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J. Biol. Chem., Vol. 278, Issue 39, 37471-37479, September 26, 2003

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Repair of UV Lesions in Silenced Chromatin Provides in Vivo Evidence for a Compact Chromatin Structure^*

Magdalena Livingstone-Zatchej , Rosanna Marcionelli , Kathrin Möller, Remko de Pril and Fritz Thoma 

From the Institut für Zellbiologie, ETH, Hönggerberg, CH-8093 Zürich, Switzerland

Genes positioned close to telomeres in yeast are silenced by a heterochromatin-like structure containing Sir proteins. To investigate whether silencing also affects DNA repair, we studied removal of UV lesions by photolyase and nucleotide excision repair (NER) in strains containing the URA3 gene inserted 2 kilobases from a telomere. URA3 was transcriptionally active in sir3 mutants, partially silenced in SIR3 cells, or completely silenced by overexpression of SIR3 or deletion of RPD3. The active URA3 showed efficient repair by both pathways. Fast repair of the promoter and 3' end by photolyase reflected a non-nucleosomal structure. Partial silencing had no remarkable effect on photolyase but reduced repair by NER, indicating differential accessibility for the two repair reactions. Complete silencing inhibits NER and photolyase in the coding region as well as in the promoter and the 3'-end. Conventional nuclease footprinting analyses revealed subtle changes in the promoter proximal nucleosome under partially silenced conditions but a pronounced reorganization of chromatin extending over the whole gene in silenced chromatin. Thus, both repair systems are sensitive to chromatin changes associated with silencing and provide direct evidence for a compact structure of heterochromatin.

Received for publication, June 16, 2003 , and in revised form, July 17, 2003.

^* This work was supported by grants of the Swiss National Science Foundation and the ETH. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Both authors contributed equally to this work.

To whom correspondence should be addressed. Tel.: 41-1-633-33-23; Fax: 41-1-6331069; E-mail: thoma{at}cell.biol.ethz.ch.

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