Identifying miRNA, RNA-binding sites in UTRs

Question

[EVR]

HI all,

I have UTRs regions of many transcripts of a non-model organism of my interest and I would like to identify the miRNA, RNA binding sites and post transcriptional regulatory elements in the UTRs. Can you suggest a database where can I download the target sequences.

Thanks in advance

[biofalconch]

Just out of curiosity, is it a plant or an animal? The type of organism makes a world of a difference, remember that searching for plant microRNAs is rather easy.

Also, what I get from your question is that you are trying to find microRNAs based on UTRs?

Answer 1

[Kevin Blighe]

For validated (or predicted) interactions, I would recommend miRWalk2.0 for this. This allows you to search for predicted or validated (via CLASH) mir-to-gene interactions. It has data for gene promotors, 5'UTR, CDS, and 3'UTR.

Alternatively, if you have a list of mirs and want to find in silico predicted gene targets, then miRNAtap is useful and is on Bioconductor. It uses information from 4 databases in order to increase confidence in predictions:

• DIANA
• PicTar
• TargetScan
• miRanda

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Finally, if you want to perform functional enrichment via GO and KEGG for each mir's predicted targets (and, thus, each mir), you can again use miRNAtap for GO (which ultimately uses topGO), and KEGGprofile for KEGG pathways.

Kevin

Answer 2

[Russ]

For non-model organisms information can be sparse. miRBase has miRNA sequences from a wide variety of species. You can try combining the sequences obtained from miRBase with TargetScan and miRanda to help predict miRNA binding sites in non-model organisms.