Computational Nature of Gene Assembly in Ciliates
Ciliates are a very diverse and ancient group of unicellular eukaryotic organisms. A feature that is essentially unique to ciliates is the nuclear dualism, meaning that they have two functionally different types of nuclei, the macronucleus and the micronucleus. During sexual reproduction a micronucleus is transformed into a macronucleus – this process is called gene assembly, and it is the most involved naturally occurring example of DNA processing that is known to us. Gene assembly is a fascinating research topic from both the biological and the computational points of view.
In this chapter, several approaches to the computational study of gene assembly are considered. This chapter is self-contained in the sense that the basic biology of gene assembly as well as mathematical preliminaries are introduced. Two of the most studied molecular models for gene assembly, intermolecular and intramolecular, are presented and the main mathematical approaches used in studying these models are discussed. The topics discussed in more detail include the string and graph rewriting models, invariant properties, template-based DNA recombination, and topology-based models. This chapter concludes with a brief discussion of a number of research topics that, because of the space restrictions, could not be covered in this chapter.
KeywordsRegular Language Assembly Strategy Gene Assembly Signed Graph Small Cover
MD and GR acknowledge support by NSF, grant 0622112. IP acknowledges support by the Academy of Finland, grants 108421 and 203667. NJ has been supported in part by the NSF grants CCF 0523928 and CCF 0726396.
- Brijder R (2008) Gene assembly and membrane systems. PhD thesis, University of LeidenGoogle Scholar
- Brijder R, Hoogeboom HJ (2008b) Extending the overlap graph for gene assembly in ciliates. In: Martín-Vide C, Otto F, Fernau H (eds) LATA 2008: 2nd international conference on language and automata theory and applications, Tarragona, Spain, March 2008. Lecture notes in computer science, vol 5196. Springer, Berlin Heidelberg, pp 137–148CrossRefGoogle Scholar
- Daley M, McQuillan I (2005a) On computational properties of template-guided DNA recombination. In: Carbone A, Pierce N (eds) DNA 11: Proceedings of 11th international meeting on DNA-based computers, London, Ontario, June 2005. Lecture notes in computer science, vol 3892. Springer, Berlin, Heidelberg, pp 27–37Google Scholar
- Daley M, McQuillan I, Stover N, Landweber LF (2010) A simple topological mechanism for gene descrambling in Stichotrichous ciliates. (under review)Google Scholar
- Dassow J, Vaszil G (2006) Ciliate bio-operations on finite string multisets. In: Ibarra OH, Dang Z (eds) 10th international conference on developments in language theory, Santa Barbara, CA, June 2006. Lecture notes in computer science, vol 4036. Springer, Berlin Heidelberg, pp 168–179CrossRefGoogle Scholar
- Ehrenfeucht A, Petre I, Prescott DM, Rozenberg G (2000) Universal and simple operations for gene assembly in ciliates. In: Mitrana V, Martin-Vide C (eds) Where mathematics, computer science, linguistics and biology meet. Kluwer, Dordrecht, pp 329–342Google Scholar
- Ehrenfeucht A, Prescott DM, Rozenberg G (2001b) Computational aspects of gene (un)scrambling in ciliates. In: Landweber LF, Winfree E (eds) Evolution as computation. Springer, Berlin, Heidelberg, New York, pp 216–256Google Scholar
- Ehrenfeucht A, Harju T, Petre I, Prescott DM, Rozenberg G (2003a) Computation in living cells: gene assembly in ciliates. Springer, Berlin, Heidelberg, New YorkGoogle Scholar
- Harju T, Petre I, Rogojin V, Rozenberg G (2006b) Simple operations for gene assembly. In: Kari L (ed) Proceedings of 11th international meeting on DNA-based computers, London, Ontario, 2005. Lecture notes in computer science, vol 3892. Springer, Berlin, pp 96–111Google Scholar
- Harju T, Li C, Petre I, Rozenberg G (2007) Complexity measures for gene assembly. In: Tuyls K, Westra R, Saeys Y, Now'e A (eds) Proceedings of the knowledge discovery and emergent complexity in bioinformatics workshop, Ghent, Belgium, May 2006. Lecture notes in bioinformaties, vol 4366. Springer, Berlin, Heidelberg, pp 42–60CrossRefGoogle Scholar
- Hausmann K, Bradbury PC (eds) (1997) Ciliates: cells as organisms. Vch Pub, Deerfield Beach, FLGoogle Scholar
- Ilie L, Solis-Oba R (2006) Strategies for DNA self-assembly in ciliates. In: Mao C, Yokomori T (eds) DNA'06: Proceedings of the 12th international meeting on DNA computing, Seoul, Korea, June 2006. Lecture notes in computer science, vol 4287. Springer, Berlin, pp 71–82Google Scholar
- Kari L, Landweber LF (1999) Computational power of gene rearrangement. In: Winfree E, Gifford DK (eds) Proceedings of DNA based computers, V. Massachusetts Institute of Technology, 1999 American Mathematical Society, Providence, RI, pp 207–216Google Scholar
- Landweber LF, Kari L (1999) The evolution of cellular computing: Nature’s solution to a computational problem. In: Kari L, Rubin H, Wood D (eds) Special issue of Biosystems: proceedings of DNA based computers IV, vol 52(1–3). Elsevier, Amsterdam, pp 3–13Google Scholar
- Petre I, Skogman S (2006) Gene assembly simulator. http://combio.abo.fi/simulator/simulator.php
- Prescott DM (1994) The DNA of ciliated protozoa. Microbiol Rev 58(2):233–267Google Scholar
- Setubal J, Meidanis J (1997) Introduction to computational molecular biology. PWS Publishing Company, Boston, MAGoogle Scholar
- White JH (1992) Geometry and topology of DNA and DNA-protein interactions. In: Sumners et al. (eds) New scientific applications of geometry and topology, American Mathematical Society, Providence, RI, pp 17–38Google Scholar