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Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Vitsios, Dimitrios M 
Davis, Matthew P 
van Dongen, Stijn 
Enright, Anton J 

Abstract

MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs. Herein, we focus on Human and Mouse for which the majority of data are available. We reanalyse sequencing data from 461 samples into a coordinated catalog of microRNA expression. We use this to perform large-scale analyses of miRNA function and biogenesis. These analyses include global expression comparison, co-expression of miRNA clusters and the prediction of miRNA strand-specificity and underlying constraints. Additionally, we report for the first time a global analysis of miRNA epi-transcriptomic modifications and assess their prevalence across tissues, samples and families. Finally, we report a list of potentially mis-annotated miRNAs in miRBase based on their aggregated modification profiles. The results have been collated into a comprehensive online repository of miRNA expression and features such as modifications and RNA editing events, which is available at: http://wwwdev.ebi.ac.uk/enright-dev/miratlas. We believe these findings will further contribute to our understanding of miRNA function in animals and benefit the miRNA community in general.

Description

Keywords

Animals, Databases, Nucleic Acid, Gene Expression, High-Throughput Nucleotide Sequencing, Humans, Mice, MicroRNAs, Molecular Sequence Annotation, Multigene Family, RNA Processing, Post-Transcriptional, Sequence Analysis, RNA, Transcriptome

Journal Title

Nucleic Acids Res

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

45

Publisher

Oxford University Press (OUP)