FIG. 3.

Requirement for Dls1p in Isw2-dependent effects on transcription. (A) Direct comparison of transcriptional profiles in isw2 rpd3 and dls1 rpd3 cells by DNA microarray analysis. Signals (pixels) normalized from six independent hybridizations were plotted. x axis, isw2 rpd3 mutant; y axis, dls1 rpd3 mutant. Note that the signals are represented by the number of pixels detected, rather than the ratio of expression to that of wild-type cells. The numbers of pixels detected are proportional to the strength of signals, hence the abundance of RNA molecules. The line in the center represents identical signals from each mutant. The two outside lines represent a twofold difference between the mutants. The two dots that are most distant from the diagonal line represent ISW2 and YJL064W genes. YJL064W is a dubious open reading frame that overlaps with the DLS1 gene (YJL065C). The DLS1 gene itself was eliminated from this analysis because of high local backgrounds in the batch of DNA microarrays used. (B) Northern blot analysis of Isw2 target genes. The genotypes of the cells used are indicated on the top. Listed vertically on the right of each blot is the gene being probed. The number under each band indicates the fold change in expression level relative to wild-type cells as determined with a phosphorimager. Signals were normalized for a loading control, ACT1. (C) Epistasis analysis of ISW2 and DLS1 genes by Northern blotting. (D) Northern blot analysis of Mata-specific genes STE2 and STE6 in Matα isw2 and dls1 mutants. As an internal positive control, the REC104 gene was also probed. WT, wild type.