Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Probing Xist RNA structure in cells using Targeted Structure-Seq

ABSTRACT: The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.

ORGANISM(S): Mus musculus

PROVIDER: GSE67667 | GEO | 2016/02/09

SECONDARY ACCESSION(S): PRJNA280605

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Probing Xist RNA structure in cells using Targeted Structure-Seq

Project description:The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.

2016-02-09 | E-GEOD-67667 | biostudies-arrayexpress

Carbodiimide reagents for the chemical probing of RNA structure in cells

Project description: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. The constitutively charged carbodiimide N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC) is widely used for probing G and U nucleotides, but has not been established for probing RNA in cells. Here, we report the use of a smaller and conditionally charged reagent, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), as a chemical probe of RNA conformation, and the first reagent validated for structure probing of unpaired G and U nucleotides in intact cells. We showed that EDC demonstrates similar reactivity to CMC when probing transcripts in vitro. We found that EDC specifically reacted with accessible nucleotides in the 7SK noncoding RNA in intact cells. We probed structured regions within the Xist lncRNA with EDC and integrated these data with DMS probing data. Together, EDC and DMS allowed us to refine predicted structure models for the 3’ extension of repeat C within Xist. These results highlight how complementing DMS probing experiments with EDC allows the analysis of Watson-Crick base-pairing at all four nucleotides of RNAs in their cellular context.

2018-12-26 | GSE118309 | GEO

Mus musculus

Project description:Probing Xist RNA structure in cells using Targeted Structure-Seq

| PRJNA280605 | ENA

HIV-1 RNA structure and heterogeneity analysis

Project description:The goal of this set of experiments is to determine the structure of HIV-1 NL4-3 and NHG RNA structure using a novel algorithm that allows for the identification of multiple RNA folding conformations. The input data used for this algorithm is DMS-MaPseq data. We focused on two specific areas of the HIV-1 genome, the Rev Response Element (RRE) and A3 splice acceptor site, as well as probing the whole HIV-1 genome. RNA is DMS-modified in vitro and in vivo as indicated. The goal of this data set was to test the novel alternative RNA structure detecting algorithm (DREEM) using RNA molecules with known structures.

2020-01-14 | GSE131506 | GEO

smartSHAPE: a low-input method for transcriptome-wide RNA structure probing uncovers RNA structure landscape in mouse colonic macrophages

Project description:Here, we report the development and application of smartSHAPE, a SHAPE-like RNA structure probing method that requires low amounts of input due to the largely reduced artefact signals of premature RT stops and increased efficiency of library construction. We used smartSHAPE to profile the global RNA secondary structures of two subtypes of mouse colonic macrophages upon inflammation, and provided evidence that RNA conformational changes at protein binding sites regulate gene expression and, in turn, immune responses. We predicted functional RNA structure elements based on smartSHAPE structure data, and discovered that PD-L1 contains a YRY-motif stem-loop structural element within the 3’UTR, which triggers RNA degradation mediated by Regnase-1.

2021-03-31 | GSE155961 | GEO

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Project description:To accelerate previous RNA structure probing approaches, which focus on analyzing one RNA sequence at a time, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing to identify single-stranded RNA (ssRNA) regions from fragments generated by nuclease P1, which is specific for single-stranded nucleic acids. In the accompanying study, we show that we can accurately and simultaneously map ssRNA regions in multiple non-coding RNAs with known structure in experiments probing the entire mouse nuclear transcriptome. We carried out probing in two cell types to assess reproducibility. We also identified and experimentally validated structured regions in ncRNAs never previously probed.

2010-11-07 | GSE24622 | GEO

In vivo structure probing of RNA in Archaea: Novel insights into the ribosome structure of Methanosarcina acetivorans

Project description:Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans. Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.

2023-06-27 | GSE229536 | GEO

PARIS analysis of mouse Xist RNA structure

Project description:PARIS analysis of mouse Xist RNA structure

| PRJNA523035 | ENA

Assaying RNA Structure with LASER-seq

Project description:structure probing of ribosomes

2018-10-16 | GSE113529 | GEO

Targeting Xist with compounds that disrupt RNA structure and X-inactivation

Project description:Although >98% of our genome is noncoding, nearly all drugs on the market target one of ~700 disease-related proteins. The historical reluctance to invest in noncoding RNA stems partly from requirements for drug targets to adopt a single stable conformation. Most RNAs can adopt several conformations of similar stabilities. RNA structures also remain challenging to determine. Nonetheless, an increasing number of diseases is now being attributed to noncoding RNA and the ability to target them would vastly expand the chemical space for drug development. Here we devise a screening strategy and identify small molecules that hit the non-coding RNA prototype, Xist. The X1 compound has drug-like properties and binds specifically to Xist’s RepA motif in vitro and in vivo. SAXS analysis reveals that RepA can adopt multiple conformations but favors one structure in solution. X1 binding reduces RepA’s conformational space, displaces cognate interacting protein factors (PRC2, SPEN), suppresses H3K27 trimethylation, and blocks initiation of X-inactivation. X1 inhibits cell differentiation and growth in a female-specific manner. Thus, RNA can be systematically targeted by drug-like compounds that disrupt RNA structure and epigenetic function.

2022-03-30 | GSE141683 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data