RNA-Binding Protein Immunoprecipitation and High-Throughput Sequencing

2020 ◽  
pp. 453-461
Author(s):  
Tino Köster ◽  
Dorothee Staiger
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS)

Methods ◽  
2017 ◽  
Vol 118-119 ◽  
pp. 171-181 ◽  
Author(s):  
Tzu-Fang Lou ◽  
Chase A. Weidmann ◽  
Jordan Killingsworth ◽  
Traci M. Tanaka Hall ◽  
Aaron C. Goldstrohm ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
In Vitro Selection ◽  
Rna Binding ◽  
Protein Complexes ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Integrated Analysis ◽  
Sequence Specificity

scholarly journals rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation

2020 ◽  
Vol 48 (W1) ◽  
pp. W300-W306 ◽  
Author(s):  
Jae Y Hwang ◽  
Sungbo Jung ◽  
Tae L Kook ◽  
Eric C Rouchka ◽  
Jinwoong Bok ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
High Throughput ◽  
Splice Site ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Retained Intron ◽  
Map Analysis

Abstract The rMAPS2 (RNA Map Analysis and Plotting Server 2) web server, freely available at http://rmaps.cecsresearch.org/, has provided the high-throughput sequencing data research community with curated tools for the identification of RNA binding protein sites. rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. The initial release of rMAPS focused only on the most common alternative splicing event, skipped exon or exon skipping. However, there was a high demand for the analysis of other major types of alternative splicing events, especially for retained intron events since this is the most common type of alternative splicing in plants, such as Arabidopsis thaliana. Here, we expanded the implementation of rMAPS2 to facilitate analyses for all five major types of alternative splicing events: skipped exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site and retained intron. In addition, by employing multi-threading, rMAPS2 has vastly improved the user experience with significant reductions in running time, ∼3.5 min for the analysis of all five major alternative splicing types at once.

scholarly journals ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

2017 ◽  
Vol 45 (19) ◽  
pp. 11004-11018 ◽  
Author(s):  
David Heller ◽  
Ralf Krestel ◽  
Uwe Ohler ◽  
Martin Vingron ◽  
Annalisa Marsico
Keyword(s):  
High Throughput ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Sequence Structure

scholarly journals An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5

2019 ◽  
Vol 20 (5) ◽  
pp. 1010 ◽  
Author(s):  
Yoshika Hayakawa-Yano ◽  
Masato Yano
Keyword(s):  
Alternative Splicing ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Neural Progenitor Cell ◽  
Conditional Knockout ◽  
Splicing Factors ◽  
Axon Development ◽  
Rna Switch

A set of tissue-specific splicing factors are thought to govern alternative splicing events during neural progenitor cell (NPC)-to-neuron transition by regulating neuron-specific exons. Here, we propose one such factor, RNA-binding protein Quaking 5 (Qki5), which is specifically expressed in the early embryonic neural stem cells. We performed mRNA-SEQ (Sequence) analysis using mRNAs obtained by developing cerebral cortices in Qk (Quaking) conditional knockout (cKO) mice. As expected, we found a large number of alternative splicing changes between control and conditional knockouts relative to changes in transcript levels. DAVID (The Database for Annotation, Visualization and Integrated Discovery) and Metascape analyses suggested that the affected spliced genes are involved in axon development and microtubule-based processes. Among these, the mRNA coding for the Ninein protein is listed as one of Qki protein-dependent alternative splicing targets. Interestingly, this exon encodes a very long polypeptide (2121 nt), and has been previously defined as a dynamic RNA switch during the NPC-to-neuron transition. Additionally, we validated that the regulation of this large exon is consistent with the Qki5-dependent alternative exon inclusion mode suggested by our previous Qki5 HITS-CLIP (high throughput sequencing-cross linking immunoprecipitation) analysis. Taken together, these data suggest that Qki5 is an important factor for alternative splicing in the NPC-to-neuron transition.

235: The RNA-Binding Protein IMP3: A Novel Molecular Marker Predicts Progression of Superficial (TA and T1) Urothelial Carcinomas of Bladder

2007 ◽  
Vol 177 (4S) ◽  
pp. 78-79
Author(s):  
Lioudmila Sitnikova ◽  
Gary Mendese ◽  
Qin Lui ◽  
Bruce A. Woda ◽  
Di Lu ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Urothelial Carcinomas

Author response for "Inhibition of osteoclastogenesis by the RNA‐binding protein QKI5: a novel approach to protect from bone resorption"

2019 ◽  
Author(s):  
Benjamin Rauwel ◽  
Yannick Degboe ◽  
Katy Diallo ◽  
Souraya Sayegh ◽  
Michel Baron ◽  
...  
Keyword(s):  
Bone Resorption ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Author Response ◽  
Novel Approach

The RNA-binding protein Musashi-2 (MSI2) controls mRNA processing and translational regulation via interactions with SFPQ and PIWIL1 during mammalian spermatogenesis

2014 ◽  
Author(s):  
Jessie M Sutherland ◽  
Alexander P Sobinoff ◽  
Kate Redgrove ◽  
Tara-Lynne Davidson ◽  
Nicole A Siddall ◽  
...  
Keyword(s):  
Translational Regulation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Mrna Processing
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