Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

Abstract

The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrated to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have performed whole-genome expression analysis, using DNA microarrays, to study mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. This analysis was performed on cells grown in both rich and minimal media. The microarray results, combined with Northern blot, computational, and genetic analyses, show that snf2Delta and swi1Delta mutations cause similar effects on mRNA levels, that Snf/Swi controls some genes differently in rich and minimal media, and that Snf/Swi control is exerted at the level of individual genes rather than over larger chromosomal domains. In addition, this work shows that Snf/Swi controls mRNA levels of MATalpha-specific genes, likely via controlling transcription of the regulators MATalpha1 and MCM1. Finally, we provide evidence that Snf/Swi acts both as an activator and as a repressor of transcription, and that neither mode of control is an indirect effect of the other.

Figure 1

Scatter plot of expression ratios of all genes in snf2Δ and swi1Δ in rich medium. The ratio of mutant to wild-type mRNA levels was calculated for every gene in both mutants. Only genes with at least 40 fluorescence units in the wild type were included. The ratios were transformed to Log₂ (ratio), such that a two-fold increase in gene expression in a mutant would equal 1 whereas a two-fold decrease would equal −1. To compare the expression of each gene in snf2Δ to that in swi1Δ, the transformed ratios for every gene in snf2Δ was plotted against those in swi1Δ.

Figure 2

Opposite effects of snf/swi mutations on mRNA levels. Northern blot analysis of SAG1 and SER3 mRNA levels in the strains FY2, FY20, FY31, FY32, FY1254, and FY1882 grown in rich medium (A) or minimal medium (B). mRNA levels of each pair of strains were averaged before normalization to the wild type. SAG1 mRNA levels are 0.13 and 0.04 in rich and minimal media, respectively, in snf2Δ and 0.11 and 0.03 in rich and minimal media, respectively, in swi1Δ, compared with the wild-type strain (1.0). SER3 mRNA levels are 21.4 and 3.19 in rich and minimal media, respectively, in snf2Δ and 6.94 and 2.36 in rich and minimal media, respectively, in swi1Δ compared with the wild-type strain (1.0).

Figure 3

(A) snf2Δ and snf1Δ mutations reduce the mRNA levels of MATα-specific genes. (B) snf2Δ and snf1Δ mutations reduce the mRNA levels of the MATα gene regulators MATα1 and MCM1. Northern blot analysis was performed in the same strains described in the legend for Fig. 3, grown in rich medium. Quantitation, performed as described in the Fig. 3 legend, is shown in Table 2.

Figure 4

The decreased mRNA levels of SAG1 and MATα1 in snf2Δ mutants are suppressed by (hta1-htb1)Δ, but the increased mRNA levels of SER3 and YOR222W are not suppressed. (A) Northern blot analysis of SAG1, MATα1, and SER3 was performed on RNA prepared from strains FY2, FY1884, FY31, and FY1885. SAG1 mRNA levels in (hta1-htb1)Δ, snf2Δ, and (hta1-htb1)Δ snf2Δ are 0.82, 0.15, and 0.51, respectively. MATα1 mRNA levels are 1.51, 0.39, and 1.20, respectively. (B) Analysis of YOR222W mRNA levels was done on strains FY57, FY710, FY458, and FY724. SER3 mRNA levels in (hta1-htb1)Δ, snf2Δ, and (hta1-htb1)Δ snf2Δ are 5.28, 23.2, and 25.1, respectively. YOR222W mRNA levels are 1.79, 7.95, and 7.99, respectively. All mRNA levels are relative to those in the wild-type strain (1.0). All strains were grown in rich medium.