GEO DataSets

(Submitter supplied) Probe rRNA structural changes during assembly with dimethyl sulfate

Organism:

Escherichia coli

Type:

Other

Platform:

GPL14548

13 Samples

Download data: TSV, TXT

(Submitter supplied) While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

22 Samples

Download data: XLSX

(Submitter supplied) Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.

Organism:

Arabidopsis thaliana; Oryza sativa Japonica Group; Oryza sativa

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL26208 GPL27860 GPL27660

17 Samples

Download data: TXT

(Submitter supplied) Ribo-T is an engineered ribosome whose small and large subunits are tethered together by insertion of circularly permutated 23S rRNA into 16S rRNA [Orelle, C., Carlson, E. D., Szal, T., Florin, T., Jewett, M. C., Mankin, A.S. Protein synthesis by ribosomes with tethered subunits. Nature 524, 119-124 (2015)]. Whether the growth defects are related to problems with Ribo-T functionality is unclear. The translation in Ribo-T cells was examined by ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq). more...

Organism:

Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21222

8 Samples

Download data: CSV, FASTA, WIG

(Submitter supplied) Yeast large ribosomal subunit (LSU) precursors are subject to substantial changes in protein composition during their maturation due to coordinated transient interactions with a large number of ribosome biogenesis factors and due to the assembly of ribosomal proteins. These compositional changes go along with stepwise processing of LSU rRNA precursors and with specific rRNA folding events, as revealed by recent cryo-electron microscopy analyses of late nuclear and cytoplasmic LSU precursors. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17143

8 Samples

Download data: XLSX

(Submitter supplied) In eukaryotes, biogenesis of ribosomes requires folding and assembly of the precursor rRNA (pre-rRNA) with a large number of proteins and snoRNPs into huge RNA-protein complexes. In spite of intense genetic, biochemical and high resolution cryo-EM studies in Saccharomyces cerevisiae, information about the conformation of the earliest 35S pre-rRNA is limited. To overcome this, we performed high-throughput SHAPE chemical probing on the 35S pre-rRNA associated with 90S pre-ribosomes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

6 Samples

Download data: FA, GTF, SGR, TAB, TXT, XLSX

(Submitter supplied) Ribosomes are among the largest folded RNAs, whose function depends on their structure. Nonetheless, in vitro studies indicate a propensity of rRNAs to misfold. We use a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics to dissect the final RNA folding steps of the small ribosomal subunit head.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

30 Samples

Download data: TXT