Although less attention was paid to understanding physical localization changes in cell nuclei recently, depicting chromatin interaction maps is a topic of high interest. Here, we focused on defining extensive physical changes in chromatin organization in the process of skeletal myoblast differentiation. Based on RNA profiling data and 3D imaging of myogenic (NCAM1, DES, MYOG, ACTN3, MYF5, MYF6, ACTN2, and MYH2) and other selected genes (HPRT1, CDH15, DPP4 and VCAM1), we observed correlations between the following: (1) expression change and localization, (2) a gene and its genomic neighbourhood expression and (3) intra-chromosome and microscopical locus-centromere distances. In particular, we demonstrated the negative regulation of DPP4 mRnA (p < 0.001) and protein (p < 0.05) in differentiated myotubes, which coincided with a localization change of the DPP4 locus towards the nuclear lamina (p < 0.001) and chromosome 2 centromere (p < 0.001). Furthermore, we discuss the possible role of DPP4 in myoblasts (supported by an inhibition assay). We also provide positive regulation examples (VCAM1 and MYH2). Overall, we describe for the first time existing mechanisms of spatial gene expression regulation in myoblasts that might explain the issue of heterogenic responses observed during muscle regenerative therapies. The changes in the localization of chromosomes and their genes in the three-dimensional nuclear space are tightly regulated but highly variable phenomena. These nuclear interactions have an impact on transcriptional regulation, cell fate and inheritance mechanisms 1-3. Recent years have led to the development of many high-throughput techniques that have vastly increased our knowledge and understanding of chromatin interaction mechanisms 4-7. However, these high-throughput techniques (called '3C techniques') rely on sequence proximity in order to map ongoing interactions. However, creating a physical map of chromatin positioning in relation to the other components of nuclei remains a challenge. To define specific position changes of chromatin in nuclei, microscopic observations of labelled material are necessary, and these techniques have been developed simultaneously with 3C techniques, ultimately combining both approaches 8-12. Human muscle-derived stem cells have been used in regenerative therapies for nearly two decades. Since pluripotent stem cell (iPSC)-based technology is still lacking clinical feasibility, myoblast-based therapies can be considered generally safe and effective for regaining muscle contraction after sphincter rupture or when used in experimental therapies of muscle dystrophies 13. One of the difficulties of cellular therapies is patient variability