In swine breeding industry, sows have been selected for decades on their prolificacy in order to maximize meat production. However, this selection is associated with a higher mortality of newborns. In this context, the skeletal fetal muscle is essential for the piglet’s survival, as it is necessary for motor functions and thermoregulation. Besides, the three-dimensional structure of the genome has been proven to play an important role in gene expression regulation. Thus, in this project, we have focused our interest on the 3D genome conformation and gene expression in porcine muscle nuclei at late gestation. We have initially developed an original approach in which we combined transcriptome data with information of nuclear locations (assessed by 3D DNA FISH) of a subset of genes, in order to build gene co-expression networks. This study has revealed interesting nuclear associations involving IGF2, DLK1 and MYH3 genes, and highlighted a network of muscle-specific interrelated genes involved in the development and maturity of fetal muscle. Then, we assessed the global 3D genome conformation in muscle nuclei at 90 days and 110 days of gestation by using the High-throughput Chromosome Conformation Capture (Hi-C) method. This study has allowed identifying thousands of genomic regions showing significant differences in 3D conformation between the two gestational ages. Interestingly, some of these genomic regions involve the telomeric regions of several chromosomes that seem to be preferentially clustered at 90 days. More important, the observed changes in genome structure are significantly associated with variations in gene expression between the 90th and the 110th days of gestation
