Background: RNA binding proteins (RBPs) play essential roles in the regulation of RNA metabolism. Recent studies have disclosed that RBPs achieve their functions via binding to their targets in a position-dependent pattern on RNAs. However, few studies have systematically addressed the associations between the RBP's functions and their positional binding preferences.
Methods: Here, we present large-scale analyses on the functional targets of human RBPs by integrating the enhanced cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) datasets and the shRNA knockdown followed by RNA-seq datasets that are deposited in the integrated ENCyclopedia of DNA Elements in the human genome (ENCODE) data portal.
Results: We found that (1) binding to the translation termination site and the 3'untranslated region is important to most human RBPs in the RNA decay regulation; (2) RBPs' binding and regulation follow a cell-type specific pattern.
Conclusions: These analysis results show the strong relationship between the binding position and the functions of RBPs, which provides novel insights into the RBPs' regulation mechanisms.
Keywords: CLIP-seq; RNA binding protein; RNA regulation; RNA-seq; knockdown.