RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database

Pierre R Bushel; Florian Caiment; Han Wu; Raegan O'Lone; Frank Day; John Calley; Aaron Smith; Jianying Li

doi:10.1186/s12864-018-5220-x

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database

BMC Genomics. 2018 Nov 19;19(1):825. doi: 10.1186/s12864-018-5220-x.

Authors

Pierre R Bushel^{1

2}, Florian Caiment³, Han Wu⁴, Raegan O'Lone⁵, Frank Day⁶, John Calley⁷, Aaron Smith⁸, Jianying Li^{9

10

11}

Affiliations

¹ Biostatistics and Computational Biology Branch, Research Triangle Park, NC, USA. bushel@niehs.nih.gov.
² Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC, 27709, USA. bushel@niehs.nih.gov.
³ Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands.
⁴ Department of Discovery and Development Statistics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, Indiana, USA.
⁵ Health and Environmental Sciences Institute, Washington, D.C., USA.
⁶ Office of Scientific Computing, National Institute of Environmental Health Sciences,, Reaserch Triangle Park, NC, USA.
⁷ Department of TTX Bioinformatics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, Indiana, USA.
⁸ Department of Investigative Toxicology, Non-Clinical Safety Assessment and Pathology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, Indiana, USA.
⁹ Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC, 27709, USA.
¹⁰ Integrative Bioinformatics, National Institute of Environmental Health Sciences,, Research Triangle Park, NC, USA.
¹¹ Kelly Government Solutions,, Research Triangle Park, NC, USA.

Abstract

Background: MicroRNAs (miRNAs) regulate gene expression and have been targeted as indicators of environmental/toxicologic stressors. Using the data from our deep sequencing of miRNAs in an extensive sampling of rat tissues, we developed a database called RATEmiRs for the Rat Atlas of Tissue-specific and Enriched miRNAs to allow users to dynamically determine mature-, iso- and pre-miR expression abundance, enrichment and specificity in rat tissues and organs.

Results: Illumina sequencing count data from mapped reads and meta data from the miRNA body atlas consisting of 21 and 23 tissues (14 organs) of toxicologic interest from 12 to 13 week old male and female Sprague Dawley rats respectively, were managed in a relational database with a user-friendly query interface. Data-driven pipelines are available to tailor the identification of tissue-enriched (TE) and tissue-specific (TS) miRNAs. Data-driven organ-specific (OS) pipelines reveal miRNAs that are expressed predominately in a given organ. A user-driven approach is also available to assess the tissue expression of user-specified miRNAs. Using one tissue vs other tissues and tissue(s) of an organ vs other organs, we illustrate the utility of RATEmiRs to facilitate the identification of candidate miRNAs. As a use case example, RATEmiRs revealed two TS miRNAs in the liver: rno-miR-122-3p and rno-miR-122-5p. When liver is compared to just the brain tissues for example, rno-miR-192-5p, rno-miR-193-3p, rno-miR-203b-3p, rno-miR-3559-5p, rno-miR-802-3p and rno-miR-802-5p are also detected as abundantly expressed in liver. As another example, 55 miRNAs from the RATEmiRs query of ileum vs brain tissues overlapped with miRNAs identified from the same comparison of tissues in an independent, publicly available dataset of 10 week old male rat microarray data suggesting that these miRNAs are likely not age-specific, platform-specific nor pipeline-dependent. Lastly, we identified 10 miRNAs that have conserved tissue/organ-specific expression between the rat and human species.

Conclusions: RATEmiRs provides a new platform for identification of TE, TS and OS miRNAs in a broad array of rat tissues. RATEmiRs is available at: https://www.niehs.nih.gov/ratemirs.

Keywords: Database; Organ-specific; RNA-Seq; Tissue-enriched; Tissue-specific; miRNA.

MeSH terms

Animals
Brain / metabolism
Databases, Genetic*
Female
Gene Expression Profiling*
Humans
Ileum / metabolism
Internet
Liver / metabolism
Male
MicroRNAs / genetics*
Oligonucleotide Array Sequence Analysis / methods
Organ Specificity / genetics*
Rats, Sprague-Dawley

Substances

MicroRNAs