Radiation-Induced DNA Damage and Repair Effects on 3D Genome Organization

Abstract

The three-dimensional structure of chromosomes plays an important role in gene expression regulation and also influences the repair of radiation-induced DNA damage. Genomic aberrations that disrupt chromosome spatial domains can lead to diseases including cancer, but how the 3D genome structure responds to DNA damage is poorly understood. Here, we investigate the impact of DNA damage response and repair on 3D genome folding using Hi-C experiments on wild type cells and ataxia telangiectasia mutated (ATM) patient cells. Fibroblasts, lymphoblasts, and ATM-deficient fibroblasts were irradiated with 5 Gy X-rays and Hi-C was performed after 30 minutes, 24 hours, or 5 days after irradiation. 3D genome changes after irradiation were cell type-specific, with lymphoblastoid cells generally showing more contact changes than irradiated fibroblasts. However, all tested repairproficient cell types exhibited an increased segregation of topologically associating domains (TADs). This TAD boundary strengthening after irradiation was not observed in ATM deficient fibroblasts and may indicate the presence of a mechanism to protect 3D genome structure integrity during DNA damage repair.2 Translocations, deletions, and other genomic aberrations that may follow DNA damage can lead to cancer by directly mutating genes or altering their regulation 7, 8 . Recently, it has become clear that the disruption of 3D genome domains can also be oncogenic 9 . Does the process of DNA repair protect the 3D folding of the genome as well as the linear DNA sequence? Certain cell types are considered to be more radiosensitive than others, but little is known about what contributes to their radiosensitivity. The possibility remains that cell type specific chromosome positioning, along with initial epigenetic chromatin and folding states can influence which translocations occur and how well DNA is able to repair after exposure to IR, helping to explain why certain cell types are more sensitive to radiation 8, 10, 11. Previous studies suggest that DNA repair efficiency may differ for heterochromatin and euchromatin 12,13 . Heterochromatic regions may be more mobile and move to DNA repair sites, where they decondense 14,15 . Condensation or decondensation of specific chromatin regions may not be determined by their preexisting histone modifications 14 , suggesting that other factors may contribute to changes in 3D genome structure after DNA damage. One previous study demonstrated spatial clustering of DSBs in active genes by inducing specific breaks and measuring their interactions with Capture Hi-C 16 . This suggests that changes in the structure of local genome domains may happen at a broader scale after IR. Additionally, CCCTC-binding factor (CTCF) and cohesin have been shown to be early responders to DNA damage induced by IR 17,18,19,20 . These proteins have also been recently demonstrated to play significant roles in chromosome folding 21,22,23,24 , contributing to the formation of topologically associating domains (TADs). These genomic domains intera...

Inferring chromosome radial organization from Hi-C data

“…On the other hand, BJ1-hTERT human skin fibroblast cell has an ellipsoidal nucleus, which shows a chromosome length based CT organization [ 17 ]. The whole genome Hi-C contact matrices were obtained from Sanders et al [ 58 ].

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Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

“…We then set to address if the increased presence of cohesin at DSBs would impact the genomic overall distribution of this protein complex following break induction. Previous work indicated a genome-wide increase of cohesin, and reinforcement of TADs following exposure to irradiation 32,33 . In agreement, we found that SCC1 enrichment was increased at cohesin-binding sites post-break induction, coinciding with an increased loop strength (Fig.…”

Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts

“…Previously, it has been discussed that IR-induced lesions can also have an impact on the 3D organization of the genome and recent results from Hi-C experiments show a decrease in interactions across TAD boundaries after exposure to IR in human fibroblasts [14]. The authors suggest that this could play a role in the ability of cells to maintain genome integrity and prevent deleterious translocations across TAD boundaries [14].…”

“…The advancement of DNA sequencing technology over the past years now allows the gathering of bulk information at the DNA sequence level [11] and to identify and visualize variants such as SNVs [12], InDels [13], and translocations [14] in the complete human genome sequence. In this study, we have explored a comprehensive dataset from human gingiva fibroblast (HGF) cells that were subjected to increasing X-radiation doses followed by repair intervals of 16 h and 7 days.…”