Zid et al. 2015 (PRJNA244101)

General Details

Title Ribosome profiling upon glucose starvation in S. cerevisiae
Organism
Number of Samples 27
Release Date 2014/04/08 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP041039
ENA SRP041039
GEO
BioProject PRJNA244101

Publication

Title
Authors Zid BM,O'Shea EK
Journal Nature
Publication Date 2014 Oct 2
Abstract A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes that encode proteins important for survival. Under many such conditions, the overall protein synthesis level is reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in Saccharomyces cerevisiae (yeast), translation is rapidly repressed, yet the transcription of many stress- and glucose-repressed genes is increased. Here we show, using ribosomal profiling and microscopy, that this transcriptionally upregulated gene set consists of two classes: one class produces messenger RNAs that are translated during glucose starvation and are diffusely localized in the cytoplasm, including many heat-shock protein mRNAs; and the other class produces mRNAs that are not efficiently translated during glucose starvation and are concentrated in foci that co-localize with P bodies and stress granules, a class that is enriched for mRNAs involved in glucose metabolism. Surprisingly, the information specifying the differential localization and protein production of these two classes of mRNA is encoded in the promoter sequence: promoter responsiveness to heat-shock factor 1 (Hsf1) specifies diffuse cytoplasmic localization and higher protein production on glucose starvation. Thus, promoter sequences can influence not only the levels of mRNAs but also the subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to the environmental conditions.
PMC PMC4184922
PMID 25119046
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1223686 PRJNA244101 Saccharomyces cerevisiae BY4741 Ribo-Seq
SRR1223687 PRJNA244101 Saccharomyces cerevisiae EY0690 Ribo-Seq
SRR1223688 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1223693 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1223694 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1223695 PRJNA244101 Saccharomyces cerevisiae RNA-Seq
SRR1223697 PRJNA244101 Saccharomyces cerevisiae BY4741 RNA-Seq
SRR1223698 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1223699 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1223700 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1223701 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1223704 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1223705 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1288391 PRJNA244101 Saccharomyces cerevisiae BY4741 RNA-Seq
SRR1288392 PRJNA244101 Saccharomyces cerevisiae EY0690 Ribo-Seq
SRR1288393 PRJNA244101 Saccharomyces cerevisiae EY0690 Ribo-Seq
SRR1288394 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288395 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288396 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288399 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1288400 PRJNA244101 Saccharomyces cerevisiae BY4741 Ribo-Seq
SRR1288401 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288402 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288403 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288404 PRJNA244101 Saccharomyces cerevisiae EY0690 RNA-Seq
SRR1288406 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
SRR1288407 PRJNA244101 Saccharomyces cerevisiae Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

ⓘ For more Information on the columns shown here see: About