Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

Abstract

Previous studies in Saccharomyces cerevisiae have demonstrated that cryptic promoters within coding regions activate transcription in particular mutants. We have performed a comprehensive analysis of cryptic transcription in order to identify factors that normally repress cryptic promoters, to determine the amount of cryptic transcription genome-wide, and to study the potential for expression of genetic information by cryptic transcription. Our results show that a large number of factors that control chromatin structure and transcription are required to repress cryptic transcription from at least 1,000 locations across the S. cerevisiae genome. Two results suggest that some cryptic transcripts are translated. First, as expected, many cryptic transcripts contain an ATG and an open reading frame of at least 100 codons. Second, several cryptic transcripts are translated into proteins. Furthermore, a subset of cryptic transcripts tested is transiently induced in wild-type cells following a nutritional shift, suggesting a possible physiological role in response to a change in growth conditions. Taken together, our results demonstrate that, during normal growth, the global integrity of gene expression is maintained by a wide range of factors and suggest that, under altered genetic or physiological conditions, the expression of alternative genetic information may occur.

Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability inSaccharomyces cerevisiae

“…Because the H2A R78A mutant induced cryptic transcription of the FLO8-HIS3 reporter gene (see Figure 2C), it is possible that some of the gene expression changes could reflect activation of cryptic transcripts. However, we did not observe a significant enrichment of yeast genes with known cryptic transcripts (Cheung et al 2008). Analysis of histone occupancy ChIP-chip data in ChromatinDB (O'Connor and Wyrick 2007) indicated that the 290 up-regulated genes had higher levels of histone occupancy in their promoter regions in wild-type cells and were depleted for permissive chromatin marks ( Figure S4).…”

“…Previous studies have discovered that the H3 R49A sprocket arginine mutant activates transcription initiation from a cryptic promoter within the FLO8-coding sequence due to a defect in Set2-dependent H3 K36 methylation (Hainer and Martens 2011). We tested the effects of this and other sprocket arginine mutants on FLO8 cryptic transcription using a FLO8-HIS3 reporter (Cheung et al 2008) and scoring for growth on media lacking histidine (SC-Leu-His; see Figure 2C). We confirmed that the H3 R49A mutant induced cryptic transcription from the FLO8-HIS3 reporter, enabling the strain to grow in media lacking histidine.…”

RNA Polymerase II Carboxyl-terminal Domain Phosphorylation Regulates Protein Stability of the Set2 Methyltransferase and Histone H3 Di- and Trimethylation at Lysine 36

“…Subsequent studies revealed that H3K36me2 is the preferred substrate for Rpd3(S) binding (12)(13)(14) and that a primary function for H3K36 methylation is to recruit the repressive activity of Rpd3(S) to genes to "reset" or reestablish chromatin structure between multiple rounds of transcription (15)(16)(17). Such resetting, or at least maintaining a more compact chromatin structure within gene bodies, also protects genes from spurious transcription from improper initiation sites (cryptic transcription) (15)(16)(17)(18). To date, no separate function has been reported for H3K36me3.…”

Structure and in Vivo Requirement of the Yeast Spt6 SH2 Domain

“…We nevertheless aimed to detect a possible global, chromatin-related function of the SH2 domain in the transcriptome data with use of correlation analysis. We first investigated whether the deregulated genes correlate to genes described to show cryptic transcription initiation in a spt6 mutant 33 that carried an internal deletion of amino acids 931-994 (corresponding to 930-993 in C. glabrata and comprising the HhH-domain that is purple in Fig. 5).…”

“…S5a). 33 We also investigated whether our set of differentially expressed genes shows any correlation with gene length or an unusual number of associated nucleosomes. 32 Again, we could not find significant correlations.…”