Epigenetic effects on yeast transcription caused by mutations in an actin-related protein present in the nucleus

Gene inactivation can result when a delta element of the Ty1 transposon inserted into the yeast HIS4 promoter (his4-912 delta) alters the transcription initiation site. Previous work has identified mutations that suppress this transcriptional defect by restoring the transcription start site to the native position, and these mutations have been implicated in transcriptional regulation and chromatin structure. We show that in a sin4 mutant such suppression is incompletely penetrant, such that genetically identical yeast cells (sin4 his4-912 delta) show either of two distinct phenotypic states, His(+) or His(-). To study this type of potential epigenetic control of gene expression, we constructed a strain with ADE2 expression under the control of the his4-912 delta promoter, as colony color provides a convenient assay for ADE2 expression. We isolated mutations in the ACT3 gene that show variegated expression of this ADE2 reporter. The act3 his4 delta-ADE2 colonies display both white and red sectors, showing that the two different phenotypes are possible in a single colony. The two phenotypic states can be inherited during clonal growth, yet are reversible. Analysis of RNA isolated from individual colonies of either red or white color demonstrates that it is the state of the promoter, as either On or Off, that is inherited and is responsible for the colony color. An act3 mutation also affects expression of the HIS4 and LYS2 genes; thus, Act3p is not a delta element-specific transcriptional regulator. Immunofluorescence microscopy experiments demonstrate that the Act3p protein is present in the nucleus. Act3p shows clear homology to actin, and possible roles for an actin-related protein in transcription are discussed.