Methods of identifying protein binding sites on RNA
AssigneeThe Regents of the University of California
InventorsEugene Yeo, Meredith Corley
Life of this patent
Estimating the term…
Abstract
Provided are methods for identifying an RNA nucleobase that interacts with an RNA binding protein (RBP) including (a) crosslinking the RNA binding protein to an RNA fragment in a biological sample; (b) detecting an RNA-RBP complex, wherein the RNA-RBP complex comprises the RNA fragment bound by the RNA binding protein; (c) isolating the RNA fragment of the RNA-RBP complex; and (d) profiling the isolated RNA fragment bound by the RNA binding protein, thereby identifying the RNA nucleobase of the RNA fragment that interacts with the RNA binding protein.
Claims6
A method of identifying an RNA nucleobase that interacts with an RNA binding protein (RBP), the method comprising:
- (a) providing a biological sample, wherein the biological sample comprises a first plurality of cells and a second plurality of cells;
- (b) contacting the first plurality of cells with an RNA structure probing agent;
- (c) crosslinking the RNA binding protein to an RNA fragment in both the first plurality of cells and the second plurality of cells;
- (d) detecting an RNA-RBP complex in both the first plurality of cells and the second plurality of cells, wherein the RNA-RBP complex comprises the RNA fragment bound by the RNA binding protein;
- (e) isolating the RNA fragment of the RNA-RBP complex in both the first plurality of cells and the second plurality of cells;
- (f) contacting the second plurality of cells with the RNA structure probing agent;
- and
- (g) profiling (i) the RNA fragment bound by the RNA binding protein from the first plurality of cells and (ii) the RNA fragment bound by the RNA binding protein from the second plurality of cells, thereby identifying the RNA nucleobase(s) of the RNA fragment that interact with the RNA binding protein via a hydrogen bond, wherein steps (a)-(g) are completed in the order presented.
Dependencies are inferred from the claim text.