Genome Wide Analysis of Porcine miRNA Editing

MicroRNAs (miRNAs) are small RNAs, usually ~23nt long, playing a prominent role in the post-transcriptional gene expression regulation. RNA editing, a post-transcription RNA modification, alters RNAs by nucleotide modifications. The most frequent and well characterized RNA editing event is conversion of adenosine (A) to inosine (I) in dsRNAs. RNA editing in miRNA seed region/target site in mRNA may affect miRNA-mRNA interaction.

The “WUR-pigENCODE” is a Dutch pilot project aiming at increasing the functional annotation of the pig genome and developing of the analytic framework needed for the FAANG (Functional Annotation of ANimal Genomes) community (see poster by Clarke, L. et al.). We have generated high-throughput whole-genome, RNA-seq, small-RNA-seq, and Reduced Representation Bisulfite Sequencing (RRBS) data from the same individuals of three commercial pig breeds (Large White, Duroc and Pietrain).

The specific objective of this study is to assess the interplay between  RNA-editing events (A to I) in miRNA seed regions and mRNA target site combined with genetic variation in the predicted target regions in the pig genome to understand how RNA-editing may change the target profile of the edited miRNAs and regulate gene expression.  We used Small RNA-seq and Stranded RNA-seq data generated from five tissues (brain-frontal loop, liver, muscle, spleen and testis) plus re-sequenced genome from the three breeds.

We plan to first perform a comparative analysis on differential expression in non-edited and edited miRNA, their targets and also look if the editing gives rise to new miRNAs. We will present the preliminary results of these analyses and outline future directions.