Specificity and nonspecificity in RNA-protein interactions.
To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.
Center for RNA Molecular Biology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.|Department of Biochemistry, Case Western Reserve University 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.|Department of Physics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
Eckhard
E
Jankowsky
Department of Biochemistry, Case Western Reserve University 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
Michael E
ME
Harris
D000818:Animals; D001483:Base Sequence; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry / Q000502:physiology*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000502:physiology*; D013816:Thermodynamics
D016601:RNA-Binding Proteins; D012313:RNA