Similar Datasets
Project description:PROPER-seq (PROtein Protein intERaction sequencing)
| PRJNA633786 | ENA
Project description: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 regulation in normal and disease processes. The majority of approaches to study RNA-protein interactions focus on single RBPs, however there are many hundreds RBPs encoded in the human genome, and each cell type expresses a different catalog of these regulatory molecules, greatly limiting the ability of these single RBP approaches to capture the global landscape of RNA-protein interactions. We and others have developed approaches to globally catalog regions of mRNAs that are bound by proteins in an unbiased manner. Here we describe a detailed protocol for performing our RNase-mediated protein footprint sequencing approach, termed protein interaction profile sequencing (PIP-seq). In this protocol, RNA-protein interactions are stabilized by cross-linking, and un-bound regions are digested with RNases, leaving only the protein-bound regions intact. To control for RNase insensitive regions, proteins are first denatured and then RNP complexes are subject to RNase treatment. After high-throughput sequencing of remaining fragments, peak calling is performed to identify protein protected sites (PPSs). We describe the application of this protocol to a human embryonic kidney cell line and perform basic quality control, reproducibility and benchmarking analyses. Finally, we describe the landscape of protein-interactions in HEK293T cells, underscoring the value of this approach. Future applications of this method to study the dynamics of RNA-protein interactions in developmental processes will help to uncover the role of RBPs in post-transcriptional regulation. Protein interaction profile sequencing (PIP-seq) in HEK293T cells. Three replicates of formaldehyde cross-linked PIP-seq are described
2014-10-20 | E-GEOD-57881 | biostudies-arrayexpress
Project description:In order to investigate the influence of m6A on RNA secondary-structure and RNA-protein interactions, we performed protein-interaction profile sequencing (PIP-seq)
2018-11-09 | GSE108767 | GEO
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
Project description:Transcriptomic analyses of renal allograft biopsies reveal conserved rejection signatures and molecular pathways
2025-01-24 | E-GEOD-9493 | ExpressionAtlas
Project description:Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.
2022-06-15 | GSE148422 | GEO
Project description:RNA-protein interactions are fundamental for bacterial homeostasis. However, we lack a system-wide understanding of their dynamics upon environmental perturbation. In this study, we have characterised the dynamics of 91% of the Escherichia coli proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and reveal novel RBP functions for proteins like the chaperone HtpG, a new tRNA-binding protein. Moreover, we characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mainly present in Proteobacteria, two of them have human orthologs in the form of mitochondrial proteins associated with rare metabolic disorders. Altogether, we provide the first dynamic RBPome of a bacterium, showcasing how this approach can reveal the function of uncharacterised proteins, and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
2024-05-08 | GSE235661 | GEO
Project description:Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy
2025-01-24 | E-GEOD-93798 | ExpressionAtlas
Project description:Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.
2022-06-15 | GSE148423 | GEO
Project description:MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing
| PRJNA1133167 | ENA