Creating AI Models to Map Oxidative Damage on Telomere DNA from Oxford Nanopore Generated DNA sequence
Telomeres cap each end of chromosomes with very long DNA sequences consisting of the repeat TTAGGG. The repeat is highly sensitive to oxidative stress, because of the many guanine residues. Oxidation of guanine forms of 8- oxo-2'-deoxyguanosine (8-oxo-dG). 8-oxo-dG is highly mutagenic and when present in telomeres can cause cellular senescence and apoptosis. Our research aims to map 8-oxo-dG mutations on telomeres using Oxford Nanopore Technology. This method sequences single strands of DNA at a time by passing DNA through nanopores on a chip monitored by an electric current. Each base perturbs the electrical current, which is analyzed by an AI model to read the sequence. We hypothesize that the precision of nanopore sequencing combined with fine-tuned neural networks enables accurate detection of 8-oxo-dG modifications. To test our hypothesis, we developed a workflow that includes PCR-based library preparation of a training set, Nanopore sequencing, basecalling with Dorado software, and model training with Remora software. Our findings demonstrate the potential of nanopore sequencing in telomere research to understand the role of oxidative DNA damage modifications at single-molecule resolution.
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