Regulated Antisense Transcription Controls Expression of Cell-Type-Specific Genes in Yeast

Transcriptome profiling studies have recently uncovered a large number of noncoding RNA transcripts (ncRNAs) in eukaryotic organisms, and there is growing interest in their role in the cell. For example, in haploidSaccharomyces cerevisiae cells, the expression of an overlapping antisense ncRNA, referred to here asRME2 (R egulator ofMe iosis2 ), preventsIME4 expression. In diploid cells, thea 1-α2 complex represses the transcription ofRME2 , allowingIME4 to be induced during meiosis. In this study we show that antisense transcription across theIME4 promoter region does not block transcription factors from binding and is not required for repression. Mutational analyses found that sequences within theIME4 open reading frame (ORF) are required for the repression mediated byRME2 transcription. These results support a model where transcription ofRME2 blocks the elongation of the full-lengthIME4 transcript but not its initiation. We have found that another antisense transcript, calledRME3 , repressesZIP2 in a cell-type-specific manner. These results suggest that regulated antisense transcription may be a widespread mechanism for the control of gene expression and may account for the roles of some of the previously uncharacterized ncRNAs in yeast.