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SRP018195
Saccharomyces cerevisiae
17 Downloadable Samples
Illumina HiSeq 2000
Description
Protein-RNA interactions are integral components of nearly every aspect of biology including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTR) covering 72% of protein-coding transcripts encoded in the genome, confirming 3' UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3' UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression. Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo. Overall design: Duplicate gPAR-CLIP and mRNA-seq libraries were sequenced from yeast strains for each of three conditions: log-phase growth, growth after 2 hour glucose starvation, and growth after 2 hour nitrogen starvation. Additional duplicate mRNA-seq libraries were sequenced from yeast strains grown in the absence of 4-thiouracil. gPAR-CLIP libraries were used to determine regions of mRNA bound by proteins. mRNA-seq libraries served as controls for mRNA abundance. A Puf3p PAR-CLIP library was sequenced to determine how well gPAR-CLIP captured the binding signatures of a single RNA-binding protein.
Publication Title
RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
FUS Regulates Activity of MicroRNA-Mediated Gene Silencing.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Individuals with the ALS-linked (amyotrophic lateral sclerosis) truncation mutation (R495X) in FUS (fused in sarcoma) are known to have a more aggressive form of the disease than those with point mutations. The underlying cause for this difference is unclear. We report that FUS is a component of miRISC (miRNA-induced silencing complex) and that overexpression of its truncation mutant R495X negatively impacts miRNA mediated RNA silencing.
Publication Title
FUS Regulates Activity of MicroRNA-Mediated Gene Silencing.
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 27 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand plant adaptation to heat stress, gene expression profiles of Arabidopsis leaves under heat stress, during recovery and control condition were obtained using microarray. Microarray data listed responsible candidate genes for glycerolipid metabolism.
Publication Title
Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana.
Sample Metadata Fields
Age, Specimen part
View Samples