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.
This research was supported by a grant from the Natural Sciences and Engineering Research Council of Canada.
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References
Bracht, J.R., Fang, W., Goldman, A.D., Dolzhenko, E., Stein, E.M., Landweber, L.F.: Genomes on the edge: programmed genome instability in ciliates. Cell 152(3), 406–416 (2013)
Cavalcanti, A.: Ciliate nuclear dimorphism pages. http://oxytricha.princeton.edu/dimorphism/ (2004)
Chen, X., Bracht, J.R., Goldman, A.D., Dolzhenko, E., Clay, D., Swart, E., Perlman, D., Doak, T., Stuart, A., Amemiya, C., Sebra, R., Landweber, L.: The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell 158(5), 1187–1198 (2014)
Ehrenfeucht, A., Prescott, D.M., Rozenberg, G.: Computational aspects of gene (un)scrambling in ciliates. In: Evolution as Computation, pp. 216–256. Natural Computing Series, Springer, Berlin Heidelberg (2002)
Jönsson, F., Postberg, J., Lipps, H.J.: The unusual way to make a genetically active nucleus. DNA Cell Biol. 28(2), 71–78 (2009)
Keil, J.M., Liu, J., McQuillan, I.: Algorithmic properties of ciliate sequence alignment. Theor. Comput. Sci. 411(6), 919–925 (2010)
Landweber, L.F., Kari, L.: The evolution of cellular computing: nature’s solution to a computational problem. Biosystems 52, 3–13 (1999)
Landweber, L.F., Kuo, T.C., Curtis, E.A.: Evolution and assembly of an extremely scrambled gene. Proc. Natl. Acad. Sci. USA 97(7), 3298–3303 (2000)
Mochizuki, K., Fine, N.A., Fujisawa, T., Gorovsky, M.A.: Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110(6), 689–699 (2002)
Möllenbeck, M., Zhou, Y., Cavalcanti, A.R.O., Jönsson, F., Higgins, B.P., Chang, W.J., Juranek, S., Doak, T.G., Rozenberg, G., Lipps, H.J., Landweber, L.F.: The pathway to detangle a scrambled gene. PLoS ONE 3(6), e2330 (2008)
Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3), 443–453 (1970)
Nowacki, M., Vijayan, V., Zhou, Y., Schotanus, K., Doak, T.G., Landweber, L.F.: RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451, 153–158 (2008)
Prescott, D.M.: The unusual organization and processing of genomic DNA in hypotrichous ciliates. Trends Genet. 8(12), 439–445 (1992)
Prescott, D.M.: The DNA of ciliated protozoa. Microbiol. Rev. 58(2), 233–267 (1994)
Prescott, D.M.: Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat. Rev. Genet. 1(3), 191–198 (2000)
Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Molecular operations for DNA processing in hypotrichous ciliates. Eur. J. Protistology 37(3), 241–260 (2001)
Prescott, D.M., Ehrenfeucht, A., Rozenberg, G.: Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates. J. Theor. Biol. 222(3), 323–330 (2003)
Verlan, S., Alhazov, A., Petre, I.: A sequence-based analysis of the pointer distribution of stichotrichous ciliates. Biosystems 101(2), 109–116 (2010)
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Mahmud, M.S.I., McQuillan, I. (2015). Simulation of the 2JLP Gene Assembly Process in Ciliates. In: Calude, C., Dinneen, M. (eds) Unconventional Computation and Natural Computation. UCNC 2015. Lecture Notes in Computer Science(), vol 9252. Springer, Cham. https://doi.org/10.1007/978-3-319-21819-9_17
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