Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins

Abstract

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.

Graphical abstract

Keywords

RNA binding protein / CLIP-seq / RNA-seq / knockdown / RNA regulation

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