Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity?

Abstract

Physical exercise is universally recognized as stressful. Among the "sport species", the horse is probably the most appropriate model for investigating the genomic response to stress due to the homogeneity of its genetic background. The aim of this work is to dissect the whole transcription modulation in Peripheral Blood Mononuclear Cells (PBMCs) after exercise with a time course framework focusing on unexplored regions related to introns and intergenic portions. PBMCs NGS from five 3 year old Sardinian Anglo-Arab racehorses collected at rest and after a 2000 m race was performed. Apart from differential gene expression ascertainment between the two time points the complexity of transcription for alternative transcripts was identified. Interestingly, we noted a transcription shift from the coding to the non-coding regions. We further investigated the possible causes of this phenomenon focusing on genomic repeats, using a differential expression approach and finding a strong general up-regulation of repetitive elements such as LINE. Since their modulation is also associated with the "exonization", the recruitment of repeats that act with regulatory functions, suggesting that there might be an active regulation of this transcriptional shift. Thanks to an innovative bioinformatic approach, our study could represent a model for the transcriptomic investigation of stress.

Keywords: exercise; gene expression; horse; intron retention; repetitive elements; stress.

Figure 1

Cartoon depicting results in the context of the method workflow.

Figure 2

Heat maps of differentially expressed genes basing on exon counts. Clustering resulted to be accurate and distinct. Legend above displays range of expression.

Figure 3

Heat maps of differentially expressed genes basing on intron counts. Like for the DEGs for the exonic compartment, also in this case there is a clear sample clustering in the two biological conditions. Legend above displays range of expression.

Figure 4

Smear plot of differentially expressed repetitive elements genome wide, red dots indicate the entries that overcome the fold change threshold (Y axes) and are significantly (q < 0.5) different between T0 and T1. X axes represent the expression value within the library.