Dose dependent transcriptional response to ionizing radiation is orchestrated with DNA repair within the nuclear space [4C-seq]

Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumor. Ionizing radiation (IR) induces dose- specific variations in transcriptional programs, implicating they are tightly regulated and critical components in the tumor response and survival. Yet, our understanding of the downstream molecular events triggered by lethal vs sublethal IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to lethal or sublethal IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. Radiation-activated genes were pre-positioned in active sub-nuclear compartments and were up-regulated following DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of events, which was linked to their spatial nuclear positioning. Thus, distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR. Overall design: To explore the genome architecture in response to irradiation, we conducted 4C-seq. U251 cells were subjected to irradiation at doses of 1Gy and 6Gy, followed by cell collection at three time points: 0 hours, 6 hours, and 12 hours post-irradiation. To capture the spatial environment of IR-responsive genes and nonresponsive genes, 4C-seq was performed using the following baits - BTG2, TRIM29, PRSS35, PPIB, HCRTR2.