Abstract
The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5' and 3' ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30 target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, a genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5' end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2, and +3 nucleosomes at the 5' end of target genes were shifted significantly, whereas the position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity-purified, single-component Fun30 exhibited a nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in the regulation of transcription and indicate that Fun30 remodels chromatin at the 5' end of genes by sliding promoter-proximal nucleosomes.
Highlights
The conserved ATP-dependent chromatin remodeling enzyme Fun30 regulates heterochromatin silencing and DNA repair
Because H2AZ nucleosomes have been implicated in regulation of gene activation or repression [50], we examined the role of Fun30 in the regulation of gene expression
We identified a role of Fun30 in the regulation of transcriptional repression by altering nucleosome positioning
Summary
The conserved ATP-dependent chromatin remodeling enzyme Fun regulates heterochromatin silencing and DNA repair. We demonstrated that affinity-purified, single-component Fun exhibited a nucleosome sliding activity in an ATP-dependent manner These results define a role for Fun in the regulation of transcription and indicate that Fun remodels chromatin at the 5 end of genes by sliding promoter-proximal nucleosomes. Control of the dynamics of nucleosomes at the 5Ј end of genes is expected to be important for transcription Both gene-specific and genome-wide studies indicate that nucleosome position and occupancy can be regulated by DNA sequence and trans-factors, including non-histone chromatin binding proteins, histone modification enzymes, and ATP-de-. Our results indicate that Fun represses transcription by sliding nucleosomes flanking the ϩ1 H2AZ-containing nucleosome at the 5Ј end of genes
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