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J. Biol. Chem., Vol. 279, Issue 53, 55520-55530, December 31, 2004

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Chromatin Domain Boundaries Delimited by a Histone-binding Protein in Yeast^*

Sélène Ferrari, Katia Carmine Simmen, Yves Dusserre, Karin Müller, Geneviève Fourel¶, Eric Gilson¶, and Nicolas Mermod||

From the Institute of Biotechnology, Center for Biotechnology UNIL-EPFL, University of Lausanne, 1015 Lausanne, Switzerland and the ^¶Laboratoire de Biologie Moléculaire et Cellulaire, UMR5665 CNRS/ENSL, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France

When located next to chromosomal elements such as telomeres, genes can be subjected to epigenetic silencing. In yeast, this is mediated by the propagation of the SIR proteins from telomeres toward more centromeric regions. Particular transcription factors can protect downstream genes from silencing when tethered between the gene and the telomere, and they may thus act as chromatin domain boundaries. Here we have studied one such transcription factor, CTF-1, that binds directly histone H3. A deletion mutagenesis localized the barrier activity to the CTF-1 histone-binding domain. A saturating point mutagenesis of this domain identified several amino acid substitutions that similarly inhibited the boundary and histone binding activities. Chromatin immunoprecipitation experiments indicated that the barrier protein efficiently prevents the spreading of SIR proteins, and that it separates domains of hypoacetylated and hyperacetylated histones. Together, these results suggest a mechanism by which proteins such as CTF-1 may interact directly with histone H3 to prevent the propagation of a silent chromatin structure, thereby defining boundaries of permissive and silent chromatin domains.

Received for publication, September 9, 2004

^* This work was supported by the Swiss National Science Foundation, the Ligue Nationale Contre le Cancer, and Etat de Vaud. 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.

The on-line version of this article (available at http://www.jbc.org) contains additional text and Fig. S1.

Both authors contributed equally to this work.

^|| To whom correspondence should be addressed: Laboratory of Molecular Biotechnology, FSB-ISP, EPFL, CH-1015 Lausanne, Switzerland. Tel.: 41-21-693-6151; Fax: 41-21-693-7610; E-mail: Nicolas.Mermod{at}unil.ch.

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