156 Epigenomics and transcriptomics of muscle and liver tissues from in vitro- and in vivo-produced dairy calves at 3 months of age
M. Rabaglino A , J. Bojsen-Møller Secher B , P. Hyttel B and H. Kadarmideen AA Technical University of Denmark, Kongens Lyngby, Denmark
B University of Copenhagen, Frederisksberg C, Denmark
Reproduction, Fertility and Development 34(2) 316-316 https://doi.org/10.1071/RDv34n2Ab156
Published: 7 December 2021
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing on behalf of the IETS
The methodologies used for producing bovine embryos through assisted reproductive technologies can induce undesirable epigenetic modifications in the conceptus, resulting in alterations in the transcriptome. Indeed, some calves born from embryos produced in vitro (IVP) suffer fetal overgrowth (known as large offspring syndrome), although most of them are born apparently healthy and phenotypically similar to calves produced in vivo. However, IVP calves might have underlying aberrations in organs at the molecular level. The objective of this study was to determine epigenomic and transcriptomic deviations in muscle and liver of healthy IVP male dairy calves compared with in vivo-produced calves. For IVP embryos, oocytes obtained after mild ovarian stimulation were fertilised and cultivated in serum-free medium. In vivo embryos were generated after ovarian superstimulation and AI. Most embryos had the same parental combination, and the recipients were of similar parity and body condition. After normal delivery, birthweight and weight at sacrifice did not differ among the in vivo or IVP calves (n = 4 per group). Samples from muscle and liver were collected at 3 months of age and subjected to RNA and genomic DNA extraction and sequencing through RNA-seq and whole-genome bisulfite sequencing (WGBS). Data were analysed by means of a bioinformatic pipeline using R software to determine differentially methylated regions (DMR) and differentially expressed genes (DEG) at a false discovery rate (FDR) < 0.05 between both groups. Enriched ontological terms associated with genes in DMR or DEG were determined using the DAVID software. The number of DMR and DEG, respectively, were 1600 and 3372 for liver and 2459 and 1563 for muscle. DEG more expressed in the liver of IVP calves were strongly associated with translation (FDR = 2.7 × 10−07), oxidative phosphorylation (FDR = 3.6 × 10−21), mitochondrial respiratory chain (FDR = 1.9 × 10−11) and non-alcoholic fatty liver disease (FDR = 1.4 × 10−09). At the same time, hypomethylated genes were related to lipid metabolism and secondary metabolites biosynthesis, transport, and catabolism (FDR = 1.7 × 10−04). Up-regulated DEG in the liver of in vivo calves were enriching for focal adhesion (FDR = 9.2 × 10−07) and ECM-receptor interaction (FDR = 2.8 × 10−06), among other terms. Notoriously, DEG with higher expression in the muscle of the IVP calves were mostly associated with the tricarboxylic acid cycle/aerobic respiration (FDR = 1.9 × 10−11), vasculature development (FDR = 6.9 × 10−10), and striated muscle tissue development (FDR = 2.3 × 10−06). Accordingly, these last two biological processes were enriched by the hypomethylated muscular genes of in vitro calves (FDR < 0.05). Up-regulated DEG in the muscle of the vivo calves were mainly related to ribosomes (FDR = 1.8 × 10−22) and translation (FDR = 6.9 × 10−10). In conclusion, these results suggest that IVP calves present a hepatic and muscular molecular profile compatible with increased metabolism and accelerated growth compared with phenotypically similar in vivo calves, at least at 3 months of age.
