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Series GSE265963 Query DataSets for GSE265963
Status Public on Apr 26, 2024
Title Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts
Organism Saccharomyces cerevisiae
Experiment type Other
Expression profiling by high throughput sequencing
Summary Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. Here we show that, in striking contrast, virtually all mRNA species condense in response to multiple unrelated stresses in budding yeast, length plays a minor role, and instead, stress-induced transcripts are preferentially excluded from condensates, enabling their selective translation. Using both endogenous genes and reporter constructs, we show that translation initiation blockade, rather than resulting ribosome-free RNA, causes condensation. These translation initiation-inhibited condensates (TIICs) are biochemically detectable even when stress granules, defined as microscopically visible foci, are absent or blocked. TIICs occur in unstressed yeast cells, and, during stress, grow before the appearance of visible stress granules. Stress-induced transcripts are excluded from TIICs primarily due to the timing of their expression, rather than their sequence features. Together, our results reveal a simple system by which cells redirect translational activity to newly synthesized transcripts during stress, with broad implications for cellular regulation in changing conditions.
 
Overall design S. cerevisiae cells were stressed, and their RNA was fractionated either using Sed-Seq (to identify RNA which sediments in a non-ribosome dependent fashion) or Polysome-Seq (to identify the ribosome association of RNA).
 
Contributor(s) Bard JA, Drummond DA
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Submission date Apr 26, 2024
Last update date Apr 27, 2024
Contact name D Allan Drummond
E-mail(s) dadrummond@uchicago.edu
Organization name University of Chicago
Street address 929 E 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (2)
GPL21656 Illumina HiSeq 4000 (Saccharomyces cerevisiae)
GPL27812 Illumina NovaSeq 6000 (Saccharomyces cerevisiae)
Samples (279)
GSM8238057 SedSeq~tg_1~L7~EW_TSPP~BY4741~30C~10min~none~BR1~Total
GSM8238058 SedSeq~tg_1~L7~EW_TSPP~BY4741~30C~10min~none~BR1~Sup
GSM8238059 SedSeq~tg_1~L7~EW_TSPP~BY4741~30C~10min~none~BR1~Pellet
Relations
BioProject PRJNA1105055

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE265963_PolysomeSeq_all_normSpike.tsv.gz 5.2 Mb (ftp)(http) TSV
GSE265963_RAW.tar 30.6 Mb (http)(custom) TAR (of TSV)
GSE265963_RNAseq_samples_byLysate.tsv.gz 829 b (ftp)(http) TSV
GSE265963_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta.gz 3.7 Mb (ftp)(http) FASTA
GSE265963_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding_Spombe_cds.fasta.gz 7.8 Mb (ftp)(http) FASTA
GSE265963_all_kallisto_counts.tsv.gz 40.2 Mb (ftp)(http) TSV
GSE265963_df_Zsup_Poly_minfilt.tsv.gz 15.2 Mb (ftp)(http) TSV
GSE265963_fastq_table.csv.gz 10.8 Kb (ftp)(http) CSV
GSE265963_saccharomyces_cerevisiae_R64-3-1_20210421_Schizosaccharomyces_pombe_all_chromosomes_relabelled.fasta.gz 7.3 Mb (ftp)(http) FASTA
GSE265963_saccharomyces_cerevisiae_R64-3-1_20210421_Schizosaccharomyces_pombe_all_chromosomes_relabelled_geneid.gff3.gz 2.3 Mb (ftp)(http) GFF3
GSE265963_saccharomyces_cerevisiae_R64-3-1_20210421_allchrom.fasta.gz 3.6 Mb (ftp)(http) FASTA
GSE265963_saccharomyces_cerevisiae_R64-3-1_20210421_nofasta_geneid.gff.gz 1.5 Mb (ftp)(http) GFF
GSE265963_sedseq_out.tsv.gz 43.0 Mb (ftp)(http) TSV
GSE265963_spike_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta.gz 3.7 Mb (ftp)(http) FASTA
GSE265963_spike_Scerevisiae_orf_coding_all_Scerevisiae_rna_coding_Spombe_cds.fasta.gz 7.8 Mb (ftp)(http) FASTA
GSE265963_spike_saccharomyces_cerevisiae_R64-3-1_20210421.fasta.gz 3.6 Mb (ftp)(http) FASTA
GSE265963_spike_saccharomyces_cerevisiae_R64-3-1_20210421_Schizosaccharomyces_pombe_all_chromosomes_relabelled.fasta.gz 7.3 Mb (ftp)(http) FASTA
GSE265963_spike_saccharomyces_cerevisiae_R64-3-1_20210421_Schizosaccharomyces_pombe_all_chromosomes_relabelled_geneid.gff3.gz 2.3 Mb (ftp)(http) GFF3
GSE265963_spike_saccharomyces_cerevisiae_R64-3-1_20210421_geneid.gff3.gz 1.5 Mb (ftp)(http) GFF3
GSE265963_stress_labels.csv.gz 632 b (ftp)(http) CSV
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