Approaches for the Identification and Characterization of RNA-Protein Interactions

2012 ◽  
pp. 199-212
Author(s):  
Saiprasad Palusa ◽  
Jeffrey Wilusz
Keyword(s):  
Protein Interactions ◽  
Identification And Characterization

Identification and characterization of protein interactions using the yeast 2-hybrid system

1998 ◽  
pp. 95-124 ◽  
Author(s):  
Susanne E. Kohalmi ◽  
Laura J. V. Reader ◽  
Alon Samach ◽  
Jacek Nowak ◽  
George W. Haughn ◽  
...  
Keyword(s):  
Hybrid System ◽  
Protein Interactions ◽  
Identification And Characterization

scholarly journals Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome

2018 ◽  
Author(s):  
Lixin Cheng ◽  
Kwong-Sak Leung
Keyword(s):  
Protein Interactions ◽  
Cellular Localization ◽  
A Priori ◽  
Specific Sequence ◽  
Nuclear Compartment ◽  
Protein Interactome ◽  
Moonlighting Proteins ◽  
Non Coding Rnas ◽  
Identification And Characterization

AbstractMoonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a methodology, MoonFinder, for the identification of moonlighting lncRNAs. MoonFinder is a statistical algorithm identifying moonlighting lncRNAs without a priori knowledge through the integration of protein interactome, RNA-protein interactions, and functional annotation of proteins. We identify 155 moonlighting lncRNA candidates and uncover that they are a distinct class of lncRNAs characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncRNAs tend to have shorter but more exons and the moonlighting lncRNAs have a localization tendency of residing in the cytoplasmic compartment in comparison with the nuclear compartment. Moreover, moonlighting lncRNAs and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

2011 ◽  
Vol 317 (15) ◽  
pp. 2183-2199 ◽  
Author(s):  
Donald B. Bloch ◽  
Rita A. Nobre ◽  
Gillian A. Bernstein ◽  
Wei-Hong Yang
Keyword(s):  
Protein Interactions ◽  
Mrna Processing ◽  
Processing Body ◽  
Identification And Characterization ◽  
Two Hybrid

scholarly journals Early Intermediates of mariner Transposition: Catalysis without Synapsis of the Transposon Ends Suggests a Novel Architecture of the Synaptic Complex

2004 ◽  
Vol 24 (18) ◽  
pp. 8301-8311 ◽  
Author(s):  
Karen Lipkow ◽  
Nicolas Buisine ◽  
David J. Lampe ◽  
Ronald Chalmers
Keyword(s):  
Protein Interactions ◽  
Reaction Mechanisms ◽  
Protein Protein Interactions ◽  
Dna Protection ◽  
Synaptic Complex ◽  
Insertion Elements ◽  
Identification And Characterization

ABSTRACT The mariner family is probably the most widely distributed family of transposons in nature. Although these transposons are related to the well-studied bacterial insertion elements, there is evidence for major differences in their reaction mechanisms. We report the identification and characterization of complexes that contain the Himar1 transposase bound to a single transposon end. Titrations and mixing experiments with the native transposase and transposase fusions suggested that they contain different numbers of transposase monomers. However, the DNA protection footprints of the two most abundant single-end complexes are identical. This indicates that some transposase monomers may be bound to the transposon end solely by protein-protein interactions. This would mean that the Himar1 transposase can dimerize independently of the second transposon end and that the architecture of the synaptic complex has more in common with V(D)J recombination than with bacterial insertion elements. Like V(D)J recombination and in contrast to the case for bacterial elements, Himar1 catalysis does not appear to depend on synapsis of the transposon ends, and the single-end complexes are active for nicking and probably for cleavage. We discuss the role of this single-end activity in generating the mutations that inactivate the vast majority of mariner elements in eukaryotes.

Identification and characterization of peptidases secreted by quahog parasite unknown (QPX), the protistan parasite of hard clams

2016 ◽  
Vol 122 (1) ◽  
pp. 21-33 ◽  
Author(s):  
E Rubin ◽  
GT Werneburg ◽  
E Pales Espinosa ◽  
DG Thanassi ◽  
B Allam
Keyword(s):  
Quahog Parasite Unknown ◽  
Hard Clams ◽  
Identification And Characterization
Sign in / Sign up

Export Citation Format

Share Document