Nuclear FKBPs, Fpr3 and Fpr4 affect genome-wide genes transcription.

Fpr3 and Fpr4 of Saccharomyces cerevisiae are nuclear FK506-binding proteins each containing an extended acidic domain in addition to the conserved FK506-binding/peptidylprolyl isomerase (PPIase) domain. Previous studies have shown that the PPIase domain regulates histone H3 methylation, while the acidic domain facilitates histone deposition and may regulate rDNA silencing. To gain insight into the role of FKBPs in maintaining chromatin structure, we examined the transcriptional profiles of fpr3 (-) and fpr4 (-) cells. Our results show that both proteins modulate the expression of a large number of genes randomly distributed throughout the genome, a pattern resembling those observed with yeast cells lacking other histone chaperones such as CAF1 and Asf1. Significant overlaps are found between nuclear FKBPs-modulated and the Asf1/CAF1-modulated genes. Thus, nuclear FKBPs appear to impact chromatin structure like other histone chaperones. Our analyses show that depleting Fpr4 causes no detectable chromatin structural change at the rDNA locus nor de-repression of transcription silencing at the locus, in contrast to a previous report. Furthermore, we demonstrate PPIase domain of the proteins represses transcription when tethered to the promoter of a reporter gene, suggesting that the PPIase domains can act on non-histone chromatin components, when brought to close proximity. The results thus provide a further demonstration for the elusive role of Fpr3 and Fpr4 in histone chaperones.