGS data for the purpose of identification of novel and expressed small noncoding RNAs and analysis of their roles in nearly all biological processes and pathways in eukaryotes. We discuss here the computational procedures and major steps for identification of microRNAs and natural antisense transcript-originated small interfering RNAs (nat-siRNAs) from NGS small-RNA profiling data.
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References
Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108
Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656–668
Moazed D (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457:413–420
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Kim VN, Nam J-W (2006) Genomics of microRNA. Trends Genet 22:165–173
Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291
Zhou X, Sunkar R, Jin H, Zhu J-K, Zhang W (2009) Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res 19:70–78
Okamura K, Lai EC (2008) Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol 9:673–678
Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453:539–543
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J-K (2012) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8:218
Jagadeeswaran G, Zheng Y, Li Y-F, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R (2009) Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol 184:85–98
Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese EL, Soulages JL, Zhang W, Sunkar R (2010) Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 11:52
Reddy AM, Zheng Y, Jagadeeswaran G, Macmil SL, Graham WB, Roe BA, Desilva U, Zhang W, Sunkar R (2009) Cloning, characterization and expression analysis of porcine microRNAs. BMC Genomics 10:65
Zhang W, Gao S, Zhou X, Xia J, Chellappan P, Zhou X, Zhang X, Jin H (2010) Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 11:R81
Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 38:6883–6894
Reese TA, Xia J, Johnson LS, Zhou X, Zhang W, Virgin HW (2010) Identification of novel MicroRNA-like molecules generated from Herpesvirus and host tRNA transcripts. J Virol 84:10344–10353
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Hofacker I, Fontana W, Stadler P, Bonhoeffer S, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem 125:167–188
Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J (2010) Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res 39:675–686
Morin RD, MD OC, Griffith M, Kuchenbauer F, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18:610–621
MacRae IJ, Doudna JA (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol 17:138–145
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98:5116–5121
Breitling R, Armengaud P, Amtmann A, Herzyk P (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573:83–92
Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33:W577–W581
Dimitrov RA, Zuker M (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J 87:215–226
Acknowledgments
This work was supported in part by NSF grant DBI-0743797, NIH grants RC1AR058681 and R01GM086412 as well as an internal grant of Fudan University to W. Zhang.
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Zhang, W., Zhou, X., Zhou, X., Xia, J. (2021). Identification of MicroRNAs and Natural Antisense Transcript-Originated Endogenous siRNAs from Small-RNA Deep Sequencing Data. In: Jin, H., Kaloshian, I. (eds) RNA Abundance Analysis . Methods in Molecular Biology, vol 2170. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0743-5_9
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DOI: https://doi.org/10.1007/978-1-0716-0743-5_9
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