T6 – DIANA Tools and Databases: In silico investigation of miRNA functions

 

Tutorial details

Date: Sunday September 9, 2018
Time: 13:30 – 17:00
Venue: TBA, room: TBA

Tutors

  • Dimitra Karagkouni, University of Thessaly, Volos, Greece
  • Spyros Tastsoglou, University of Thessaly, Volos, Greece
  • Nikos Perdikopanis, University of Thessaly, Volos, Greece
  • Giorgos Skoufos, University of Thessaly, Volos, Greece
  • Ioannis Kavakiotis, University of Thessaly, Volos, Greece

Summary

Our view of non-coding RNA biology has been transformed during the past two decades, due to the emergence of microRNAs (miRNAs) and other non-coding RNA species (e.g. long non-coding RNAs, lncRNAs) as important regulators of gene expression, actively researched for their role in most physiological and pathological conditions. miRNAs are small single-stranded non-coding RNA molecules that post-transcriptionally regulate gene expression, through target cleavage, degradation and/or translational suppression. By binding on miRNA Recognition Elements (MREs) on the transcript sequence, each miRNA has the capacity to target numerous coding and non-coding transcripts. lncRNAs have been also shown to harbor MREs and their sponge-like repressive function against miRNAs has been established.

Characterization of the miRNA interactome required extensive computational and wet-lab research efforts mainly because of the complex rules that govern miRNA targeting. Sophisticated in silico approaches have been employed in order to predict their coding and non-coding targets as well as for the identification of elements regulating their own transcription. Concurrently, a vast array of high-throughput/specific techniques have been utilized to experimentally verify miRNA-gene interactions across different species, cell types and conditions. Databases of experimentally supported interactions have become indispensable tools in miRNA research that facilitate the retrieval of miRNA targets of interest and lay the groundwork for the elucidation of miRNA roles.

The tutorial will provide an A-to-Z overview of the DIANA-tools suite. Upon completion, participants will be able to utilize TarBase, LncBase, microT-CDS and miRGen to retrieve predicted and experimentally supported mRNA and lncRNA targets, as well as miRNA-TF interactions. Insights will be provided to aid the critical evaluation of the meta-information complementing each interaction. Finally, participants will explore the capabilities of miRPath and mirExTra, web-applications for the investigation of miRNA functions.

Target audience

The tutorial is aimed at researchers in the fields of molecular biology, systems biology, non-coding RNA research and bioinformatics. No programming experience is required.

Detailed Schedule

13:30 – 15:00 Part 1: DIANA resources for miRNA targets and regulators

  • Experimentally verified and predicted miRNA-mRNA interactions (DIANA-TarBase, DIANA-microT-CDS) and miRNA-lncRNA interactions (DIANA-LncBase)
  • Tissue/cell-line specific pri-miRNA Transcription Start Sites and TF-miRNA interactions (DIANA-miRGen)

15:00 – 15:30 Coffee Break

15:30 – 17:00 Part 2: Analyses of miRNA function

  • Investigations of the combinatorial effects of miRNAs using semantic annotation sources (DIANA-miRPath)
  • Identifying miRNAs and TFs of importance in (s)RNA-Seq data sets (DIANA-mirExTra)

 

Requirements & material

Participants are required to bring their personal laptop. Apart from a conventional web browser, there are no specific software requirements. The relevant material will be provided a week before the conference in www.microrna.gr/eccb.