Recently, we documented that human cytomegalovirus (HCMV) and herpes simplex virus (HSV) infections lead to a robust induction of HSATII RNA, among other satellite repeat transcripts. HSATII RNA positively affects viral gene expression, DNA accumulation and yield, as well as has a broad influence on host cell biology. Our report also provided evidence that cooperation between at least two HCMV immediate-early proteins (IE1, IE2) is necessary for the robust induction of HSATII RNA expression. However, cellular processes contributing to the virus-induced HSATII RNA were still unknown. Here, we report that the strength with which HSATII RNA affects virus replication cycle is cell-type specific with retinal pigment epithelial cells being markedly more sensitive to levels of HSATII RNA than fibroblasts. We demonstrate that the HCMV IE1 and IE2 proteins regulate HSATII expression via the E2F3a transcription factor. Moreover, treatment of cells with DNA damaging agents also induced HSATII expression, and we determined that a rerouted DNA damage response (DDR) pathway, based on kinase independent ATM regulation, plays a central role in the expression of HSATII in HCMV-infected cells. Importantly, we discovered that, depending on the HSATII RNA levels, breast cancer cells showed differential sensitivity to DNA damaging drugs with enhanced cell migration seen in less metastatic cells. Additionally, we demonstrate that highly motile and proliferative phenotype of metastatic breast cancer cells can be effectively inhibited by knocking down HSATII RNA. Together, our investigation provides the molecular mechanism that links a high expression of HSATII RNA to the E2F3a-initiated induction of DDR, centered on kinase-independent functions of ATM, and to processes critical for efficient viral infection, cancer cell migration and proliferation.