Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces

ABSTRACT: The cellular function of RNA is intimately linked to its structure. The 3D structure of RNA is intricate and compact, and is often complexed with other macromolecules for regulatory interaction. These interactions frequently lead to occluded environments that block structure probing by current reagents. Our RNA infrastructure profiling method (RISP) quantitatively compares standard acylation probes to new small-sized probes, and reveals ca. 80% more structural data for intracellular RNAs underlying protein contacts. Comparative analysis also reveals information about close contacts in ribonucleoprotein complexes such as small nuclear RNAs in the spliceosome. In addition, RISP analysis with small agent AcIm reveals pronounced signals for m6A methylation sites of RNAs in their native cellular setting, even in crowded environments.

ORGANISM(S): Homo sapiens

PROVIDER: GSE243544 | GEO | 2024/10/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces

Project description:RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces

| PRJNA1018899 | ENA

HyPro-MS analysis of proteins proximal to nuclear noncoding RNAs in HeLa cells

Project description:The ability of RNAs to form specific contacts with other macromolecules provides an important mechanism for subcellular compartmentalization. We developed a suite of hybridization-proximity (HyPro) labeling technologies for unbiased discovery of proteins (HyPro-MS) and transcripts (HyPro-seq) associated with RNAs of interest in genetically unperturbed cells. To generate the HyPro-MS dataset reported here, fixed and permeabilized HeLa cells were hybridized with digoxigenin-labeled oligonucleotide probes against noncoding RNAs 45S, NEAT1 or PNCTR and proteins co-localizing with these RNAs were biotinylated in situ using a custom-engineered HyPro enzyme containing a digoxigenin-binding domain. Biotinylated proteins were then captured on streptavidin beads and analyzed by LC-MS/MS.

2021-11-08 | PXD025264 | Pride

Expression analysis of Antirrhinum majus inflorescence meristems grown under control and crowding conditions

Project description:Investigation of gene expression level changes as a result of crowding growth conditions. A five-chip study using total RNA recovered from samples of inflorescence meristems of Antirrhinum majus cv.165E, grown as single plant per pot (control) and 10 plants per pot (crowded conditions). Each chip measures the expression level of 11,959 ESTs with up to six 60-mer probes per target.

2015-09-10 | E-GEOD-72818 | biostudies-arrayexpress

RNA-seq analysis in RISP WT and KO hematopoietic stem cells

Project description:Adult and fetal hematopoietic stem cells (HSCs) display a glycolytic phenotype required to maintain stem cell properties; however, whether mitochondrial respiration is required to maintain HSC function is not known. Here we report that loss of the mitochondrial complex III subunit Rieske iron sulfur protein (RISP), encoded by the Uqcrfs1 gene, in fetal mouse HSCs, results in anemia and prenatal death. RISP null fetal HSCs displayed impaired respiration, resulting in a decreased NAD+/NADH ratio and an increase in glycolysis. While they were viable and able to robustly proliferate in vivo, RISP null fetal HSCs had impaired differentiation, resulting in a depletion of the progenitor pool. RNA-seq analysis revealed widespread changes in gene expression due to loss of RISP in fetal HSCs. Furthermore, RISP null fetal HSCs and progenitors exhibited an increase in both DNA and histone methylation concomitant with increases in 2-hydroxyglutarate (2-HG), a metabolite known to inhibit DNA and histone demethylases. RISP inactivation in adult HSCs also impaired respiration, resulting in a decreased NAD+/NADH ratio, increased glycolysis and loss of quiescence, followed by rapid depletion resulting in severe pancytopenia and lethality. The effect of RISP ablation in fetal or adult HSCs was cell-autonomous. Together, these data indicate that respiration is dispensable for HSC proliferation, but essential for HSC differentiation and maintenance of adult HSC quiescence.

2017-05-15 | GSE95341 | GEO

Cohesin and CTCF control chromosomal contact dynamics in living cells [integration sites]

Project description:Mammalian chromosomes are partitioned into topologically associating domains (TADs) by the loop-extrusion activity of cohesin that is blocked at specific DNA sites bound by CTCF. Chromosome structure inside TADs is highly variable in single cells, yet little is known about its temporal dynamics, how it influences the rates and durations of chromosomal contacts, and how it depends on CTCF and cohesin. To address these questions we combine two quantitative live-cell imaging strategies that minimize locus-specific confounding effects. We show that loop extrusion by cohesin globally reduces the mobility of the chromatin fiber in living cells, while also increasing the rates of formation and durations of contacts between sequences inside the same TAD. Quantitative analysis of high-resolution microscopy data reveals that contacts assemble and disassemble frequently in the course of the cell cycle, and become substantially more frequent and longer in the presence of convergent CTCF sites. Comparison with polymer modeling additionally reveals that cohesin-mediated CTCF loops last around 10 minutes on average. Our data support the notion that chromosome structure within TADs is highly dynamic and provide a quantitative framework for understanding the principles that link chromosome structure to biological function.

2022-02-27 | GSE197237 | GEO

Cohesin and CTCF control chromosomal contact dynamics in living cells [Hi-C]

2022-02-27 | GSE197231 | GEO

Cohesin and CTCF control chromosomal contact dynamics in living cells [capture C]

2022-02-27 | GSE197234 | GEO

Cohesin and CTCF control chromosomal contact dynamics in living cells [4C-seq]

2022-02-27 | GSE197226 | GEO

AlphaLink: bringing protein structure prediction in situ with in-cell photo-crosslinking mass spectrometry, crosslinking mass spectrometry, XL-MS,

Project description:The protein structure prediction problem has been revolutionised by AlphaFold2, an algorithm that uses neural networks and evolutionary information to predict accurate models from the primary sequence. However, some proteins remain difficult to predict. Moreover, proteins are dynamic entities that exist in complex environments in vivo. Here, we use the noncanonical amino acid Photo-Leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. We then introduce AlphaLink, a modified version of the AlphaFold2 algorithm that synergistically incorporates experimental distance restraint information into its network architecture. AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets in both synthetic and real-world scenarios by employing sparse experimental contacts as anchor points. The program can predict individual conformations of proteins based on the distance restraints provided. The noise-tolerant framework presented here for integrating data in protein structure prediction opens a path to accurate characterisation of protein structures from in-cell data.

2023-02-22 | PXD036833 | JPOST Repository

HyPro-seq analysis of HeLa and ARPE-19 cells

Project description:The ability of RNAs to form specific contacts with other macromolecules provides an important mechanism for subcellular compartmentalization. We developed a suite of hybridization-proximity (HyPro) labeling technologies for unbiased discovery of proteins (HyPro-MS) and transcripts (HyPro-seq) associated with RNAs of interest in genetically unperturbed cells. To generate the HyPro-seq dataset reported here, fixed and permeabilized human cells were hybridized with digoxigenin-labeled oligonucleotide probes against noncoding RNAs 45S, NEAT1 or PNCTR and transcripts co-localizing with these RNAs were biotinylated in situ using a custom-engineered HyPro enzyme containing a digoxigenin-binding domain. Biotinylated RNAs were then purified and sequenced using the NextSeq 500 Illumina platform.

2021-11-05 | E-MTAB-10365 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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