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Originally published as Genetics Published Articles Ahead of Print on June 14, 2005.
Genetics, Vol. 170, 1611-1621, August 2005, Copyright © 2005
doi:10.1534/genetics.104.031401
Genome-Wide Characterization of Tetrahymena thermophila Chromosome Breakage Sites. I. Cloning and Identification of Functional Sites
Eileen Hamilton*,1,
Peter Bruns
,
Cindy Lin*,2,
Virginia Merriam
,
Eduardo Orias*,
Linh Vong*,3 and
Donna Cassidy-Hanley
* Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106
Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
Department of Biology, Loyola Marymount University, Los Angeles, California 90045
Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853
1 Corresponding author: Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106.
E-mail: ehamilto{at}lifesci.ucsb.edu
The chromosomes of the macronuclear (expressed) genome of Tetrahymena thermophila are generated by developmental fragmentation of the five micronuclear (germline) chromosomes. This fragmentation is site specific and directed by a conserved 15-bp chromosome breakage sequence (Cbs element). This article reports the construction of a library enriched for chromosome breakage junctions and the development of a successful scheme for the genome-wide isolation and characterization of functional Cbs junctions. Twenty-three new Cbs junctions were characterized and each was assigned to a specific micronuclear chromosome or chromosome arm. Two distinct previously unreported variant chromosome breakage sequences were found, each in two or more functional Cbs elements. Analysis of natural Cbs junctions confirmed that microheterogeneity in the macronuclear telomere addition site is associated with chromosome fragmentation. The physical and genetic characterization of these functional chromosome breakage junctions is reported in the accompanying article in this issue. The whole-genome shotgun sequencing and auto-assembly phase of the Tetrahymena Genome Initiative has recently been completed at The Institute for Genome Research (TIGR). By providing unique sequence from the natural ends of macronuclear chromosomes, Cbs junctions characterized in the work reported here will serve as useful sequence tags for relating macro- and micronuclear genetic, physical, and sequence maps.
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