miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Top Cited Papers
Open Access
- 10 September 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (1), 37-52
- https://doi.org/10.1093/nar/gkr688
Abstract
MicroRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression of a large fraction of all animal genes and are important in a wide range of biological processes. Recent advances in high-throughput sequencing allow miRNA detection at unprecedented sensitivity, but the computational task of accurately identifying the miRNAs in the background of sequenced RNAs remains challenging. For this purpose, we have designed miRDeep2, a substantially improved algorithm which identifies canonical and non-canonical miRNAs such as those derived from transposable elements and informs on high-confidence candidates that are detected in multiple independent samples. Analyzing data from seven animal species representing the major animal clades, miRDeep2 identified miRNAs with an accuracy of 98.6–99.9% and reported hundreds of novel miRNAs. To test the accuracy of miRDeep2, we knocked down the miRNA biogenesis pathway in a human cell line and sequenced small RNAs before and after. The vast majority of the >100 novel miRNAs expressed in this cell line were indeed specifically downregulated, validating most miRDeep2 predictions. Last, a new miRNA expression profiling routine, low time and memory usage and user-friendly interactive graphic output can make miRDeep2 useful to a wide range of researchers.Keywords
Funding Information
- Helmholtz Association
This publication has 54 references indexed in Scilit:
- A Human snoRNA with MicroRNA-Like FunctionsMolecular Cell, 2008
- Early origins and evolution of microRNAs and Piwi-interacting RNAs in animalsNature, 2008
- Discovering microRNAs from deep sequencing data using miRDeepNature Biotechnology, 2008
- Small non-coding RNAs in animal developmentNature Reviews Molecular Cell Biology, 2008
- Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA lociJournal of Bone and Joint Surgery, 2008
- Database resources of the National Center for Biotechnology InformationNucleic Acids Research, 2007
- Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAsGenome Research, 2007
- microRNA FunctionsAnnual Review of Cell and Developmental Biology, 2007
- The evolution of gene regulation by transcription factors and microRNAsNature Reviews Genetics, 2007
- Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegansCell, 2006