Campus

 

Kathleen M. Karrer

Professor Emeritus

B.S. 1971, Marquette University, Milwaukee, WI
Ph.D. 1976, Yale University, New Haven, CT
Postdoctoral Fellow, Indiana University, Bloomington, IN


 

Genome Remodeling and Developmental Programming

The ciliated protozoan, Tetrahymena, is a single celled organism that contains two nuclei: a diploid, germ line micronucleus and transcriptionally active macronucleus. During sexual reproduction, the macronucleus is degraded and a new one develops from a mitotic product of the micronucleus. The development of the new macronucleus involves extensive genome remodeling, including elimination of about 15% of the genome through 5000 or more site specific DNA deletions, de novo DNA methylation and multiple rounds of endoreduplication of the macronuclear genome. Since mating can be easily synchronized in Tetrahymena, the organism provides an unusually good system for analysis of the molecular machinery required for these events (8).

Our long term goal is to understand the molecular mechanisms of genome remodeling. We have characterized families of sequences that are eliminated from the macronuclear genome. One of these encodes homing endonucleases-like proteins with apetala2 DNA binding domains, the only example of this domain outside the plant kingdom (4). Another family, designated Tlr elements, were the first example of the Maverick elements, which are characterized by moderate copy number, long inverted terminal repeats, and a high degree of sequence identity among the family members (7). In vivo rearrangement experiments showed that any part of the Tlr element can serve to promote developmentally regulated deletion from a processing vector (5). This suggested that the machinery for genome remodeling operates via a genome surveillance mechanism. We propose that rather than recognizing specific sequences, the cellular machinery targets some general feature of the germ line limited DNA, such as repetition of the sequence in the micronuclear genome. Experimental evidence confirmed that foreign DNA sequences can be eliminated from the developing macronucleus and the efficiency of their deletion increases with the copy number of the element in the micronucleus (3). 

The molecular machinery for genome remodeling is developmental stage specific. This characteristic was used to isolate genes that are up-regulated at the time of DNA rearrangement (2,6). One of them, ASI2, is nonessential for vegetative growth but is required in the germ line micronucleus to complete the program of sexual reproduction.  Germ line knockouts of ASI2 with wild type macronuclei develop new macronuclei and undergo both DNA rearrangement and de novo DNA methylation, but they fail to complete endoreduplication of the DNA and die before the first postzygotic division (2). The deduced protein encoded by ASI2 resembles a signal transduction receptor. We propose that Asi2p is a regulator of endocycling (1), the occurrence of multiple rounds of DNA replication in the absence of nuclear or cell division.  Current experiments are directed at identifying downstream targets of ASI2.

 

Selected Publications

Karrer, K.M. 2012. Nuclear Dualism in Methods in Cell Biology: Tetrahymena thermophila.  Eds.  K. Collins and E. Orias. 109: 29-52.

Yin, L., S.T. Gater and K.M. Karrer. 2010.  A developmentally regulated gene, ASI2, is required for endocycling in the macronuclear anlagen of Tetrahymena.  Eukaryotic Cell.  9:1343-1353.

Li, S., L. Yin, E. S. Cole, R. A. Udani and K. M. Karrer. 2006. Progeny of germ line knockouts of ASI2, a gene encoding a putative signal transduction receptor in Tetrahymena thermophila, fail to make the transition from sexual reproduction to vegetative growth. Developmental Biology 295: 633-646 

Liu, Y., X. Song, M.A. Gorovsky and K.M. Karrer. 2005. Elimination of foreign DNA during somatic differentiation in Tetrahymena is dosage dependent and involves double-stranded RNA. Euk Cell. 4:421-431 

Wuitschick, J.D., P.R. Lindstrom, A.E. Meyer and K.M. Karrer. 2004. Homing endonucleases encoded by germ line limited genes in the ciliate Tetrahymena have APETELA2 DNA binding domains. Euk. Cell 3:685-694.  

Wuitschick, J.D. and K.M. Karrer. 2003. Diverse sequences within Tlr elements target programmed DNA elimination in Tetrahymena thermophila. Euk. Cell 2:678-689.

Udani, R.A. and K.M. Karrer. 2002. ASI1, a gene encoding a novel leucine zipper protein, is induced during development of the macronucleus in Tetrahymena. Mech. Dev. 118:215-218. 

Wuitschick, J.D., J.A. Gershan, A.J. Lochowicz, S. Li and K.M. Karrer. 2002. A novel family of mobile genetic elements are limited to the germ line genome in Tetrahymena thermophila. Nucleic Acids Res. 30:2524-2537. 

Karrer, K.M. 2000. Tetrahymena genetics: Two nuclei are better than one. In: Methods in Cell Biology series: Tetrahymena thermophila. Ed. D. Asai and J. Forney. Vol. 62 pp. 127-186.


Meeting Presentations

Karrer, K.M.  Control of Endocycling in Tetrahymena.  Gall 85th Birthday Symposium. Baltimore, MD, April 13-14, 2013

 

Invited Talks

Genome remodeling in Tetrahymena: Developmentally programmed DNA deletion and endocycling.  Southern Illinois University, Carbondale, IL September 2, 2011.

 

Awards

Nora Finnigan Werra Faculty Achievement Award (2009)

John P. Raynor, S.J., Faculty Award for Teaching Excellence (1999)

Clare Booth Luce Professor (1989-1994)

 

Current Students

Dr. Karrer is not currently accepting new Ph.D. students into her lab

 

 



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