Eu-heterochromatic rearrangements transfer genes into the heterochromatin and cause their variegated inactivation (PEV). Genes affected by PEV often demonstrate association with heterochromatic nuclear compartment (a distinct area composed of heterochromatin sequences like satellite DNA and enriched in specific chromatin proteins, e.g., HP1). Here, we investigate the nuclear localization and the expression levels of the genes subjected to PEV caused by chromosome inversion, In(2)A4. We demonstrate that the degree of PEV-caused gene inactivation depends on a developmental stage, and the maximum of repression corresponds to the gene expression activation period. In the case of In(2)A4 rearrangement, we detect the dragging of the affected euchromatin region into the nuclear compartment of heterochromatin and the increase in HP1 occupancy in this region. We developed a protocol for simultaneous RNA-DNA-protein staining in order to demonstrate the strong correlation between the transcriptional activity of the affected gene and its distance from chromosome 2 satellite DNA in a single cell.