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TranscriptomicsA transcriptome-wide atlas of RNP compositions reveals diverse classes of mRNAs and lncRNAs
Aim: To determine how different classes of transcript (e.g. lncRNAs and mRNAs) are defined in the cell. Approach: We determined the transcriptome-wide targets of key RNA packaging, maturation, export and turnover factors. We used the CRAC technique, whereby RNA:protein interactions are fixed by UV ...
ORGANISM(S): Saccharomyces cerevisiae 
2013-08-29 | E-GEOD-46742 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of thermosensitive exosome mutants from permissive temperature and various time exposure to restrictive temperature
Transcriptome analyses of thermosensitive exosome mutants from permissive temperature to various time exposure to restrictive temperature.
ORGANISM(S): Saccharomyces cerevisiae 
2006-02-28 | E-MEXP-537 | biostudies-arrayexpress
TranscriptomicsTranscriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae
Purpose: The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. We applied an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between individu...
ORGANISM(S): Saccharomyces cerevisiae 
2012-09-25 | E-GEOD-40046 | biostudies-arrayexpress
ProteomicsImproved detection and quantitation of RNA-interactome using DIA SILAC
Detection and quantitation of the RNA-interacting proteome is commonly achieved applying SILAC labeling, following by data-dependent acquisition (DDA) of the proteomic data. However, the limited sensitivity of the DDA approach often restricts protein detection to those with higher expression in cell...
ORGANISM(S): Homo sapiens (Human) 
2023-12-19 | PXD045318 | Pride
Hek cells Dia-silac Rna-interactome 
ProteomicsSubstrate Specificity of the TRAMP Nuclear Surveillance Complexes
During nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyze...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-07-02 | PXD017114 | Pride
Trf4 Trf5 Nuclear surveillance Tramp complexes Rna-binding proteins 
ProteomicsA disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis
Mutations in the human RMRP gene cause Cartilage Hair Hypoplasia (CHH), an autosomal recessive disorder characterized by skeletal abnormalities and impaired T-cell activation. RMRP encodes a non-coding RNA, which forms the core of the RNase MRP ribonucleoprotein complex. In budding yeast, RMRP cleav...
ORGANISM(S): Homo sapiens (Human) 
2021-03-30 | PXD025029 | Pride
Protein-rna interaction  rna-binding sites  uv crosslinking  mass spectrometry  genetic disease  cartilage hair hypoplasia  ribosome synthesis  t cell activation 
ProteomicsDefining the RNA Interactome by Total RNA-Associated Protein Purification
UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), r...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2019-03-26 | PXD011071 | Pride
Trapp rna-protein uv 
ProteomicsStress-induced translation inhibition through displacement of scanning initiation factors
Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the protein:RNA interactome, without correspo...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-10-13 | PXD019141 | Pride
Translational control. Heat shock Glucose starvation Environmental stress Initiation factors Rna-binding proteins Mrna Translation 
ProteomicsIntegrative Vectors for Regulated Expression of SARS-CoV-2 Proteins Implicated in RNA Metabolism
Infection with SARS-CoV-2 is expected to result in substantial reorganization of host cell RNA metabolism. We identified 14 proteins that were predicted to interact with host RNAs and/or RNA binding proteins, based on published data for SARS-CoV and SARS-CoV-2. Here, we describe a series of affinity...
ORGANISM(S): Homo sapiens (Human) 
2020-09-25 | PXD020339 | Pride
Covid-19  fusion proteins  uv crosslinking  rna 
ProteomicsThe type 6 secretion system immunity protein RhsFI has been repurposed for small RNA regulation in pathogenic E. coli
RNA-binding proteins (RBPs) play key roles in regulating virulence gene expression in pathogenic, enterohaemorrhagic E. coli (EHEC). Under virulence-inducing conditions total RNA associated protein purification (TRAPP) identified 443 RNA-associated proteins in EHEC included 35 encoded within pathoge...
ORGANISM(S): Escherichia coli 
2026-02-23 | PXD063410 | Pride
Label-free quantitation Small rna Rna-binding proteins Data dependent acquisition E.coli 
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