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the IES and joins the MDSs through one copy of the pointer, in this case by
application of the ld excision operation. The template molecule emerges intact
and can be used repeatedly to guide more recombinations in the multiple DNA
molecules in a polytene chromosome.
TEMPORAL ORDER OF EVENTS IN GENE ASSEMBLY
There are at least three possible models, distinguished by their temporal pro-
grams, for IES excisions and MDS ligations during macronuclear development:
(1) all IESs might be excised at the same time, with simultaneous joining of
all MDSs; (2) IESs might be excised and MDSs ligated in a fixed temporal
order, creating one or more partially processed intermediates; (3) IESs might
be excised and MDSs ligated in an order that is not fixed, with different orders
in different developing macronuclei or even with different orders in different
DNA molecules within the same developing macronucleus. One experimental
result so far suggests IESs are excised and MDSs are ligated in a fixed temporal
order. IES 6 in the actin I gene of
Sterkiella histriomuscorum
, which separates
MDS 9 from MDS 10, is invariably the first to be excised, followed some hours
later by excision of the remaining eight IESs and MDS reordering/ligation.
Whether these remaining events occur in a fixed temporal order has not yet
been determined.
CONCLUSIONS
In this chapter we described in detail the decryption of micronuclear genes
in ciliates. We considered the gene assembly process from a computational
perspective and introduced the template-guided model. The temporal order of
events in gene assembly was also briefly considered, and we highlighted some
open questions on this matter. In the next chapter, Kari and Landweber further
develop the decryption of macronuclear DNA from a computational standpoint.
Acknowledgments
This work is supported by NIGMS research grant R01 GM 56161
and NSF research grant MCB-9974680 to D.M. Prescott. We are grateful to Gayle
Prescott for her patience in typing several versions of the manuscript and to Beth Hewitt
for constructing the figures.
References
[1] S. Duharcourt, A-M. Keller, and E. Meyer. Homology-dependent maternal inhi-
bition of developmental excision of internal eliminated sequences in
Paramecium
tetraurelia
.
Mol. Cell. Biol.
, 18:7075-7085, 1998.
