Abstract
Small noncoding RNAs (sncRNAs) are widely expressed in the cell of almost all known species. Most sncRNAs appear to have regulatory roles, ranging from facilitating RNA production and modifications (e.g., snoRNAs) to control of mRNA stability and translational efficiency (e.g., miRNAs and endo-siRNA) and to transposon silencing (e.g., piRNAs). The affordability and efficiency of next-generation RNA deep sequencing (RNA-Seq) technologies have made sncRNA deep sequencing (sncRNA-Seq) analyses a routine in biomedical research. SncRNA-Seq analyses generate millions of reads and gigabytes of data; annotation of sncRNA-Seq data remains challenging due to a lack of comprehensive sncRNA annotation pipelines. To solve this problem, we have developed a computer-assisted sncRNA annotation pipeline, which uses open-source software and allows for not only proper classification of known sncRNAs, but also discovery of novel sncRNA species. In this chapter, we describe our sncRNA annotation protocol in detail.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T (2004) Identification of virus-encoded microRNAs. Science 304: 734–736. doi:10.1126/science.1096781
Bourc’his D, Voinnet O (2010) A small-RNA perspective on gametogenesis, fertilization, and early zygotic development. Science 330: 617–622. doi:10.1126/science.1194776
Czech B, Hannon GJ (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12:19–31. doi:10.1038/nrg2916
Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2:919–929
Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126–139
Siomi H, Siomi MC (2009) On the road to reading the RNA-interference code. Nature 457:396–404
Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355. doi:10.1038/nature02871nature02871 [pii]
Ro S, Ma HY, Park C, Ortogero N, Song R, Hennig GW, Zheng H, Lin YM, Moro L, Hsieh JT, Yan W (2013) The mitochondrial genome encodes abundant small noncoding RNAs. Cell Res 23:759–774. doi:10.1038/cr.2013.37
Smith CM, Steitz JA (1997) Sno storm in the nucleolus: new roles for myriad small RNPs. Cell 89:669–672
Ganot P, Bortolin ML, Kiss T (1997) Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89:799–809
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854
Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30:363–364. doi:10.1038/ng865
Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264. doi:10.1016/j.ygeno.2008.07.001
Kozomara A, Griffiths-Jones S (2013) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 39:D152–D157. doi:10.1093/nar/gkt1181
Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–D157. doi:10.1093/nar/gkq1027
Ortogero N, Hennig GW, Langille C, Ro S, McCarrey JR, Yan W (2013) Computer-assisted annotation of murine sertoli cell small RNA transcriptome. Biol Reprod 88:3. doi:10.1095/biolreprod.112.102269
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMB J 17:10–12
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. doi:10.1186/gb-2009-10-3-r25
Chen X, Fau-Li Q, Li Q, Fau-Wang J, Wang J, Fau-Guo X, Guo X, Fau-Jiang X, Jiang X, Fau-Ren Z, Ren Z, Fau-Weng C, Weng C, Fau-Sun G, Sun G, Fau-Wang X, Wang X, Fau-Liu Y, Liu Y, Fau-Ma L, Ma L, Fau-Chen J.-Y, Chen Jy Fau-Wang J, Wang J, Fau-Zen K, Zen K, Fau-Zhang J, Zhang J, Fau-Zhang C.-Y.C.Y. Z (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10:17
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
Hertel J, Hofacker IL, Stadler PF (2008) SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24:158–164. doi:10.1093/bioinformatics/ btm464
Chan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37:D93–D97. doi:10.1093/nar/gkn787
Acknowledgements
This work was supported by NIH grants (HD060858, HD071736, and HD074573) to W.Y. Software was developed in the Imaging Core (Core D) with support by the COBRE grant P20 RR-18751 from the NIH.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Ortogero, N., Hennig, G.W., Luong, D., Yan, W. (2015). Computer-Assisted Annotation of Small RNA Transcriptomes. In: Sioud, M. (eds) RNA Interference. Methods in Molecular Biology, vol 1218. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1538-5_22
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1538-5_22
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1537-8
Online ISBN: 978-1-4939-1538-5
eBook Packages: Springer Protocols