FIG. 3.

Nested nonintronic genes in the budding yeast genome. (A) Gene organization at the rDNA repeat locus of S. cerevisiae chromosome (Chr.) XII. The TAR1 gene (represented by the red arrow) is nested opposite and within the 25S rRNA gene. For simplicity, a single repeat unit of the rDNA locus is presented here; approximately 140 tandem copies of this unit are present on chromosome XII. (B) TAR1 encodes a protein product and is conserved among related fungi. The TAR1 gene was originally identified by transposon-based gene trapping in S. cerevisiae. Twenty-three different sites of transposon insertion identified within TAR1 are represented here by vertical blue lines along the arrow representing the TAR1 gene. Transposon insertions at each of these sites within TAR1 resulted in detectable levels of β-galactosidase (β-Gal) activity under vegetative growth conditions, as indicated by the blue circle. The protein-coding potential of TAR1 was confirmed by Western blotting, and the Tar1p product was localized to yeast mitochondria. TAR1 is conserved among hemiascomycetous species, and a sampling of these species is shown here. The similarity of the indicated orthologous sequence to that of S. cerevisiae Tar1p is indicated by the intensity of the shaded ellipse; the darkest colors indicate the strongest sequence similarity. (C) Gene organization at the YGR031W locus on S. cerevisiae chromosome VII. Transcription of the nested gene NAG1 is regulated by Rlm1p binding at the indicated site shared with the GSC2 promoter. The consensus sequence for Rlm1p binding is shown here. (D) NAG1 encodes a protein product with two predicted transmembrane (TM) domains. A Nag1p-green fluorescent protein (GFP) chimera localizes to the yeast cell periphery, consistent with its likely role as a plasma membrane protein contributing to yeast cell wall biogenesis.