The dynamic nature of chromatin and its modifications play a critical role in transcriptional gene regulation and thus can affect several cellular functions such as differentiation, replication, DNA damage response and activation of cell death. Alterations in cellular epigenetic and genetic structure after IR can lead to long term effects, such as survival and genomic instability. Additionally, DSB repair is thought to be differentially regulated in euchromatin and heterochromatin. Histone methylation is an important modification related to the compactness and transcriptional activity of chromatin. Thus histone methyltransferases (HMT) play a pivotal role in determining the functional status of chromatin. The human HMT SUV39h1 and SUV39h2 are altered in various types of human cancers. Here we show that the knockout Suv39h1/2 mice fibroblasts (Fbs) have significantly lower clonogenic survival, which is attributed to reduced DSB repair capacity of these cells. The downregulation of HMT SUV39H1 in human lung cancer cell lines leads to significantly reduced number of radiation-induced residual γH2AX. However, the effect of SUV39H1 downregulation on clonogenical survival was less marked as compared to the mouse knockout model. Additionally, the HMT inhibitor Chaetocin, significantly reduces the radiation dose necessary to control 50% of a plaque-monolayer culture after treatment with low concentrations, reduces the cell proliferation and significantly increased apoptosis in lung cancer cell lines. Moreover Chaetocin was found to remodel the nuclear chromatin structure by forming chaetocin-induced chromatin condensation/clustering which is mainly associated with heterochromatin domains in primary human Fbs, transformed mFbs and in the tumour cell line H1299.