Simulation of the 2JLP gene assembly process in ciliates

Abstract

The gene assembly process in ciliates consists of a massive amount of DNA excision from the micronucleus and sometimes the rearrangement of the rest of the DNA sequences. Several models exist that describe certain parts of this process. In this research, a simulation is created and tested with real data to test the feasibility of the 2JLP model. Several parameters are introduced in the model that are used to test ambiguities or edge cases of the biological model. Parameters are systematically varied within the simulation to try to find their optimal values. Interestingly, a negative correlation is found between the degree to which the simulation successfully descrambles genes, and a parameter that is used to filter out scnRNAs that are similar to IES specific sequences from the macronucleus. This provides in silico evidence that if a scnRNA consists of both a portion of MDS and IES, then from the perspective of maximizing the accuracy of the descrambling, it is desirable to filter out this scnRNA. The simulator successfully performs the gene assembly process whether the inputs are scrambled or unscrambled DNA sequences. On average, before the proof checking stage that is in the model, the descrambling intermediate genes are 91.1% similar to the descrambled genes. After the proof checking stage, the intermediate genes are 99.4% similar. We hope that this work and further simulations can serve as a foundation for future computational and mathematical study of descrambling, and to help inform and refine the biological model.