Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [perturb_seq]

ABSTRACT: RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action, yet the regulatory grammar that underlies RBP-mediated functions remains underexplored. Here, we performed a multi-omic data integration to systematically decipher the context-specific functions of RBPs. First, we report a compendium of in vivo proximity-dependent biotinylation (BioID) datasets of 50 human RBPs, which we used to generate a large-scale map of RBP protein neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (Perturb-seq) to capture rich transcriptomic phenotypes downstream of each RBP knockdown. By combining these physical and functional interaction readouts, along with the ENCODE transcriptome-wide atlas of RBP binding sites from eCLIP assays, we generated an integrated map of functional RBP interactions. This map not only captures well-studied post-transcriptional processes, but also reveals numerous previously unknown RBP-mediated regulatory functions. For a number of these cases, we have validated their predicted context-specific RBP functions using biochemical and genetic approaches. By deciphering these complex modes of functional interactions between RBPs, we have taken the first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

ORGANISM(S): Homo sapiens

PROVIDER: GSE225807 | GEO | 2024/02/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [Ribosomal profiling]

Project description:RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action, yet the regulatory grammar that underlies RBP-mediated functions remains underexplored. Here, we performed a multi-omic data integration to systematically decipher the context-specific functions of RBPs. First, we report a compendium of in vivo proximity-dependent biotinylation (BioID) datasets of 50 human RBPs, which we used to generate a large-scale map of RBP protein neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (Perturb-seq) to capture rich transcriptomic phenotypes downstream of each RBP knockdown. By combining these physical and functional interaction readouts, along with the ENCODE transcriptome-wide atlas of RBP binding sites from eCLIP assays, we generated an integrated map of functional RBP interactions. This map not only captures well-studied post-transcriptional processes, but also reveals numerous previously unknown RBP-mediated regulatory functions. For a number of these cases, we have validated their predicted context-specific RBP functions using biochemical and genetic approaches. By deciphering these complex modes of functional interactions between RBPs, we have taken the first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

2024-02-21 | GSE225808 | GEO

A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [ATAC-Seq]

2024-02-21 | GSE225806 | GEO

rec-Y2H matrix in S. cerevisiae screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins

Project description:RNA-binding proteins (RBPs) are crucial factors of post-transcriptional gene regulation and their modes of action are intensely investigated. At the center of attention are RNA motifs that guide where RBPs bind. However, sequence motifs recognized by RBPs are typically a poor predictor of RBP-RNA interactions in vivo. It is hence believed that many RBPs recognize RNAs as complexes, to increase specificity and regulatory potential. To probe the potential for RBP–RBP complex formation, we assembled a library of 978 mammalian RBPs and used rec-Y2H screening to detect direct interactions between RBPs, sampling >1M possible interactions. We discovered 1994 new interactions and demonstrate that our interaction screening discovers RBP pairs that bind RNAs adjacently. We further find that the mRNA binding region preferences of an RBP can deviate, depending on its adjacently binding interaction partner. Finally, we reveal novel RBP–RBP interaction networks among major RNA processing steps and show that RBP mutations observed in cancer rewire spliceosomal interaction networks.

2021-09-01 | E-MTAB-9612 | biostudies-arrayexpress

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

Project description:RNA-binding proteins (RBPs) target RNA in a context-dependent manner to regulate gene expression. Protein-protein interaction (PPI) maps of RBP complexes and networks are critical for defining RBP function and RNA targeting. Yet, PPI networks under-represent RBP baits and need more information about RNA-driven interactions. Therefore, we generated an RNA-aware, RBP-interactome map combining two strategies that use systematic proteomic methods to identify 1) protein interactions using co-immunoprecipitation in the presence or absence of RNase treatment of a ~100 RBPs across the RNA life-cycle and 2) RNA-dependent complexes using Size Exclusion Chromatography. Together, this dataset provides proteome-wide, cell-type specific, and quantitative identification of RNA-protein interactions across multiple RNA processing events. In the resulting PPI network, several hundred database-supported interactions establish many complexes operating at each of these mRNA life-cycle stages. Nearly a thousand novel interactions imply new functions for RBPs across multiple steps of the RNA life cycle. Overlapping our network with eCLIP data, we find RNA targets between interactors and uncover complex-driven binding signatures. Betweenness-centrality scores identify multi-functional RBPs that participate across multiple mRNA life-cycle steps. We characterize the novel interactions and functions of different classes of multi-functional proteins. We find the scaffolding protein, ERH, interacts with numerous nuclear speckle proteins and facilitates splicing and mRNA export. Finally, we show that the splicing factor, SNRNP200, interacts with nuclear export, localization, and translation proteins and is an essential factor of RNA granule formation during stress. Our large-scale RBP interaction network provides new insights and a valuable resource for exploring new RBP complexes operating to control gene expression.

2023-08-14 | GSE230717 | GEO

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

Project description:RNAs are continuously associated with RNA-binding proteins (RBPs), and these interactions are necessary for many key cellular processes ranging from splicing to chromatin regulation. Although numerous approaches have been developed to map RNA-binding sites of individual RBPs, few methods exist that allow assessment of global RBP-RNA interactions. Here, we describe a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites throughout a transcriptome of interest. We apply this method to the HeLa transcriptome and compare RBP binding sites found using different cross-linkers and ribonucleases. From this analysis, we identify numerous putative RBP binding motifs, reveal novel insights into co-binding by RBPs, and uncover a significant enrichment for disease-associated polymorphisms within RBP interaction sites. Protein interaction profile sequencing (PIP-seq) in HeLa cells. Two crosslinkers (formaldehyde and UV) with two RNases (dsRNase and ssRNase) each, as well as a no-crosslink sample. Performed with and without proteins. Three replicates for formaldehyde, two replicates for UV, single replicate for no crosslinker.

2013-11-06 | E-GEOD-49309 | biostudies-arrayexpress

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]

Project description:Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also showed strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription. As part of the ENCODE consortium, we embarked on a large-scale RBP ChIP-seq analysis, revealing broad presence of RBPs in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also show great preference for hotspots in the genome, particularly gene promoters, where their binding is frequently linked to transcriptional output. Self-organizing map reveals extensive co-binding events between TFs and RBPs, as exemplified by those between YY1, a known RNA-dependent TF, and RBM25, an RBP involved in alternative splicing. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may bridge specific TF-RNA interactions to control transcription.

2019-06-27 | GSE120105 | GEO

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:RNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions such as CLIP rely on purifying single proteins at a time. Methods to identify transcriptome wide binding of RBPs without purifying individual RBPs are gaining interest. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale in an RBP agnostic manner. Our method allows precise mapping of the 5’ end of the RBP binding site and uncovers RBPs that are differentially activated during cell fate transitions.

2024-03-04 | GSE230097 | GEO

Coordinating Expression of RNA Binding Proteins with Their mRNA Targets

Project description:Post-transcriptional regulation by RNA binding proteins (RBPs) plays prominent roles in a variety of biological processes. In this study, by analyzing the global regulatory relationship between RBPs and their target mRNAs in yeast, we discovered that most RBP genes are co-regulated with their target genes, but the RBPs tend to dampen expression variation among their target mRNAs. We further examined a well-studied RBP gene, PUF3, and found that the protein decreases the variation of its target mRNAs by differentially affecting their decay. Our results provided new insights into the functional importance of RBPs in coordinating their target genes expression. Both the PUF3 deletion strain and wild type BY4742 (MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0) strain were cultured overnight in YPD media. 0.01 OD cells were transferred into fresh YPEG media until 1.0 OD. Total RNA was extracted by the standard Trizol protocol. mRNA was then purified using oligo-dT DynaBeads. cDNA sequencing library was constructed according to the protocol described by Wang et al. After sequencing, the reads were also mapped into S. cerevisiae genome by SOAP2 with no more than two mismatches. RPKM was used to represent the expression level of each gene.

2014-06-01 | E-GEOD-55419 | biostudies-arrayexpress

Coordinating Expression of RNA Binding Proteins with Their mRNA Targets

2014-06-01 | GSE55419 | GEO

Global signatures of protein binding on structural RNAs in Saccharomyces cerevisiae

Project description:Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellelar functions and dynamics upon changing environmental condictions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical ncRNAs and ~11% of long ncRNA (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responces. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured noncoding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. Duplicate gPAR-CLIP libraries were sequenced from yeast strains for each of three conditions: log-phase growth, growth after 2 hour glucose starvation, and growth after 2 hour nitrogen starvation. polyA RNAs were isolated for all conditions. Total RNA were isolated from log phase growth conditions. Sucrose gradient fractionation was performed: some RNAs were isolated from the "light" fraction (lighter than 40S ribosome) and some from the "heavy" fraction. gPAR-CLIP libraries were used to determine regions of RNA bound by proteins.

2013-07-15 | E-GEOD-48888 | biostudies-arrayexpress

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