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

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

doi:10.1074/jbc.m410346200

Abstract

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.

Highlights

When located next to chromosomal elements such as telomeres, genes can be subjected to epigenetic silencing
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
Boundary elements have been defined functionally by their ability to protect against position effect when flanking the assayed gene

Summary

Introduction

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. The expression state of a eukaryotic gene depends in part on its location in the chromosome This position effect results from the organization of eukaryotic genomes into discrete functional domains, defined by local differences in chromatin structure. Transcriptional repression of the yeast Saccharomyces cerevisiae subtelomeric regions is one of the best-studied examples of position-dependent gene expression. This phenomenon is referred to as telomere position effect and is similar to the position effect variegation (PEV) initially described in Drosophila [6]. Silencing in natural subtelomeric regions further involves auxiliary recruitment at protosilencer relay elements found in the middle-repetitive X and YЈ subtelomeric elements [1, 8, 16]

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Conclusion