: A Tool for the Detection of Annotated and Novel Small RNAs

Overview

Journal Noncoding RNA

Date 2022 Jan 25

PMID 35076605

Authors

Jin Zhang

Abdallah M Eteleeb

Emily B Rozycki

Matthew J Inkman

Amy Ly

Russell E Scharf

Kay Jayachandran

Bradley A Krasnick

Thomas Mazur

Nicole M White

Ryan C Fields

Christopher A Maher

Affiliations

Soon will be listed here.

Abstract

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17-35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36-200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17-200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

Citing Articles

Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration.

Chaudhary U, Banerjee S ACS Pharmacol Transl Sci. 2024; 7(7):1901-1915.

PMID: 39022352 PMC: 11249652. DOI: 10.1021/acsptsci.3c00388.

References

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

Zhang C, Zhao L, Wu H, Tian G, Dai S, Zhao R . C/D-Box Snord105b Promotes Tumorigenesis in Gastric Cancer via ALDOA/C-Myc Pathway. Cell Physiol Biochem. 2018; 45(6):2471-2482. DOI: 10.1159/000488265. View

Sun C, Fu Z, Wang S, Li J, Li Y, Zhang Y . Roles of tRNA-derived fragments in human cancers. Cancer Lett. 2017; 414:16-25. DOI: 10.1016/j.canlet.2017.10.031. View

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L . The Ensembl genome database project. Nucleic Acids Res. 2001; 30(1):38-41. PMC: 99161. DOI: 10.1093/nar/30.1.38. View

Zhang J, Griffith M, Miller C, Griffith O, Spencer D, Walker J . Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. Exp Hematol. 2017; 55:19-33. PMC: 5772960. DOI: 10.1016/j.exphem.2017.07.008. View

. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012; 487(7407):330-7. PMC: 3401966. DOI: 10.1038/nature11252. View

Handzlik J, Tastsoglou S, Vlachos I, Hatzigeorgiou A . Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data. Sci Rep. 2020; 10(1):705. PMC: 6971259. DOI: 10.1038/s41598-020-57495-9. View

Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

10.

Matera A, Terns R, Terns M . Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007; 8(3):209-20. DOI: 10.1038/nrm2124. View

11.

Aparicio-Puerta E, Lebron R, Rueda A, Gomez-Martin C, Giannoukakos S, Jaspez D . sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. Nucleic Acids Res. 2019; 47(W1):W530-W535. PMC: 6602500. DOI: 10.1093/nar/gkz415. View

12.

Sharp S, Schaack J, Cooley L, Burke D, Soll D . Structure and transcription of eukaryotic tRNA genes. CRC Crit Rev Biochem. 1985; 19(2):107-44. DOI: 10.3109/10409238509082541. View

13.

Seto A, Kingston R, Lau N . The coming of age for Piwi proteins. Mol Cell. 2007; 26(5):603-9. DOI: 10.1016/j.molcel.2007.05.021. View

14.

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

15.

. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 2020; 49(D1):D212-D220. PMC: 7779037. DOI: 10.1093/nar/gkaa921. View

16.

Goodarzi H, Nguyen H, Zhang S, Dill B, Molina H, Tavazoie S . Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. Cell. 2016; 165(6):1416-1427. PMC: 4915377. DOI: 10.1016/j.cell.2016.05.046. View

17.

Cech T, Steitz J . The noncoding RNA revolution-trashing old rules to forge new ones. Cell. 2014; 157(1):77-94. DOI: 10.1016/j.cell.2014.03.008. View

18.

Li Z, Ender C, Meister G, Moore P, Chang Y, John B . Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res. 2012; 40(14):6787-99. PMC: 3413118. DOI: 10.1093/nar/gks307. View

19.

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

20.

Wu J, Liu Q, Wang X, Zheng J, Wang T, You M . mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing. RNA Biol. 2013; 10(7):1087-92. PMC: 3849156. DOI: 10.4161/rna.25193. View