Crosstalk of Epitranscriptomic RNA Modifications and DNA Damage Repair

About This Grant

Project Summary Environmental and endogenous genotoxic stressors can induce DNA and RNA damage and misdeposition of the epitranscriptomic mark, N6-methyladenosine (m6A), leading to genome instability, gene dysregulation, and cancer and neurodegeneration. However, it remains unknown how DNA and RNA damage can synergize to modulate genome and epitranscriptome stability. In this project, we aim to understand the mechanisms underlying the crosstalk of RNA damage and m6A with DNA damage and repair. Our hypothesis is that environmentally-induced RNA damage, m6A, and DNA base damage and repair can interplay on R-loops to modulate RNA and DNA integrity. To test the hypothesis, we will pursue three Specific Aims. Aim 1 is to determine if environmentally-induced RNA damage can modulate RNA-guided DNA base damage repair and its fidelity on R-loops. First, we will determine if the environmental genotoxicant KBrO3 and occupational exposure level of Mn2+ can induce RNA and DNA base damage on R-loops to disrupt the expression of R-loop hotspot genes, MALAT1 and unfolded protein response regulator X-box binding protein 1 (XBP1) genes in human kidney cancer and iPSC-differentiated neural cells. Second, we will determine if RNA base damage can promote KBrO3- and Mn2+-induced DNA base damage by reducing the efficiency and fidelity of RNA-guided BER using circular RNA-mediated RNA damage systems, the artificial intelligence tool AlphaFold3, molecular dynamics simulation (MD), and steady-state enzyme kinetics. Aim 2 is to determine if m6A can modulate environmentally-induced DNA base damage repair by regulating RNA-guided DNA synthesis on R-loops. First, we will determine if KBrO3 and Mn2+ can cause the unique m6A deposition on R-loops, leading to dysregulation of the MALAT1 and XBP1 genes in kidney cancer and neural cells. Second, we will determine if m6A can disrupt DNA base damage repair induced by KBrO3 and Mn2+ on the R-loops of the MALAT1 and XBP1 genes by altering BER efficiency and fidelity using circRNA-mediated gene-targeted m6A deposition systems, AlphaFold3, MD, and enzyme kinetics. Aim 3 is to determine if environmentally-induced DNA base damage and repair can modulate m6A deposition on R-loops to disrupt RNA transcriptomic integrity. First, we will determine if KBrO3- and Mn2+-induced DNA base damage can alter m6A deposition on R-loops of the MALAT1 and XBP1 genes by disrupting the recruitment of m6A writers METTL3/METTL14 and eraser FTO and their substrate interaction on R-loops, suppressing R-loop resolution and expression of the genes in cancer and neural cells. Second, we will determine if DNA base damage can synergize with Mn2+ to cause m6A misdeposition on R-loops of the MALAT1 and XBP1 genes. Our study will create a new paradigm to reveal the crosstalk between environmentally-induced oxidative RNA damage and m6A deposition and DNA base damage and repair on R-loops in modulating genomic and transcriptomic integrity. Our results will facilitate the discovery of novel targets for RNA-based gene-targeted therapy and biomarkers for the prevention of environmentally-induced cancer and neurodegenerative diseases.