Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oligonucleotide-mediated proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.

ABSTRACT: Within all cells, RNA molecules form complex networks of molecular interactions that are central to their function, but discovering these interactions remains challenging. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable DNA probes to deliver proximity-biotinylating enzymes to a target RNA, enabling molecules within that RNA's subcellular microcompartment to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its RNA-targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs, and enabled systematic discovery of nucleolar-chromatin interactions across multiple cell lines. O-MAP uses exclusively off-the-shelf parts requiring no genetic- or cell-line engineering and is easily portable across diverse specimen-types and target RNAs. We therefore anticipate its application to a broad array of RNA phenomena.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: David Shechner

PROVIDER: MSV000094186 | MassIVE | Tue Feb 27 12:46:00 GMT 2024

SECONDARY ACCESSION(S): PXD050197

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP ChIP]

Project description:Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA, enabling nearby molecules to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise RNA-localized in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs and enabled systematic characterization of nucleolar-chromatin interactions across multiple cell lines. O-MAP is portable to cultured cells, organoids, and tissues, and to RNAs of various lengths, abundances, and sequence composition. And, O-MAP requires no genetic manipulation and uses exclusively off-the-shelf parts. We therefore anticipate its application to a broad array of RNA phenomena.

2024-08-22 | GSE217562 | GEO

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [Xist OMAP RIP]

2024-08-22 | GSE217565 | GEO

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [Xist OMAP ChIP]

2024-08-22 | GSE217564 | GEO

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP RIP]

2024-08-22 | GSE217563 | GEO

Nascent transcript O-MAP reveals the molecular architecture a single-locus subnuclear compartment built by RBM20 and the TTN noncoding RNA

Project description:We here adapt Oligonucleotide-mediated proximity-interactome mapping (O-MAP), a novel RNA-targeted microenvironment-mapping method, to biochemically characterize the molecular neighborhoods near individual genomic loci. By targeting O-MAP to introns within the TTN pre-mRNA, we have systematically mapped the chromatin loci, RNAs, and proteins within a cardiomyocyte-specific "RNA factory" nucleated on these TTN-derived noncoding transcripts. This revealed an unanticipated compartmental architecture that organizes trans-chromosomal domains into a hub of transcriptionally silenced chromatin, and which recruits dozens of unique RNA-binding and chromatin-scaffolding factors, including QKI and SAFB, along with their target transcripts. Loss of the cardiac-specific splicing factor RBM20, a master regulator of TTN splicing, remodels nearly every facet of factor architecture, suggesting new mechanisms in RBM20-driven dilated cardiomyopathy. This establishes O-MAP as a pioneering method for probing single-locus, microcompartment-level interactions that are opaque to conventional tools, and suggests new mechanisms by which coding genes can "moonlight" as nuclear-architectural noncoding RNAs.

2024-10-08 | MSV000096046 | MassIVE

Chem-Seq of chemical derivatives in MM1S cells

Project description:An ability to map the global interactions of a chemical entity with chromatin genome-wide could provide new insights into the mechanisms by which a small molecule perturbs cellular functions. we developed a method that uses chemical derivatives and massively parallel DNA sequencing (Chem-Seq) to identify the sites bound by small chemical molecules throughout the human genome.

2013-12-13 | GSE44098 | GEO

Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions

Project description:Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells, and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus, and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome, and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.

2023-08-09 | GSE240435 | GEO

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (RADICL-seq)

Project description:Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs,, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However they present still some limitations. Here, we introduce RNA and DNA interacting complexes ligated and sequenced (RADICL-seq), a novel technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation based methodology that reduces the bias for nascent transcription, increases genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

2019-12-05 | GSE132190 | GEO

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (CAGE)

2019-12-05 | GSE132191 | GEO

Characterization of chromatin associated RNA-binding proteins by SPACE

Project description:Chromatin processes such as DNA replication, transcription and RNA processing are mediated by intermolecular transactions among proteins, RNAs and the genome. Although DNA-protein and RNA-protein interactions have been studied extensively, reliable and efficient identification of chromatin-associated RNA-binding proteins (caRBPs) has remained technically challenging; especially using limited sample material. Here, we present SPACE (Silica Particle Assisted Chromatin Enrichment), a stringent and straightforward chromatin-purification method, which works efficiently with as few as 100,000 cells. Using SPACE we have enriched 1825 chromatin-associated proteins in mES cells. Among many known and novel chromatin-associated proteins, we identified 743 RBPs. Considering protein counts RBPs consist 40% of the chromatin composition, while, weighted by their abundances they comprise ~70% of the chromatome. Furthermore, using a double tryptic digestion strategy (SPACE2) we have determined how the caRBPs bind to chromatin. By applying SPACE to mES cells in 2i and serum conditions, we have detected significant changes in the chromatome of the cells that are neglected in traditional full proteome analyses. Overall, SPACE and SPACE2 are sensitive and powerful methods for providing a global view of chromatin composition and RBP-chromatin interactions.

2021-11-25 | PXD023903 | Pride

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