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ProteomicsFormaldehyde-crosslinking enables comprehensive profiling of in vivo RNA-interactome in UV-impermeable samples
Development of UV-crosslinking based RNA-interactome capture protocol have expanded the repertoire of RBPs. Apparent limitations of UV-crosslinking, however, have made the RBP profiling to be incomplete and inapplicable to many of the biological samples in physiological contexts. Here we developed f...
ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog) 
2020-11-25 | PXD010046 | Pride
Rbp formaldehyde 
TranscriptomicsGlobal analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any or...
ORGANISM(S): Arabidopsis thaliana 
2014-12-16 | E-GEOD-58974 | biostudies-arrayexpress
GenomicsMouse spleen: Histone modification patterns in spleens from wild type and leukemic mice
ChIP-Seq for H3K4me3 and H3K27me3 in wild type spleens and spleens from mice having deletion of RBP-J in cells of the renin lineage, which results in B-cell leukemia. Examination of 2 different histone modifications in wild type and mutant spleens.
ORGANISM(S): Mus musculus 
2014-02-17 | E-GEOD-46566 | biostudies-arrayexpress
TranscriptomicsRNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
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 ...
ORGANISM(S): Homo sapiens 
2013-11-06 | E-GEOD-49309 | biostudies-arrayexpress
TranscriptomicsDynamic binding of RBPJ is determined by Notch signalling status
Notch signalling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to a neighbouring cell. The DNA-binding protein RBPJ is the principle effector of this pathway in mammals and together with the transcription ...
ORGANISM(S): Mus musculus 
2013-05-13 | E-GEOD-37184 | biostudies-arrayexpress
ProteomicsFAX-RIC enables robust RNA interactome profiling in multicellular organisms in vivo
Formaldehyde crosslinking based profiling of RNA interactome in the mosue tissue, liver.
ORGANISM(S): Mus musculus (Mouse) 
2020-11-25 | PXD022023 | Pride
Mouse liver rbp rna interactome 
ProteomicsProtein-RNA interaction dynamics downstream of KRAS activation reveals key regulators of oncogenic KRAS driven cancers.
Oncogenic KRAS mutations rewires cellular signaling, leading to significant alterations in gene expression. RNA-binding proteins (RBPs) play a pivotal role in gene expression regulation by post-transcriptionally controlling various aspects of RNA metabolism. It becomes clear that interactions betw...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD053310 | Pride
Human Lung Rbp 
TranscriptomicsProfiling of RNA-binding protein binding sites by in-situ reverse transcription-based sequencing
RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA substrates are still lacking, especially when the interaction is dynamic or materials a...
ORGANISM(S): Homo sapiens Mus musculus 
2023-11-05 | GSE226161 | GEO
TranscriptomicsTranscriptome-wide ribonuclease footprinting to identify RNA-protein interaction sites
RNA-binding proteins (RBPs) are intimately involved in all aspects of RNA processing and regulation and are linked to neurodegenerative diseases and cancer. Therefore, understanding the relationship between RBPs and their RNA targets is critical for a broader understanding of post-transcriptional re...
ORGANISM(S): Homo sapiens 
2014-10-20 | E-GEOD-57881 | biostudies-arrayexpress
TranscriptomicsTranposable elements modulate human mRNAs and lncRNAs via specific RNA-protein interactions.
Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively inve...
ORGANISM(S): Homo sapiens 
2014-09-10 | E-GEOD-61238 | biostudies-arrayexpress
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