GEO DataSets

(Submitter supplied) A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. While dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at Adenine (A) and Cytosine (C) at neutral pH. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL32081

33 Samples

Download data: TXT

(Submitter supplied) Deciphering the conformations of RNAs in their cellular environment allows identification of RNA elements with potentially functional roles within biological contexts. Insight into the conformation of RNA in cells has been achieved using chemical probes that were developed to react specifically with flexible RNA nucleotides, or the Watson-Crick face of single-stranded nucleotides. The most widely used probes are either selective SHAPE (2'-hydroxyl acylation and primer extension) reagents that probe nucleotide flexibility, or dimethyl sulfate (DMS), which probes the base-pairing at adenine and cytosine but is unable to interrogate guanine or uracil. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL16791 GPL17021

42 Samples

Download data: CSV

(Submitter supplied) We develop an enhanced MaP protocol based on MarathonRT and bioinformatic optimizations which enables robust DMS probing of all four RNA nucleotides within living cells. We demonstrate this on RNA from E. coli and HEK293 cell lines.

Organism:

Escherichia coli; Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL16085

73 Samples

Download data: TAR

(Submitter supplied) Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. more...

Organism:

Homo sapiens; Drosophila melanogaster; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

10 related Platforms

29 Samples

Download data: TXT

(Submitter supplied) Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.

Organism:

Vibrio vulnificus; Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL16085 GPL27000 GPL15520

23 Samples

Download data

(Submitter supplied) We present an approach for globally monitoring RNA structure in native conditions in vivo with single nucleotide precision. This method is based on in vivo modification with dimethyl sulfate (DMS), which reacts with unpaired adenine and cytosine residues9, followed by deep sequencing to monitor modifications. Our data from yeast and mammalian cells are in excellent agreement with known mRNA structures and with the high-resolution crystal structure of the Saccharomyces cerevisiae ribosome10. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens

Type:

Other

Platforms:

GPL13821 GPL11154

25 Samples

Download data: TXT, WIG

(Submitter supplied) In this study, we conducted a thermodynamic analysis of RNA helix stability in the Eco80 artificial cytoplasm, which mimics in vivo conditions. Eco80 contains 80% of Escherichia coli metabolites, with biological concentrations of metal ions including 2 mM free Mg2+ and 29 mM metabolite-chelated Mg2+. We determined a set of Watson-Crick free energy nearest-neighbor parameters in Eco80 and found that helices are less stable by ∆∆Go37 ~ 1 kcal/mol in comparison to the traditional 1 M NaCl condition. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL33080

9 Samples

Download data: TSV, TXT

(Submitter supplied) Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates’ secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16085 GPL21222

10 Samples

Download data: BEDGRAPH, TAR

(Submitter supplied) structure probing of ribosomes

Organism:

Saccharomyces cerevisiae; Escherichia coli; Homo sapiens

Type:

Other

Platforms:

GPL17342 GPL18133 GPL16791

37 Samples

Download data: TSV

(Submitter supplied) RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3′ untranslated region. more...

Organism:

Severe acute respiratory syndrome coronavirus 2

Type:

Other

Platform:

GPL28588

2 Samples

Download data: JSON, TAR, WIG

(Submitter supplied) Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown in the presence and absence of amino acids. We show that the change in global RNA structurome is inversely proportional to the change in abundance upon amino acid starvation and that this trend is pronounced in the stringent response and codY regulons. We also use this data to characterize known and novel RNA switches.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18561

14 Samples

Download data: TXT

(Submitter supplied) Due to the mounting evidence that RNA structure plays a critical role in regulating almost any essential physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 performs comparably well to NAI on naked RNA under in vitro conditions and it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. more...

Organism:

Homo sapiens; Escherichia coli; Bacillus subtilis

Type:

Other

Platforms:

GPL21222 GPL18573 GPL24109

36 Samples

Download data: WIG