Abstract
Ciliates, a very ancient group of organisms, have evolved extraordinary ways of organizing, manipulating, and replicating the DNA in their micronuclear genomes. The way that ciliates transform genes from their micronuclear (storage) form into their macronuclear (expression) form constitutes a very interesting case of “DNA computing in vivo”. In this paper we investigate in detail one aspect of this transformation, viz., gene (un)scrambling. In particular, we use the formal framework of pointer reduction systems to investigate the computational aspects of gene (un)scrambling.
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References
Adleman, L. (1994) Molecular computation of solutions to combinatorial problems, Science, 266:1021–1024.
Duharcourt, S., A-M. Keller, and E. Meyer (1998) Homology-dependent maternal inhibition of developmental excision of internal eliminated sequences in Paramecium tetraurelia. Mol. Cell. Biol. 18:7075–7085.
Hoffman, D.C. and D.M. Prescott (1996) A germline gene encoding DNA polymerase α in the hypotrichous ciliate Oxytricha nova is extremely scrambled. Nucl. Acids Res. 24:3337–3340.
Kari, L., Rubin, H., and D.H. Wood (1998) Proceedings of the 4th DIMACS meeting on DNA Based Computers, Philadelphia.
Landweber, L.F. and Kari, L. (1998) The evolution of cellular computing: nature’s solution to a computational problem. In Proceedings of the 4th DIMACS meeting on DNA Based Computers, Philadelphia, pp. 3–15.
Landweber, L.F. and Kari, L. (2000) Universal molecular computation in cillates. This volume.
Mitcham, J.L., D.M. Prescott, and M.K. Miller (1994) The micronuclear gene-encoding β-telomere binding protein in Oxytricha nova. J. Euk. Microbiol. 41:478–480.
Mitcham, J.D., A.J. Lynn, and D.M. Prescott (1992) Analysis of a scrambled gene: the gene encoding α-telomere-binding protein in Oxytricha nova. Genes & Develop. 6:788–800.
Paun, G., Rozenberg, G., and A. Salomaa (1998) DNA Computing Springer-Verlag, Berlin, Heidelberg.
10. Prescott, D.M. (1999) The evolutionary scrambling and developmental unscrambling of germline genes in hypotrichous ciliates. Nucl. Acids Res., in press.
Prescott, D.M. and M.L. DuBois (1996) Internal eliminated segments (IESs) of Oxytrichidae. J. Euk. Microbiol. 43:432–441.
Prescott, D.M. (1992) The unusual organization and processing of genomic DNA in hypotrichous ciliates. Trends in Genet. 8:439–445.
Prescott, D.M. and A.F. Greslin (1992) Scrambled actin I gene in the micronucleus of Oxytricha nova. Develop. Genet. 13:66–74.
Wright, A-D.G. and D.H. Lynn (1997) Maximum ages of ciliate lineages estimated using a small subunit rRNA molecular clock: Crown eukaryotes date back to the Paleoproterozoic. Arch. Protistenkd. 148:329–341.
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Ehrenfeucht, A., Prescott, D.M., Rozenberg, G. (2002). Computational Aspects of Gene (Un)Scrambling in Ciliates. In: Landweber, L.F., Winfree, E. (eds) Evolution as Computation. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55606-7_12
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DOI: https://doi.org/10.1007/978-3-642-55606-7_12
Publisher Name: Springer, Berlin, Heidelberg
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