Next Generation Sequencing Transcriptomic Analysis (RNA-seq) of Thoroughbred horse at rest, after exercise and after training
ABSTRACT: A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. Our study is a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses before and after a bout of high-intensity exercise and again after an extended period of training. We hypothesized that regular high-intensity exercise training primes the transcriptome for the demands of high-intensity exercise.
Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptome profiling of blood was performed for untrained horses and horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) – 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling. Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2, FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds. The blood transcriptome sequencing was performed for 37 samples collected form Arabian horses using Illumina HiScan SQ in75 single-end cycles and in 3-4 technical repetitions.repetitions.
Project description:Consequence of physical exercise in skeletal muscle was investigated in C57BL/6 mice after 4 weeks of exercise training and compared to sedentary controls. Exercised mice received four 4 weeks of regular exercise training on a motorized treadmill and were compared to sedentary controls. 6 mice of each Treatment were used to extract RNA from the quadriceps muscle three hours after the last training bout
Project description:10 male subjects performed ~45 min one-legged cycling and 4 x 7 maximal concentric-eccentric knee extensions for each leg 15 min later. Thus, one limb performed aerobic and resistance exercise (AE+RE), while the opposing leg did resistance exercise only (RE). Biopsies were obtained from m. vastus lateralis of each leg 3 h after the resistance exercise bout. Gene expression analysis was carried out on the Affymetrix HuGene-2.1-st platform. Overall design: Skeletal muscle gene expression after a single bout of one-legged resistance type exercise only or one bout of one-legged resistance type exercise combined with one bout of aerobic exercise
Project description:Regulated in DNA Damage and Development 1 (REDD1) is a stress induced protein whose expression is highly induced in skeletal muscle following a single bout of aerobic exercise. However, the role of this induction is unknown We used microarrays to detail the change in gene signature within skeletal muscle following a single bout of aerobic exercise in wild type and REDD1 null mice Overall design: Wild type and REDD1 knockout mice were randomized to remain sedentary or undergo a single bout of aerobic exercise. One hour following the completion of the exercise protocol, the plantaris from sedentary and exercised mice was extracted and frozen.
Project description:Background: Exercise has a positive effect on overall health. This study was performed to get an overview of the effects of mixed exercise training on skeletal muscl 18 middle-aged men performed 12 weeks of exercise training (2x endurance training and 1x resistance training), muscle biopsies were taken at baseline and 3 days after the last training session
Project description:We examined global mRNA expression using cDNA microarrays in skeletal muscle of humans before, and 3h and 48h after a single bout of exhaustive endurance exercise (cycling). Keywords: Time course Overall design: Healthy, non-trained university-aged subjects performed a single bout of exhaustive cycling. Skeletal muscle biopsies were taken from the vastus lateralis before, 3h and 48h after the exercise bout. Total RNA was extracted, amplified, reverse transcribed, and cDNA was analyzed on a custom made cDNA microarray. Four subjects were analyzed, and samples were not pooled between subjects (i.e. individual microarrays were used for baseline vs. 3H and baseline vs. 48h for EACH subject; repeated measures design).
Project description:This SuperSeries is composed of the following subset Series: GSE14239: MESSAGE 2 space experiment with Rhodospirillum rubrum S1H GSE14241: BASE-A space experiment with Rhodospirillum rubrum S1H Refer to individual Series
Project description:R. rubrum S1H inoculated on solid agar rich media was sent to the ISS in October 2003 (MESSAGE-part 2 experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.
Project description:STRRIDE is an exercise intervention study of different doses and intensities in overweight women and men with the metabolic syndrome. We profiled biopsies from 3 female and 3 male STRRIDE subjects in the “high” exercise group (2,200 kCal/wk). Muscle biopsies were profiled at entry (0h), and after 9 months of aerobic training (24 hrs post-last bout, 96 hrs post last bout, and 336h (14 days) de-training). Included also are pilot expression data from 3 male subjects. Keywords: other
Project description:We examined global mRNA expression using cDNA microarrays in skeletal muscle of humans before, and 3h and 48h after a single bout of exhaustive endurance exercise (cycling). Keywords: Time course Healthy, non-trained university-aged subjects performed a single bout of exhaustive cycling. Skeletal muscle biopsies were taken from the vastus lateralis before, 3h and 48h after the exercise bout. Total RNA was extracted, amplified, reverse transcribed, and cDNA was analyzed on a custom made cDNA microarray. Four subjects were analyzed, and samples were not pooled between subjects (i.e. individual microarrays were used for baseline vs. 3H and baseline vs. 48h for EACH subject; repeated measures design).