Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP) v1

protocols.io ◽  
2020 ◽  
Author(s):  
Eric L. Van Nostrand ◽  
Thai B. Nguyen ◽  
Chelsea Gelboin-Burkhart ◽  
Ruth Wang ◽  
Steven M. Blue ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cost Effective ◽  
Protein Targets

Erratum to: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)

2017 ◽  
pp. E1-E1 ◽  
Author(s):  
Eric L. Van Nostrand ◽  
Thai B. Nguyen ◽  
Chelsea Gelboin-Burkhart ◽  
Ruth Wang ◽  
Steven M. Blue ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cost Effective ◽  
Protein Targets

scholarly journals Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)

2017 ◽  
pp. 177-200 ◽  
Author(s):  
Eric L. Van Nostrand ◽  
Thai B. Nguyen ◽  
Chelsea Gelboin-Burkhart ◽  
Ruth Wang ◽  
Steven M. Blue ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cost Effective ◽  
Protein Targets

scholarly journals A deep learning framework for modeling structural features of RNA-binding protein targets

2015 ◽  
Vol 44 (4) ◽  
pp. e32-e32 ◽  
Author(s):  
Sai Zhang ◽  
Jingtian Zhou ◽  
Hailin Hu ◽  
Haipeng Gong ◽  
Ligong Chen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Structural Features ◽  
Protein Targets ◽  
Learning Framework

Hermes RNA-binding protein targets RNAs-encoding proteins involved in meiotic maturation, early cleavage, and germline development

2007 ◽  
Vol 75 (6) ◽  
pp. 519-528 ◽  
Author(s):  
Hye-Won Song ◽  
Karen Cauffman ◽  
Agnes P. Chan ◽  
Yi Zhou ◽  
Mary Lou King ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Meiotic Maturation ◽  
Early Cleavage ◽  
Germline Development ◽  
Protein Targets

scholarly journals Mechanistic Implications of Enhanced Editing by a HyperTRIBE RNA-binding protein

2017 ◽  
Author(s):  
Weijin Xu ◽  
Reazur Rahman ◽  
Michael Rosbash
Keyword(s):  
Rna Editing ◽  
Rna Binding ◽  
Catalytic Domain ◽  
Target Identification ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Protein Targets ◽  
Rna Targets ◽  
Editing Activity ◽  
Editing Enzyme

AbstractWe previously developed TRIBE, a method for the identification of cell-specific RNA binding protein targets. TRIBE expresses an RBP of interest fused to the catalytic domain (cd) of the RNA editing enzyme ADAR and performs Adenosine-to-Inosine editing on RNA targets of the RBP. However, target identification is limited by the low editing efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites, many of which are also edited by TRIBE but at a much lower editing frequency. HyperTRIBE therefore more faithfully recapitulates the known binding specificity of its RBP than TRIBE. In addition, separating RNA binding from the enhanced editing activity of the HyperTRIBE ADAR catalytic domain sheds light on the mechanism of ADARcd editing as well as the enhanced activity of the HyperADARcd.

scholarly journals Identification of RNA-binding protein targets with HyperTRIBE

2018 ◽  
Vol 13 (8) ◽  
pp. 1829-1849 ◽  
Author(s):  
Reazur Rahman ◽  
Weijin Xu ◽  
Hua Jin ◽  
Michael Rosbash
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Protein Targets

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
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