Global identification of RNA-binding proteins and RNA-binding domains in methicillin-resistant Staphylococcus aureus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA785458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17091006_1.fastq.gz | Fastqsanger.gz | |||
| SRR17091006_2.fastq.gz | Fastqsanger.gz | |||
| SRR17091007_1.fastq.gz | Fastqsanger.gz | |||
| SRR17091007_2.fastq.gz | Fastqsanger.gz | |||
| SRR17091008_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:Using improved and robust biochemical methods, we present the first global analysis of RNA-binding proteins (RBPs) and RNA-binding domains (RBDs) in clinically relevant and multi-drug resistant Gram-positive bacteria. To validate our results in silico, we developed novel bioinformatics tools that compare RBDome data with ligand-binding site predictions generated by five different algorithms on a large number of S. aureus crystal structures. This revealed that the putative RBDs are highly enriched for predicted RNA-binding sites and basic and aliphatic amino acids, demonstrating the robustness of our approach. Surprisingly, we found that HTH-type DNA-binding and NAD and P-loop type Rossmann-fold proteins may also play a prominent role in post-transcriptional regulation in Gram-positive bacteria and we identified a common mode of RNA recognition for these domains. Subsequent in vivo validation studies showed that the HTH-type transcription factor CcpA, a master regulator of carbon metabolism in Gram-positive bacteria, is also a global post-transcriptional regulator and binds its RNA substrates at very specific distances from transcription terminators. Our novel experimental and computations tools are widely applicable, and our work provides an extremely valuable resource for groups studying post-transcriptional regulation and RNA-binding proteins in bacteria.
2022-05-04 | GSE189977 | GEO
Project description:RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific
| PRJNA889324 | ENA
Project description:Thousands of RNA-binding proteins (RBPs) crosslink to cellular mRNA. Among these are numerous unconventional RBPs (ucRBPs)—proteins that associate with RNA but lack known RNA-binding domains (RBDs). The vast majority of ucRBPs have uncharacterized RNA-binding specificities. We analyzed 492 human ucRBPs for intrinsic RNA-binding in vitro and identified 23 that bind specific RNA sequences. Most (17/23), including 8 ribosomal proteins, were previously associated with RNA-related function. We identified the RBDs responsible for sequence-specific RNA-binding for several of these 23 ucRBPs and surveyed whether corresponding domains from homologous proteins also display RNA sequence specificity. CCHC-zf domains from seven human proteins recognized specific RNA motifs, indicating that this is a major class of RBD. For Nudix, HABP4, TPR, RanBP2-zf, and L7Ae domains, however, only isolated members or closely related homologs yielded motifs, consistent with RNA-binding as a derived function. The lack of sequence specificity for most ucRBPs is striking, and we suggest that many may function analogously to chromatin factors, which often crosslink efficiently to cellular DNA, presumably via indirect recruitment. Finally, we show that ucRBPs tend to be highly abundant proteins and suggest their identification in RNA interactome capture studies could also result from weak nonspecific interactions with RNA.
2023-03-31 | GSE215198 | GEO
Project description:Dissecting RNA Selectivity Mediated by Tandem RNA-Binding Domains
| PRJNA1176144 | ENA
Project description:In the current work, we present a comprehensive coverage of the RNA-binding protein (RBP) interactome of Drosophila at four levels of resolution. The highest level tackled in our study represents the RNA-protein complexes, which we address by combining formaldehyde crosslinking of Drosophila S2 cells followed by polyA+ pulldown using oligo-dT beads. On the second level of resolution we identified direct RBPs in the cell using UV crosslinking. Given the paucity of information available on the RNA-binding regions in the Drosophila RBPs that we uncovered, we developed the CAPRI methodology to dissect RNA binding domains (RBDs) on a systematic level. The CAPRI technique provided the final two levels of resolution of our study. The protocol utilised FASP to enable isolation of peptides crosslinked to RNA and peptides adjacent to these crosslinked sites. The CAPRI pipeline mapped both the peptides in proximity to RNA and the precise amino acids contacting RNA. The RNA crosslinked peptide analysis was made by de novo peptide analysis software, PEAKS (Bioinformatics Solutions Inc). In a separate analysis, we also applied FA crosslinking to RBD capture and showed it to be a viable complementary method to the CAPRI workflow. We next applied CAPRI interactome capture to human cells in order to analyse the evolutionary conservation of newly identified RNA binding domains between the two species. These interactome capture techniques and the datasets acquired using them are discussed in detail in the following sections. In summary, we present a comprehensive resource for the study of RNA-protein interactions at a high throughput scale.
2019-07-02 | PXD013338 | Pride
Project description:Global mapping of RNA-binding domains in multi-drug resistant Staphylococcus aureus
| PRJNA687253 | ENA
Project description:RNA regulation plays an integral role in tuning gene expression and is controlled by thousands of RNA-binding proteins (RBPs). While some RBPs require most of their sequence to accomplish their functions, some examples exist of modularity: small protein domains that serve as molecular glues to recruit larger RNA regulatory complexes. Mapping these RNA-regulatory effector domains is important for understanding RBP function and for developing compact synthetic tools for precisely tuning RNA levels. We developed a high-throughput recruitment assay (HT-RNA-Recruit) to identify RNA-down-regulatory effector domains within human RBPs. By recruiting over 30,000 protein tiles from 367 RBPs to a reporter mRNA, we discovered over 100 unique RNA-down-regulatory effector domains in 86 distinct RBPs. We identified some domains that downregulate gene expression both when recruited to DNA and RNA, and dissected their mechanisms of regulation. Finally, we built inducible synthetic RNA regulators that can target endogenous RNAs or stably maintain reporter gene expression at desired levels, and developed a mathematical model to predict their dynamics. This work serves as a resource for human RNA regulators and expands the synthetic repertoire of RNA-based genetic control tools.
2025-08-05 | GSE303955 | GEO
Project description:The RNA interactomes of HeLa and HEK293 cells jointly comprise 1106 RNA-binding proteins (RBPs), with almost half of these lacking well-defined RNA-binding domains (RBDs), suggesting the existence of numerous unknown RNA-binding architectures. Here, we report on “RBDmap”, a new method built on interactome capture, to comprehensively identify the RBDs of native RBPs in HeLa cells. Making use of in vivo UV-crosslinking of RBPs to polyadenylated RNAs, capture on oligo(dT) magnetic beads, sequential proteolytic digestion and LC-MS/MS combined with a sophisticated scoring algorithm, RBDmap “re-discoveres” many known RNA-binding sites (e.g. RRM, KH) of numerous well characterized RBPs and suggests novel RBDs.
2016-08-08 | PXD000883 | Pride
Project description:Using improved and robust biochemical methods, we present the first global analysis of RNA-binding proteins (RBPs) and RNA-binding domains (RBDs) in clinically relevant and multi-drug resistant Gram-positive bacteria. To validate our results in silico, we developed novel bioinformatics tools that compare RBDome data with ligand-binding site predictions generated by five different algorithms on a large number of S. aureus crystal structures. This revealed that the putative RBDs are highly enriched for predicted RNA-binding sites and basic and aliphatic amino acids, demonstrating the robustness of our approach. Surprisingly, we found that HTH-type DNA-binding and NAD and P-loop type Rossmann-fold proteins may also play a prominent role in post-transcriptional regulation in Gram-positive bacteria and we identified a common mode of RNA recognition for these domains. Subsequent in vivo validation studies showed that the HTH-type transcription factor CcpA, a master regulator of carbon metabolism in Gram-positive bacteria, is also a global post-transcriptional regulator and binds its RNA substrates at very specific distances from transcription terminators. Our novel experimental and computations tools are widely applicable, and our work provides an extremely valuable resource for groups studying post-transcriptional regulation and RNA-binding proteins in bacteria.
2022-05-04 | GSE163719 | GEO
Project description:Differential binding of PARP-1 domains
| PRJNA923684 | ENA