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Originally published as Genetics Published Articles Ahead of Print on September 14, 2008.
Genetics, Vol. 180, 1407-1418, November 2008, Copyright © 2008
doi:10.1534/genetics.108.094490
The DNA End-Binding Protein Ku Regulates Silencing at the Internal HML and HMR Loci in Saccharomyces cerevisiae
Catherine L. Vandre*,
Rohinton T. Kamakaka
and
David H. Rivier*,1
* Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois 61801 and Department of MCD Biology, University of California, Santa Cruz, California 95064
1 Corresponding author: Department of Cell and Developmental Biology, B107 Chemical and Life Science Bldg., University of Illinois, 601 S. Goodwin Ave., Urbana, Illinois 61801.
E-mail: rivier{at}uiuc.edu
Heterochromatin resides near yeast telomeres and at the cryptic mating-type loci, HML and HMR, where it silences transcription of the 
- and a-mating-type genes, respectively. Ku is a conserved DNA end-binding protein that binds telomeres and regulates silencing in yeast. The role of Ku in silencing is thought to be limited to telomeric silencing. Here, we tested whether Ku contributes to silencing at HML or HMR. Mutant analysis revealed that yKu70 and Sir1 act collectively to silence the mating-type genes at HML and HMR. In addition, loss of yKu70 function leads to expression of different reporter genes inserted at HMR. Quantitative chromatin-immunoprecipitation experiments revealed that yKu70 binds to HML and HMR and that binding of Ku to these internal loci is dependent on Sir4. The interaction between yKu70 and Sir4 was characterized further and found to be dependent on Sir2 but not on Sir1, Sir3, or yKu80. These observations reveal that, in addition to its ability to bind telomeric DNA ends and aid in the silencing of genes at telomeres, Ku binds to internal silent loci via protein–protein interactions and contributes to the efficient silencing of these loci.
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Genetics 2008 180: NP.
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