The integration of genetic information in the cellular and nuclear environments is crucial for deciphering how the genome functions in physiological conditions. By combining 3D nuclear mapping, high-flow transcriptomic data analyses, and statistical methods for the development of co-regulated gene networks, it becomes possible to develop an integrated approach to depict the regulation of gene expression. For this purpose, we focused on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late fetal development in pig (90 and 110 days), a critical period for survival. We published a muscle transcriptomic analysis performed during this perinatal period (Voillet et al. 2014). Data from this previous study obtained from two extreme genetic lines in terms of mortality at birth (Large White and Meishan), were used to construct networks of differentially co-expressed genes. As co-expressed genes are not necessary related to a common biological process, we used information of gene co-localizations (3D DNA FISH) to reinforce observed links in the co-expressed gene network. The innovative network inference method developed, sequentially incorporates biological knowledge on gene spatial co-localization to construct robust networks gathering co-regulated genes. Clustering of nodes (genes) becomes more and more biologically consistent in each iteration. Interestingly, by means of the final network, we particularly uncovered unexpected gene associations in the nuclear space between IGF2 and MYH3 suggesting that they could be subject to similar transcriptional regulation.