The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders
© Law et al.; licensee BioMed Central Ltd. 2005
Received: 2 September 2005
Accepted: 21 November 2005
Published: 3 January 2006
Translational efficiencies in Saccharomyces cerevisiae vary from transcript to transcript by approximately two orders of magnitude. Many of the poorly translated transcripts were found to respond to the appropriate external stimulus by recruiting ribosomes. Unexpectedly, a high frequency of these transcripts showed the appearance of altered 5' leaders that coincide with increased ribosome loading.
Of the detectable transcripts in S. cerevisiae, 8% were found to be underloaded with ribosomes. Gene ontology categories of responses to stress or external stimuli were overrepresented in this population of transcripts. Seventeen poorly loaded transcripts involved in responses to pheromone, nitrogen starvation, and osmotic stress were selected for detailed study and were found to respond to the appropriate environmental signal with increased ribosome loading. Twelve of these regulated transcripts exhibited structural changes in their 5' transcript leaders in response to the environmental signal. In many of these the coding region remained intact, whereas regulated shortening of the 5' end truncated the open reading frame in others. Colinearity between the gene and transcript sequences eliminated regulated splicing as a mechanism for these alterations in structure.
Frequent occurrence of coordinated changes in transcript structure and translation efficiency, in at least three different gene regulatory networks, suggests a widespread phenomenon. It is likely that many of these altered 5' leaders arose from changes in promoter usage. We speculate that production of translationally silenced transcripts may be one mechanism for allowing low-level transcription activity necessary for maintaining an open chromatin structure while not allowing inappropriate protein production.
Across a cellular transcriptome the loading of ribosomes onto individual mRNA species varies broadly [1–3], consistent with each transcript having a uniquely defined efficiency of translation. Translational efficiencies across the transcriptome of Saccharomyces cerevisiae have been estimated to vary from transcript to transcript by approximately two orders of magnitude (as reported by MacKay and coworkers  and herein). Many factors contribute to transcript-specific translation efficiencies, including those intrinsic and extrinsic to mRNA structure . Extrinsic factors include regulation of the activities of translation initiation factors through phosphorylation [5, 6] and regulation of the binding of transacting molecules [7–9]. Factors intrinsic to the specific mRNA include features of the 5' untranslated region (UTR) that inhibit ribosome scanning such as secondary structure  and upstream open reading frames (ORFs) . In addition, altered translational efficiency can arise from regulated changes in mRNA structure, such as modifications in transcript structures occurring through alternative use of promoters and splice sites within the nucleus , as well as RNA splicing and polyadenylation mechanisms occurring in the cytosol [13, 14]. The relative importance of these various regulatory mechanisms differs widely from transcript to transcript in a given cell or tissue.
In the present study, we identified a set of under-translated transcripts of S. cerevisiae. Within this group of transcripts, we found over-representation of the Gene Ontology (GO) categories related to environmental responses of the organism, suggesting that mRNA translatability may be controlled in response to exogenous stresses. Transcripts from three of these GO categories, namely responses to pheromone, nitrogen starvation, and osmotic stress, were selected to test this hypothesis. Many of the under-translated transcripts selected were found to respond to the appropriate environmental signal with a change in ribosome loading. Remarkably, we found that a majority of these alterations in translation are accompanied by a change in the 5' UTR of the transcript. These findings suggest that changes in translational efficiency as a consequence of altered transcript structure are much more common than was previously suspected. Furthermore, those alterations that arise from changes in promoter usage have implications with regard to the fate of intergenic transcripts involved in regulation of gene expression.
The under-translated transcriptome
For the purposes of subsequent analysis, those transcripts with translation efficiencies below 0.25 of the mean were arbitrarily defined as under-translated. By this definition, of the 3,916 transcripts for which reliable polysome profiles could be modeled, fewer than 10% (298 transcripts) were found to be under-translated . Two experimentally accessible characteristics combine to achieve inefficient translation of these transcripts: the fraction of a transcript in the act of being translated (for example, associated with ribosomes) and the average spacing of ribosomes along a translating mRNA. Across the entire transcriptome, the average fraction of transcripts associated with ribosomes is 0.82 and the average ribosome density is 4.4 ribosomes per 1,000 nucleotides. For most members of the under-translated transcriptome, both parameters lie below these population means (Figure 1b, filled symbols). At the extremes of the distribution, a few of the under-translated transcripts are more than 90% associated with ribosomes but sparsely loaded. Likewise, a few others possess ribosome densities that are average or above, but with less than 20% of the transcripts actually present in polysomes.
In the under-translated transcriptome, 213 of the 298 transcripts are the products of named genes. The biologic processes associated with this poorly translated group are explored in Figure 1c. Because the analysis was restricted to just the subset of named genes, the category 'process unknown' represents only 3.5% of this selected group of transcripts, in contrast to 13.9% in the complete dataset. The GO categories significantly (P < 0.01) over-represented or under-represented in the under-translated transcriptome are specifically broken down in the figure, whereas all others are combined in the 'other' category. The processes of protein synthesis, ribosome biogenesis, and RNA metabolism are under-represented in the under-translated transcriptome, which was expected because the transcripts analyzed were derived from steady-state growing cells, where protein synthesis is vigorous. In contrast, responses to environmental changes such as 'response to stress', 'cell cycle', 'signal transduction', and 'sporulation, meiosis and pseudohyphal growth' were significantly over-represented in the population of under-translated transcripts. Individual representatives from these environmental response categories were selected from the under-translated population, and their responses to external stimuli were evaluated.
Translational responses of the transcriptome to mating pheromone
Influence of pheromone treatment, nitrogen starvation and osmotic stress on 5' leader structure and ribosome loading
RNase protection assays (Figure 2d) revealed that the long SAG1 transcript has a 5' end greater than 484 nucleotides upstream of the ORF. The short form exhibits a ladder of protected fragments (Figure 2d), probably resulting from either multiple, closely placed transcriptional starts or breathing of the RNA double helix during the assay. The size of the predominant short species is consistent with the 5' end being located at approximately -40 nucleotides relative to the start of the ORF. Results of 5' rapid amplification of cDNA ends (RACE; Table 1), performed on total RNA from either growing cells or cells treated with α-factor for 30 minutes, revealed major 5' termini at positions -826 and -38. Therefore, RNase protection and 5' RACE are consistent with both transcripts containing the initiation codon for the known form of Sag1 protein. The size of the short transcript is consistent with the presence of a pheromone-response element  and a TATA box  in this region of the genome.
Exploring further the apparent difference in translational efficiency between the two SAG1 transcripts, His3p tagged with the HA epitope was used as a reporter  in constructs containing either the 826-nucleotide or 38-nucleotide 5' leader of SAG1 under the control of a heterologous constitutive promoter. Western blot analysis revealed much higher levels of protein produced from the construct with the short 5' leader (Figure 2e; compare lanes 1 and 3). Because the same protein was produced from both transcripts, the difference in level must have resulted from altered rates of synthesis rather than differences in protein stability. Transcript levels were determined using QPCR (data not shown) and the calculated translation efficiency (protein/mRNA) of the transcript with the short SAG1 leader was found to be 4.9 times that of the long SAG1 construct, which is consistent with the qualitative assessment of ribosome loading by sucrose gradient centrifugation (Figure 2a, and Table 1). Thus, production of a new transcript with elevated translational efficiency amplifies the protein response resulting from transcriptional induction of the SAG1 gene (Figure 2c).
Other transcripts in addition to HO and SAG1 were found to change their association with ribosomes in response to mating pheromone . These include CRH1, KAR5, PRM2, PRP39, and PRY3, which - like HO and SAG1 - all show concomitant alterations in their 5' leaders (Table 1). Interestingly, the poorly loaded forms of these particular transcripts all have their 5' termini located within the protein encoding regions, precluding synthesis of the full-length proteins (see Discussion, below).
Many genes respond to α-factor with increases in transcript level, but corresponding alterations in transcript structure were not universally found. For example, four genes - BAR1, FAR1, PRM4, and STE2 - all exhibited elevated transcript levels after exposure to α-factor, but none of these showed a modified 5' leader (Table 1). Of these four genes, only PRM4 exhibited significantly altered ribosome loading , and this transcript is seemingly 'poised' to respond rapidly at the translational level to pheromone. It should be emphasized that, of the pheromone-responsive cohort of genes examined in this paper, PRM4 is the only one that showed a change in ribosome loading with no concomitant change in transcript structure.
Influence of nitrogen starvation on the translation state of the transcriptome
Under-translated genes involved in responses to nitrogen stress
Regulation of arginine and ornithine utilization
Regulation of aromatic amino acid catabolism
Regulates amino acid permease Gap1p
General control of amino acid biosynthesis
Regulates nitrogen catabolic gene expression
Regulates amino acid permease Gap1p
Regulator of amino acid permease genes
The 5' termini of eight transcripts related to nitrogen stress were examined before and after starvation (Table 1). The ASP1 and GDH1 transcripts follow the general reduction in ribosome loading after nitrogen starvation and are unaltered in structure. This is in contrast to a group of transcripts with enhanced ribosome loading, namely AMD2, ASP3, DAL5, and DAL7, which all exhibit clear alterations in the 5' termini of their transcripts. The 5' end of the short form of ASP3 lies within the ORF, as was noted above for some of the pheromone-regulated transcripts. Two other transcripts, UGA1 and MON1, were found to have unaltered 5' termini after starvation, although they exhibit enhanced ribosome loading with nitrogen starvation.
Influence of osmotic stress on the under-translated transcriptome
Under-translated osmoregulatory genes
Salt induced aldo-keto reductase
Aldehyde dehydrogenase, activity increased by osmotic shock
MAPKKK in the PKC pathway
Present with Hot1p at GPD1 promoter only during osmostress
Transcription factor, high osmolarity
Negative effector of halotolerance
MAPKK osmosensing, redundant w/SSK2
osmosensing activator of MAPK pathway
Involved in vacuole biogenesis and osmoregulation
MAPK in osmolarity response
Glycerone kinase, response to stress
Osmoregulation in vacuole
Poorly translated cytosolic transcripts are usually found predominantly within mRNP particles  or with single ribosomes arrested on them , depending on the mechanism of regulation. Conversely, transcripts in the process of being translated into protein are generally associated with multiple actively translating ribosomes (polysomes). Because the average rate of movement of translating ribosomes along mRNAs (for example, polypeptide elongation) tends to be constant among different transcript species , it follows that the spacing of ribosomes along an mRNA is generally proportional to the rate of synthesis of the encoded protein. These considerations enable estimates of relative rates of synthesis of individual proteins across transcriptomes [1, 3], which in turn allowed us to define a class of transcripts that are under-loaded with ribosomes and thus apparently translated at lower efficiencies than the majority of the transcriptome. However, this definition is not all-inclusive, because those transcripts whose translation is regulated through arrest of elongation would be located in the polysomal fraction and therefore would not be identified as under-translated by this analysis. Transcripts regulated at the level of polypeptide elongation may be prominent during early embryonic development [29, 30] and among transcripts regulated by micro-RNAs . Because of these considerations, the definition of less than 10% of the transcripts as 'under-translated' in growing yeast being may be an under-estimate.
Mechanisms for generating alternate 5' untranslated regions
For a significant number of the genes implied to be under-translated during normal growth conditions, ribosome loading increased under the appropriate stress conditions, suggesting the existence of specific regulatory mechanisms that are responsive to environmental signals. One possible mechanism for this enhanced translation is suggested by the surprising frequency of regulated alterations in transcript structure. Of the 17 poorly loaded, translationally controlled transcripts examined in detail here, 12 exhibited structural changes coincident with altered ribosome loading in response to exogenous cues. The remaining five (PRM4, UGA1, MON1, GCY1, and PGM2) are likely to be solely under translational control.
The observed structural alterations were detected exclusively at the 5' ends of the transcripts. The sequences of 5' RACE products, together with RNase protection assays, demonstrated co-linearity between transcript and genomic sequences, providing no evidence for a regulated splicing mechanism similar to that involved in regulation of HAC1 in response to endoplasmic reticulum stress . Excluding regulated splicing as a mechanism, the alternative forms seemingly arose either transcriptionally, through use of different promoters, or post-transcriptionally, either as normal intermediates of mRNA decay or through a new RNA cleavage mechanism. The requirement for STE12 revealed by this work points to a role for transcription in the pheromone-induced transcript changes described here, but this role could be direct or indirect. Consistent with a direct role for Ste12p-mediated promoter activation, TATA boxes and Ste12p binding sequences are found appropriately placed relative to the putative transcription starts of the pheromone-induced forms of the HO, PRM2, PRY3, and SAG1 transcripts (K.S. Bickel, unpublished observation). Previously, altered promoter usage was demonstrated directly for the nitrogen-regulated gene CAN1 and was suggested for DAL5, although the translatability of the alternative transcript forms was not assessed . Promoter elements implicated in regulation of CAN1 and DAL5 are also found in the promoter regions of AMD2 and DAL7, suggesting the possibility of a similar switch in promoter usage.
Considering possible post-transcriptional mechanisms, the normal process of mRNA decay in the cytosol involves removal of the 5' cap, followed by 5'-3' exonucleolytic degradation . A block to exonuclease action could produce some of the 5' truncated products described here. Perhaps related to this is that accumulation of 5' truncated transcripts in Arabidopsis was recently found to result from ribosome arrest mediated by nascent peptide . Importantly, all known nonsplicing post-transcriptional mechanisms would be predicted to generate uncapped 5' ends, in contrast to the termini generated by RNA polymerase II initiation.
Implications of altered 5'-untranslated regions for protein production
Because this is the first large-scale study relating ribosome loading to transcript structure, the frequency with which these regulated changes in transcript structure occur across nature is unknown. However, the suggestion that 9-18% of mammalian transcripts may have alternative first exons  is provocative. Two mammalian genes, in which alternative first exons were found to modify translation, are the gene encoding TIMP (tissue inhibitor of metalloproteinases) and the oncogene mdm2. With both of these genes, the translational efficiencies of the transcripts are regulated by changes in promoter utilization, which lead to altered 5' leaders [36, 37].
In yeast, use of alternative promoters has been shown in some cases to produce different proteins. The SUC2 and KAR4 genes both contain multiple promoters, which generate different protein products with different biologic activities [38, 39]. Similarly, the short forms of the CRH1, KAR5, PRM2, PRP39, PRY3, ASP3, and AQY1 mRNAs identified in this study lack the primary initiation codon, resulting in 5' truncated ORFs. These seven genes have the potential to create short protein products from internal AUG codons within the truncated mRNAs in the same ORFs as the primary products, although existence of these protein products has not been proven. With PRM2, CRH1, and PRY3, the putative amino-terminal truncated proteins lack signal sequences that target these three proteins to the endoplasmic reticulum. Therefore, if produced, the short protein products of these three genes probably differ in intracellular location, and possibly in function, from the full-length proteins. Similarly, the single transmembrane domain of the full-length Kar5 protein, which localizes it in the endoplasmic reticulum membrane, would be missing from the shorter, poorly translated form. These changes in protein targeting potentially could play roles in regulating cellular responses to pheromone.
With several other transcripts identified here - HO, SAG1, AMD2, DAL5, and DAL7 - the altered 5' leaders did not modify the protein encoding regions but profoundly altered the loading of ribosomes on the resulting transcripts. Although one can posit functional explanations for the truncated protein products produced from alternate transcripts, the biologic significance of 5' leaders with repressed translational activity is less obvious. The HO gene represents an extreme example in which a 5' leader as long as 2 kilobases is produced in response to pheromone treatment and the long transcripts are located primarily in untranslated mRNP particles. Likewise, poor translation of the SAG1 transcript in growing cells is mediated by an inhibitory 826-nucleotide 5' UTR. A similar situation seems to occur with the nitrogen-regulated AMD2, DAL5, and DAL7 transcripts. In addition to the changes in ribosome loading observed here, the levels of all five of these transcripts are regulated at the transcriptional level. One outcome of these parallel changes in transcript level and translation efficiency is to amplify the biologic consequence of transcriptional control by accentuating the upregulation or downregulation of protein production. This is surely one mechanism for the 'homodirectional' changes in transcript level and ribosome loading that have been noted by others on a global level in yeast . However, this rationalization neglects the conundrum of why the cell does not simply enhance an expression response by switching transcription completely off.
Implications for transcriptional mechanisms
Why should the cell produce a transcript that is either poorly translated or not translated at all? One speculative role for the continued synthesis of translationally inactive transcripts, under conditions in which the protein product is not needed, could involve regulation of accessibility to the promoter regions of these genes. One suggested role for the 'intergenic' transcription, which has been found widely in eukaryotes [40, 41], is to assist in maintaining an open chromatin state required for facile transcriptional activation. Intergenic transcription has been found in the locus control regions of the mammalian β-globin and MHC (major histocompatibility complex) class II loci [42, 43], in the promoter regions of the interleukin-4 and interleukin-13 genes , in the V(D)J region of the mouse immunoglobulin heavy chain locus  and within the Drosophila bithorax complex . RNA polymerase II is found upstream of many apparently inactive genes in stationary phase S. cerevisiae . It is noteworthy that the 5' leader of the long HO transcript extends 2,000 nucleotides upstream of the coding region through a region that is devoid of genes (for example, intergenic) and which contains a multitude of transcription factor binding sites that mediate the complex transcriptional control of the HO gene (discussed by Krebs and coworkers ). Maintenance of this extended region in an open state through continued low level transcription of the translationally inactive transcript species could allow rapid reactivation of HO transcription upon removal of pheromone.
In addition to keeping chromatin in an active state, transcription from intergenic regions can also be involved in repressing transcription from promoters. This has been found to occur either by local competition between promoters  or through interference by elongating polymerases coming from an upstream promoter . The competition model applies equally to promoters located upstream or downstream of the primary promoter, which is consistent with the occurrence of both longer and shorter 5' UTRs in this study.
Very little is known of the mechanisms that prevent inappropriate protein production from intergenic transcripts. Some 'cryptic' RNA polymerase II products are removed within the nucleus through a highly conserved process utilizing a unique poly(A) polymerase and the nuclear exosome . Nonsense-mediated decay [52, 53], another highly conserved process [54, 55], removes those transcripts that are recognized as having premature translation termination codons. This paper describes a third process, translational silencing, wherein continuing synthesis of transcripts with inhibitory 5' leaders contributes to an open chromatin structure while protecting the cell from inappropriate protein production. At this time, we have no evidence defining the inhibitory elements in the 5' leaders of the silenced transcripts. As discussed in the Background section (above), possible inhibitory features could be secondary structure, protein binding sites, or ATG codons upstream of the coding region. With regard to the latter mechanism, we have noted ATG sequences in all of the long, inhibitory 5' leaders. For example, the long forms of the DAL5 and AMD2 5' leaders contain five and two ATG codons, respectively, whereas neither short form contains an ATG upstream of the start codon. Further experimental work will be required to establish the inhibitory elements in the translationally silenced transcripts.
Materials and methods
Yeast cultures and polysome fractionation
All experiments used strain BY2125 (MATa ade2-1 his3-11,15 leu2-3,112 ura3-1 can1-100 ssd1-d : W303 background). Strains VM1906 (Δfus3::LEU2 Δkss1::TRP1), VM1718 (Δste12::TRP1) and LL1 (Δgcn2::TRP1) were derived from BY2125 by gene disruption .
Cells were grown at 30°C in rich glucose medium, YPD (1% yeast extract, 2% peptone and 2% glucose) , to mid-log phase (approximately 1 × 107 cells/ml) before harvesting. Preparations of cell lysates and polysome fractionation were described previously, as was pheromone treatment of yeast cultures . For nitrogen starvation, cultures were grown at 30°C in minimal glucose medium  with necessary supplements to mid-log phase, washed once with 10 mmol/l potassium phosphate (pH 7.0), and then incubated for 30 minutes at 30°C in pre-warmed nitrogen starvation medium (0.2% yeast nitrogen base [without amino acids or ammonium sulfate], 3% glucose, 20 mmol/l potassium phosphate [pH 7.0], and adenine and uracil added at 40 and 20 µg/ml, respectively) . For osmotic stress, exponential phase YPD cultures (approximately 8 × 106 cells/ml) were diluted into an equal volume of pre-warmed YPD or YPD + 2 mol/l sorbitol. Incubation at 30°C was continued for 30 minutes before the cultures were harvested.
RNA was isolated using Qiagen RNeasy mini-columns (Qiagen Corp., Valencia, CA, USA). An equal proportion of the RNA isolated from each sucrose gradient fraction was used directly in reverse transcription reactions using anchored oligo(dT)25 primers. When comparing changes in total RNA isolated from different culture conditions or treatments, equal quantities of total RNA were used for reverse transcription reactions. QPCR was performed as described previously .
Northern blot analysis followed a procedure described previously , as did the RNase protection assays . The SAG1 RNase protection assay probe was 631 bases long and contained 484 nucleotides 5' of the coding region and 55 nucleotides into the coding region. 5' RACE was carried out as described by Frohman  using gene specific primers for the reverse transcription reaction. The Thermoscript RT-PCR system (Invitrogen, Carlsbad, CA, USA) was used allowing for the reverse transcription reaction to be done at 55°C to minimize reverse transcriptase stops due to secondary structure in the RNA. To estimate the HO 5' leader in cells treated with α-factor for 30 minutes, reverse transcription reactions were done as described above and the products were used as DNA template in a series of PCR reactions. Two reverse primers, located -500 and -1493 nucleotides relative to the initiation codon of the HO ORF and 10 different forward primers, spaced roughly 200 nucleotides apart starting at -700, were used.
Determination of ribosome loading ratio
Using QPCR, relative levels of mRNA across polysome gradients were determined for the indicated genes in growing cells or treated cells. The treatment was either pheromone treatment for 30 minutes, nitrogen starvation for 30 minutes or osmotic stress for 30 minutes. Using the Abs260 nm traces from the polysome gradients, the number of ribosomes associated with a specific mRNA in each fraction was determined. The ribosome loading ratio was calculated by dividing the average number of ribosomes associated with a transcript from a polysome gradient from treated cells divided by the average number of ribosomes associated with a transcript from a polysome gradient from growing cells. A number greater than 1 indicates an increase in ribosome loading with treatment and conversely a number less than 1 indicates a decrease in ribosome loading with treatment.
Construction of HIS3-HAreporter plasmids
A HIS3-HA reporter plasmid (pVW12) was constructed by insertion of the HIS3-HA sequence from pVW06  between the Bam HI and Eco RI sites of the multiple cloning sequence of plasmid pRS416ADH1p , so that HIS3-HA transcription is from the constitutive ADH1 promoter. The ADH1 5' leader in pVW12 (nucleotides -48 to -1) was replaced with either the SAG1 short 5' leader (nucleotides -48 to -1, plasmid pVW13) or the SAG1 long 5' leader (nucleotides -836 to -1, plasmid pVW14) using plasmid gap repair . Specifically, pVW12 was cleaved in the 5' leader with Spe I and Xba I and transformed into strain BY2125 with PCR fragments bearing the short or long SAG1 5' leader flanked with 5' and 3' sequences homologous to the ADH1 promoter (-91 to -49) and HIS3-HA (+1 to +48). Ura+ yeast transformants were screened by PCR to identify plasmids repaired with the SAG1 fragments and confirmed by DNA sequencing. S1 nuclease protection assays were carried out as described [64, 65], using gel purified oligonucleotides (Qiagen Corp.), on RNA isolated from pVW13 or pVW14 to confirm the 5' ends of each transcript.
Yeast transformed with pRS416ADH1, pVW13, or pVW14 were grown in selective medium (synthetic complete medium with casamino acids and lacking uracil) to mid-exponential phase, harvested, and lysed as described previously . Protein samples (5 µg for the pVW13 lysate and 50 µg each for the pVW14 and pRS416ADH1p lysates) were separated by electrophoresis on a 10% polyacrylamide gel and transferred electrophoretically to PVDF membrane. The membrane was incubated with anti-HA mouse monoclonal antibody HA.11 (Covance Research Products, Berkeley, CA, USA) and sheep anti-mouse immunoglobulin conjugated with horseradish peroxidase (Amersham Biosciences, Piscataway, NJ, USA), then developed with ECL Plus Western Blotting Detection System (Amersham Biosciences). His-HA protein was quantitated using a Storm 840 phosphorimager (Amersham Biosciences).
Additional data files
The following additional data are included with the online version of this article: A text file containing the data used to construct Figure 1, parts a and b (Additional data file 1); a text file containing the data used to construct Figure 1, parts c (Additional data file 2); and a text file containing the data used to determine ribosome loading ratio in Figure 1 (Additional data file 3).
This study were supported by research grants from the National Institutes of Health (CA89807 and CA71453). KSB was supported under a National Science Foundation Graduate Research Fellowship and in part by PHS NRSA T32 GM07270 from NIGMS. We are grateful to Eileen Turcott for technical assistance and to Marnie Gelbart and Stephanie Namciu for helpful suggestions on the possible impacts of the alternative transcripts on transcriptional control.
- Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D: Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2003, 100: 3889-3894. 10.1073/pnas.0635171100.PubMedPubMed CentralView ArticleGoogle Scholar
- Preiss T, Baron-Benhamou J, Ansorge W, Hentze MW: Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat Struct Biol. 2003, 10: 1039-1047. 10.1038/nsb1015.PubMedView ArticleGoogle Scholar
- MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR: Gene expression in yeast responding to mating pheromone: Analysis by high-resolution translation state analysis and quantitative proteomics. Mol Cell Proteomics. 2004, 3: 478-489. 10.1074/mcp.M300129-MCP200.PubMedView ArticleGoogle Scholar
- Sonenberg N, Hershey JWB, Mathews MB: Translational Control of Gene Expression. 2000, Cold Spring Harbor, NY: Cold Spring Harbor PressGoogle Scholar
- Hinnebusch AG, Asano K, Olsen DS, Phan L, Nielsen KH, Valasek L: Study of translational control of eukaryotic gene expression using yeast. Ann N Y Acad Sci. 2004, 1038: 60-74. 10.1196/annals.1315.012.PubMedView ArticleGoogle Scholar
- Hay N, Sonenberg N: Upstream and downstream of mTOR. Genes Dev. 2004, 18: 1926-1945. 10.1101/gad.1212704.PubMedView ArticleGoogle Scholar
- Wilkie GS, Dickson KS, Gray NK: Regulation of mRNA translation by 5' and 3'-UTR-binding factors. Trends Biochem Sci. 2003, 28: 182-188. 10.1016/S0968-0004(03)00051-3.PubMedView ArticleGoogle Scholar
- Bartel DP: MicroRNAs. Genomics, biogenesis, mechanism, and function. Cell. 2004, 116: 281-297. 10.1016/S0092-8674(04)00045-5.PubMedView ArticleGoogle Scholar
- de Moor CH, Meijer H, Lissenden S: Mechanisms of translational control by the 3' UTR in development and differentiation. Semin Cell Dev Biol. 2005, 16: 49-58. 10.1016/j.semcdb.2004.11.007.PubMedView ArticleGoogle Scholar
- Kozak M: Structural features in eukaryotic messenger RNAs that modulate the initiation of translation. J Biol Chem. 1991, 266: 19867-19870.PubMedGoogle Scholar
- Morris DR, Geballe AP: Upstream open reading frames as regulators of mRNA translation. Mol Cell Biol. 2000, 20: 8635-8642. 10.1128/MCB.20.23.8635-8642.2000.PubMedPubMed CentralView ArticleGoogle Scholar
- Landry JR, Mager DL, Wilhelm BT: Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet. 2003, 19: 640-648. 10.1016/j.tig.2003.09.014.PubMedView ArticleGoogle Scholar
- Patil C, Walter P: Intracellular signaling from the endoplasmic reticulum to the nucleus: the unfolded protein response in yeast and mammals. Curr Opin Cell Biol. 2001, 13: 349-356. 10.1016/S0955-0674(00)00219-2.PubMedView ArticleGoogle Scholar
- Mendez R, Richter JD: Translational control by CPEB: a means to the end. Nat Rev Mol Cell Biol. 2001, 2: 521-529. 10.1038/35080081.PubMedView ArticleGoogle Scholar
- Lipke PN, Wojciechowicz D, Kurjan J: AG alpha 1 is the structural gene for the Saccharomyces cerevisiae alpha-agglutinin, a cell surface glycoprotein involved in cell-cell interactions during mating. Mol Cell Biol. 1989, 9: 3155-3165.PubMedPubMed CentralView ArticleGoogle Scholar
- Lipke PN, Kurjan J: Sexual agglutination in budding yeasts: structure, function, and regulation of adhesion glycoproteins. Microbiol Rev. 1992, 56: 180-194.PubMedPubMed CentralGoogle Scholar
- Hagen DC, Bruhn L, Westby CA, Sprague GF: Transcription of alpha-specific genes in Saccharomyces cerevisiae : DNA sequence requirements for activity of the coregulator alpha 1. Mol Cell Biol. 1993, 13: 6866-6875.PubMedPubMed CentralView ArticleGoogle Scholar
- Haber JE: Mating-type gene switching in Saccharomyces cerevisiae. Trends Genet. 1992, 8: 446-452.PubMedView ArticleGoogle Scholar
- Klar AJ: Lineage-dependent mating-type transposition in fission and budding yeast. Curr Opin Genet Dev. 1993, 3: 745-751. 10.1016/S0959-437X(05)80093-0.PubMedView ArticleGoogle Scholar
- Nasmyth K: Regulating the HO endonuclease in yeast. Curr Opin Genet Dev. 1993, 3: 286-294. 10.1016/0959-437X(93)90036-O.PubMedView ArticleGoogle Scholar
- Breeden L, Nasmyth K: Cell cycle control of the yeast HO gene: cis - and trans -acting regulators. Cell. 1987, 48: 389-397. 10.1016/0092-8674(87)90190-5.PubMedView ArticleGoogle Scholar
- Elion EA: Pheromone response, mating and cell biology. Curr Opin Microbiol. 2000, 3: 573-581. 10.1016/S1369-5274(00)00143-0.PubMedView ArticleGoogle Scholar
- Dohlman HG, Thorner JW: Regulation of G protein-initiated signal transduction in yeast: paradigms and principles. Annu Rev Biochem. 2001, 70: 703-754. 10.1146/annurev.biochem.70.1.703.PubMedView ArticleGoogle Scholar
- Klionsky DJ, Emr SD: Autophagy as a regulated pathway of cellular degradation. Science. 2000, 290: 1717-1721. 10.1126/science.290.5497.1717.PubMedPubMed CentralView ArticleGoogle Scholar
- Abeliovich H, Klionsky DJ: Autophagy in yeast: mechanistic insights and physiological function. Microbiol Mol Biol Rev. 2001, 65: 463-479. 10.1128/MMBR.65.3.463-479.2001.PubMedPubMed CentralView ArticleGoogle Scholar
- Cherkasova VA, Hinnebusch AG: Translational control by TOR and TAP42 through dephosphorylation of eIF2alpha kinase GCN2. Genes Dev. 2003, 17: 859-872. 10.1101/gad.1069003.PubMedPubMed CentralView ArticleGoogle Scholar
- Stefl R, Skrisovska L, Allain FH: RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle. EMBO Rep. 2005, 6: 33-38. 10.1038/sj.embor.7400325.PubMedPubMed CentralView ArticleGoogle Scholar
- Mathews MB, Sonenberg N, Hershey JWB: Origins and targets of translational control. Translational Control. Edited by: Hershey JWB, Mathews MB, Sonenberg N. 1996, Cold Spring Harbor, NY: Cold Spring Harbor Press, 1-29.Google Scholar
- Braat AK, Yan N, Arn E, Harrison D, Macdonald PM: Localization-dependent oskar protein accumulation; control after the initiation of translation. Dev Cell. 2004, 7: 125-131. 10.1016/j.devcel.2004.06.009.PubMedView ArticleGoogle Scholar
- Clark IE, Wyckoff D, Gavis ER: Synthesis of the posterior determinant Nanos is spatially restricted by a novel cotranslational regulatory mechanism. Curr Biol. 2000, 10: 1311-1314. 10.1016/S0960-9822(00)00754-5.PubMedView ArticleGoogle Scholar
- Olsen PH, Ambros V: The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol. 1999, 216: 671-680. 10.1006/dbio.1999.9523.PubMedView ArticleGoogle Scholar
- Ruegsegger U, Leber JH, Walter P: Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell. 2001, 107: 103-114. 10.1016/S0092-8674(01)00505-0.PubMedView ArticleGoogle Scholar
- Cox KH, Rai R, Distler M, Daugherty JR, Coffman JA, Cooper TG: Saccharomyces cerevisiae GATA sequences function as TATA elements during nitrogen catabolite repression and when Gln3p is excluded from the nucleus by overproduction of Ure2p. J Biol Chem. 2000, 275: 17611-17618. 10.1074/jbc.M001648200.PubMedPubMed CentralView ArticleGoogle Scholar
- Coller J, Parker R: Eukaryotic mRNA decapping. Annu Rev Biochem. 2004, 73: 861-890. 10.1146/annurev.biochem.73.011303.074032.PubMedView ArticleGoogle Scholar
- Onouchi H, Nagami Y, Haraguchi Y, Nakamoto M, Nishimura Y, Sakurai R, Nagao N, Kawasaki D, Kadokura Y, Naito S: Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis. Genes Dev. 2005, 19: 1799-1810. 10.1101/gad.1317105.PubMedPubMed CentralView ArticleGoogle Scholar
- Waterhouse P, Khokha R, Denhardt DT: Modulation of translation by the 5' leader sequence of the messenger RNA encoding murine tissue inhibitor of metalloproteinases. J Biol Chem. 1990, 265: 5585-5589.PubMedGoogle Scholar
- Brown CY, Mize GJ, Pineda M, George DL, Morris DR: Role of two upstream open reading frames in the translational control of oncogene mdm2. Oncogene. 1999, 18: 5631-5637. 10.1038/sj.onc.1202949.PubMedView ArticleGoogle Scholar
- Carlson M, Botstein D: Two differentially regulated mRNAs with different 5' ends encode secreted and intracellular forms of yeast invertase. Cell. 1982, 28: 145-154. 10.1016/0092-8674(82)90384-1.PubMedView ArticleGoogle Scholar
- Gammie AE, Stewart BG, Scott CF, Rose MD: The two forms of karyogamy transcription factor Kar4p are regulated by differential initiation of transcription, translation, and protein turnover. Mol Cell Biol. 1999, 19: 817-825.PubMedPubMed CentralView ArticleGoogle Scholar
- Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005, 308: 1149-1154. 10.1126/science.1108625.PubMedView ArticleGoogle Scholar
- Johnson JM, Edwards S, Shoemaker D, Schadt EE: Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 2005, 21: 93-102. 10.1016/j.tig.2004.12.009.PubMedView ArticleGoogle Scholar
- Routledge SJ, Proudfoot NJ: Definition of transcriptional promoters in the human beta globin locus control region. J Mol Biol. 2002, 323: 601-611. 10.1016/S0022-2836(02)01011-2.PubMedView ArticleGoogle Scholar
- Masternak K, Peyraud N, Krawczyk M, Barras E, Reith W: Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nat Immunol. 2003, 4: 132-137. 10.1038/ni883.PubMedView ArticleGoogle Scholar
- Rogan DF, Cousins DJ, Santangelo S, Ioannou PA, Antoniou M, Lee TH, Staynov DZ: Analysis of intergenic transcription in the human IL-4/IL-13 gene cluster. Proc Natl Acad Sci USA. 2004, 101: 2446-2451. 10.1073/pnas.0308327100.PubMedPubMed CentralView ArticleGoogle Scholar
- Bolland DJ, Wood AL, Johnston CM, Bunting SF, Morgan G, Chakalova L, Fraser PJ, Corcoran AE: Antisense intergenic transcription in V(D)J recombination. Nat Immunol. 2004, 5: 630-637. 10.1038/ni1068.PubMedView ArticleGoogle Scholar
- Schmitt S, Prestel M, Paro R: Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev. 2005, 19: 697-708. 10.1101/gad.326205.PubMedPubMed CentralView ArticleGoogle Scholar
- Radonjic M, Andrau J-C, Lijnzaad P, Kemmeren P, Kockelkorn TTJP, van Leenen D, van Berkum NL, Holstege FCP: Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol Cell. 2005, 18: 171-183. 10.1016/j.molcel.2005.03.010.PubMedView ArticleGoogle Scholar
- Krebs JE, Kuo MH, Allis CD, Peterson CL: Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev. 1999, 13: 1412-1421.PubMedPubMed CentralView ArticleGoogle Scholar
- Hirschman JE, Durbin KJ, Winston F: Genetic evidence for promoter competition in Saccharomyces cerevisiae. Mol Cell Biol. 1988, 8: 4608-4615.PubMedPubMed CentralView ArticleGoogle Scholar
- Martens JA, Laprade L, Winston F: Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature. 2004, 429: 571-574. 10.1038/nature02538.PubMedView ArticleGoogle Scholar
- Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, et al: Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell. 2005, 121: 725-737. 10.1016/j.cell.2005.04.030.PubMedView ArticleGoogle Scholar
- He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A: Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol Cell. 2003, 12: 1439-1452. 10.1016/S1097-2765(03)00446-5.PubMedView ArticleGoogle Scholar
- Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC: Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet. 2004, 36: 1073-1078. 10.1038/ng1429.PubMedView ArticleGoogle Scholar
- Lejeune F, Maquat LE: Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr Opin Cell Biol. 2005, 17: 309-315. 10.1016/j.ceb.2005.03.002.PubMedView ArticleGoogle Scholar
- Conti E, Izaurralde E: Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol. 2005, 17: 316-325. 10.1016/j.ceb.2005.04.005.PubMedView ArticleGoogle Scholar
- Rothstein R: Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 1991, 194: 281-301.PubMedView ArticleGoogle Scholar
- Sherman F: Getting started with yeast. Methods Enzymol. 1991, 194: 3-21.PubMedView ArticleGoogle Scholar
- Roon RJ, Murdoch M, Kunze B, Dunlop PC: Derepression of asparaginase II during exponential growth of Saccharomyces cerevisiae on ammonium ion. Arch Biochem Biophys. 1982, 219: 101-109. 10.1016/0003-9861(82)90138-2.PubMedView ArticleGoogle Scholar
- MacKay VL, Mai B, Waters L, Breeden LL: Early cell cycle box-mediated transcription of CLN3 and SWI4 contributes to the proper timing of the G1-to-S transition in budding yeast. Mol Cell Biol. 2001, 21: 4140-4148. 10.1128/MCB.21.13.4140-4148.2001.PubMedPubMed CentralView ArticleGoogle Scholar
- Ruan HJ, Brown CY, Morris DR: Analysis of ribosome loading onto mRNA species: implications for translational control. Analysis of mRNA Formation and Function. Edited by: Richter JD. 1997, New York: Academic Press, 305-321.View ArticleGoogle Scholar
- Frohman MA: Rapid amplification of complementary DNA ends for generation of full-length complementary DNAs: thermal RACE. Methods Enzymol. 1993, 218: 340-356.PubMedView ArticleGoogle Scholar
- Mumberg D, Muller R, Funk M: Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene. 1995, 156: 119-122. 10.1016/0378-1119(95)00037-7.PubMedView ArticleGoogle Scholar
- Cormack B, Castano I: Introduction of point mutations into cloned genes. Methods Enzymol. 2002, 350: 199-218.PubMedView ArticleGoogle Scholar
- Mai B, Miles S, Breeden LL: Characterization of the ECB binding complex responsible for the M/G1-specific transcription of CLN3 and SWI4. Mol Cell Biol. 2002, 22: 430-441. 10.1128/MCB.22.2.430-441.2002.PubMedPubMed CentralView ArticleGoogle Scholar
- Iyer V, Struhl K: Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 1996, 93: 5208-5212. 10.1073/pnas.93.11.5208.PubMedPubMed CentralView ArticleGoogle Scholar
- Saccharomyces Genome Database. [http://www.yeastgenome.org/]
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