Deletions of three yeast genes, SET2, CDC73, and DST1, involved in transcriptional elongation and/or chromatin metabolism were used in conjunction with genetic array technology to screen approximately 4700 yeast deletions and identify double deletion mutants that produce synthetic growth defects. Of the five deletions interacting genetically with all three starting mutations, one encoded the histone H2A variant Htz1 and three encoded components of a novel 13 protein complex, SWR-C, containing the Snf2 family ATPase, Swr1. The SWR-C also copurified with Htz1 and Bdf1, a TFIID-interacting protein that recognizes acetylated histone tails. Deletions of the genes encoding Htz1 and seven nonessential SWR-C components caused a similar spectrum of synthetic growth defects when combined with deletions of 384 genes involved in transcription, suggesting that Htz1 and SWR-C belong to the same pathway. We show that recruitment of Htz1 to chromatin requires the SWR-C. Moreover, like Htz1 and Bdf1, the SWR-C promotes gene expression near silent heterochromatin.

Using DNA microarrays, we compared global transcript stability profiles following chemical inhibition of transcription to rpb1-1 (a temperature-sensitive allele of yeast RNA polymerase II). Among the five inhibitors tested, the effects of thiolutin and 1,10-phenanthroline were most similar to rpb1-1. A comparison to various microarray data already in the literature revealed similarity between mRNA stability profiles and the transcriptional response to stresses such as heat shock, consistent with the fact that the general stress response includes a transient shutoff of general mRNA transcription. Genes encoding factors involved in rRNA synthesis and ribosome assembly, which are often observed to be coordinately down-regulated in yeast microarray data, were among the least stable transcripts. We examined the effects of deletions of genes encoding deadenylase components Ccr4p and Pan2p and putative RNA-binding proteins Pub1p and Puf4p on the genome-wide pattern of mRNA stability after inhibition of transcription by chemicals and/or heat stress. This examination showed that Ccr4p, the major yeast mRNA deadenylase, contributes to the degradation of transcripts encoding both ribosomal proteins and rRNA synthesis and ribosome assembly factors and mediates a large part of the transcriptional response to heat stress. Pan2p and Puf4p also contributed to the degradation rate of these mRNAs following transcriptional shutoff, while Pub1p preferentially stabilized transcripts encoding ribosomal proteins. Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level of mRNA stability. mRNA turnover is an important factor in the regulation of gene expression in eukaryotic cells and complements transcriptional regulation by endowing the cell with the capability to rapidly vary the levels of existing transcripts (7,27). mRNA half-lives range from 3 min to more than 100 min in Saccharomyces cerevisiae (20,58) and from ϳ15 min to more than 10 h in mammals (27). The details of the eukaryotic mRNA decay pathway are best understood in S. cerevisiae, where many of the major proteins involved have been identified and characterized (53, 60). Deadenylation and decapping are the two most important steps in the mRNA degradation pathway and typically occur sequentially (10, 55, 60), although decapping is not absolutely dependent upon deadenylation (54). Deadenylation is carried out by the Pan2/Pan3 and the Ccr4/Caf1 poly(A) nuclease complexes (54), and decapping is carried out by the decapping enzymes Dcp1 and/or Dcp2, all of which are conserved among eukaryotes (33, 44). A deadenylated and decapped mRNA is degraded by the 5Ј33Ј exonuclease Rat1 and/or Xrn1 (22) and by a 3Ј35Ј exonucleolytic protein complex known as the exosome (26).Transcript stability is traditionally thought to be regulated by specific sequences or structures in the 3Ј or 5Ј untranslated region (UTR) and by cognate trans-acting factors that recognize, and in some cases may bind to, these elements (40). The identification of cis-and tran...