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.
Highlights
During the last few years, transcriptomic analysis has experienced a tremendous boost and it’s the gold standard for fully characterize the RNA molecules expressed in a certain tissue in a specific physiological time.Great efforts and resources have been invested in defining the functional part of the genome through the extensive use of RNA-Sequencing (RNA-Seq) technologyGenes 2020, 11, 410; doi:10.3390/genes11040410 www.mdpi.com/journal/genesGenes 2020, 11, 410 in humans [1] and in animals with other ongoing initiatives such Functional Annotation of AnimalGenomes (FAANG) [2].Despite new knowledge has been produced and genome annotations significantly improved, the genome response, in terms of gene expression modulation, is far from being understood
With our experimental design we tried to dissect the transcription modulation in horse Peripheral Blood Mononuclear Cells (PBMCs) after exercise focusing on unexplored regions related to introns and intergenic portions
Repetitive elements are known to influence the surrounding sequences once activated [38]. All these mechanisms represent a sort of genomic response to external stimuli, and we tried to search for signs of them in exercise induced stress
Summary
During the last few years, transcriptomic analysis has experienced a tremendous boost and it’s the gold standard for fully characterize the RNA molecules expressed in a certain tissue in a specific physiological time.Great efforts and resources have been invested in defining the functional part of the genome (which turned out to be remarkable) through the extensive use of RNA-Sequencing (RNA-Seq) technologyGenes 2020, 11, 410; doi:10.3390/genes11040410 www.mdpi.com/journal/genesGenes 2020, 11, 410 in humans [1] and in animals with other ongoing initiatives such Functional Annotation of AnimalGenomes (FAANG) [2].Despite new knowledge has been produced and genome annotations significantly improved, the genome response, in terms of gene expression modulation, is far from being understood. Great efforts and resources have been invested in defining the functional part of the genome (which turned out to be remarkable) through the extensive use of RNA-Sequencing (RNA-Seq) technology. Genes 2020, 11, 410 in humans [1] and in animals with other ongoing initiatives such Functional Annotation of Animal. Despite new knowledge has been produced and genome annotations significantly improved, the genome response, in terms of gene expression modulation, is far from being understood. Variation, intended as variation of expression in different cells and tissues, while the “temporal” one, physiological and pathological variation through time, has been left behind. Different studies (Genome Wide Association Studies—GWAS) pointed towards the intergenic and intronic fraction of the genome [4] where the most regulatory molecules lie and are transcribed
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call