Visualization of the Small RNA Transcriptome Using SeqclusterViz

Overview

Journal F1000Res

Specialties Biomedical Engineering
Science

Date 2019 Jul 12

PMID 30984380

Citations 4

Authors

Lorena Pantano

Francisco Pantano

Eulalia Marti

Shannan Ho Sui

Affiliations

Soon will be listed here.

Abstract

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson's disease.

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References

Bartel D . MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116(2):281-97. DOI: 10.1016/s0092-8674(04)00045-5. View

Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S . Hidden layers of human small RNAs. BMC Genomics. 2008; 9:157. PMC: 2359750. DOI: 10.1186/1471-2164-9-157. View

Gonzalez S, Pisano D, Serrano M . Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs. Cell Cycle. 2008; 7(16):2601-8. DOI: 10.4161/cc.7.16.6541. View

Okamura K, Lai E . Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol. 2008; 9(9):673-8. PMC: 2729316. DOI: 10.1038/nrm2479. View

Kim D, Saetrom P, Snove Jr O, Rossi J . MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A. 2008; 105(42):16230-5. PMC: 2571020. DOI: 10.1073/pnas.0808830105. View

Moazed D . Small RNAs in transcriptional gene silencing and genome defence. Nature. 2009; 457(7228):413-20. PMC: 3246369. DOI: 10.1038/nature07756. View

Kim V, Han J, Siomi M . Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 2009; 10(2):126-39. DOI: 10.1038/nrm2632. View

Cole C, Sobala A, Lu C, Thatcher S, Bowman A, Brown J . Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 2009; 15(12):2147-60. PMC: 2779667. DOI: 10.1261/rna.1738409. View

Huang P, Liu Y, Lee C, Lin W, Gan R, Lyu P . DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res. 2010; 38(Web Server issue):W385-91. PMC: 2896168. DOI: 10.1093/nar/gkq392. View

10.

Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J . Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 2010; 39(2):675-86. PMC: 3025573. DOI: 10.1093/nar/gkq776. View

11.

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

12.

Yang J, Qu L . DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data. Methods Mol Biol. 2011; 822:233-48. DOI: 10.1007/978-1-61779-427-8_16. View

13.

Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X . CPSS: a computational platform for the analysis of small RNA deep sequencing data. Bioinformatics. 2012; 28(14):1925-7. DOI: 10.1093/bioinformatics/bts282. View

14.

Stocks M, Moxon S, Mapleson D, Woolfenden H, Mohorianu I, Folkes L . The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics. 2012; 28(15):2059-61. PMC: 3400958. DOI: 10.1093/bioinformatics/bts311. View

15.

Feng Y, Zhang X, Graves P, Zeng Y . A comprehensive analysis of precursor microRNA cleavage by human Dicer. RNA. 2012; 18(11):2083-92. PMC: 3479397. DOI: 10.1261/rna.033688.112. View

16.

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

17.

Martens-Uzunova E, Olvedy M, Jenster G . Beyond microRNA--novel RNAs derived from small non-coding RNA and their implication in cancer. Cancer Lett. 2013; 340(2):201-11. DOI: 10.1016/j.canlet.2012.11.058. View

18.

Giurato G, Filippo M, Rinaldi A, Hashim A, Nassa G, Ravo M . iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq. BMC Bioinformatics. 2013; 14:362. PMC: 3878829. DOI: 10.1186/1471-2105-14-362. View

19.

Rueda A, Barturen G, Lebron R, Gomez-Martin C, Alganza A, Oliver J . sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acids Res. 2015; 43(W1):W467-73. PMC: 4489306. DOI: 10.1093/nar/gkv555. View

20.

Telonis A, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y . Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015; 6(28):24797-822. PMC: 4694795. DOI: 10.18632/oncotarget.4695. View