scholarly journals Proximity of 5.8 S RNA-binding proteins and A-site proteins in yeast ribosomes inferred from cross-linking.

1984 ◽  
Vol 259 (16) ◽  
pp. 9971-9974 ◽  
Author(s):  
J C Lee ◽  
R R Traut
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cross Linking ◽  
Yeast Ribosomes ◽  
A Site

scholarly journals Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

2014 ◽  
Vol 11 (10) ◽  
pp. 1064-1070 ◽  
Author(s):  
Katharina Kramer ◽  
Timo Sachsenberg ◽  
Benedikt M Beckmann ◽  
Saadia Qamar ◽  
Kum-Loong Boon ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Binding Sites ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
High Resolution Mass Spectrometry ◽  
Cross Linking ◽  
High Resolution Mass ◽  
Resolution Mass

scholarly journals Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP

2022 ◽  
Author(s):  
Maciej Bak ◽  
Erik van Nimwegen ◽  
Ralf Schmidt ◽  
Mihaela Zavolan ◽  
Andreas J Gruber
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cell Types ◽  
Mrna Processing ◽  
Sequence Motif ◽  
Rna Seq ◽  
Global Regulators ◽  
Polypyrimidine Tract Binding Protein ◽  
A Site

Maturation of eukaryotic pre-mRNAs via splicing, 3' end cleavage and polyadenylation is modulated across cell types and conditions by a variety of RNA-binding proteins (RBPs). Although over 1'500 proteins are associated with RNAs in human cells, their binding motifs, targets and functions still remain to be elucidated, especially in the complex environment of human tissues and in the context of diseases. To overcome the lack of methods for systematic and automated detection of sequence motif-guided changes in pre-mRNA processing based on RNA sequencing (RNA-seq) data we have developed MAPP (Motif Activity on Pre-mRNA Processing). We demonstrate MAPP's functionality by applying it to RNA-seq data from 284 RBP knock-down experiments in the ENCODE project, from which MAPP not only infers position-dependent impact profiles of known regulators, but also reveals RBPs that modulate both the inclusion of cassette exons and the poly(A) site choice. Among these, the Polypyrimidine Tract Binding Protein 1 (PTBP1) has a similar activity in glioblastoma samples. This highlights the ability of MAPP to unveil global regulators of mRNA processing under physiological and pathological conditions.

scholarly journals Denaturing cross-linking immunoprecipitation to identify footprints for RNA-binding proteins

2021 ◽  
Vol 2 (4) ◽  
pp. 100819
Author(s):  
Michael Rosenberg ◽  
Vered Levy ◽  
Verena K. Maier ◽  
Barry Kesner ◽  
Roy Blum ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cross Linking
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