SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

Fan Chen,Sündüz Keleş

doi:10.1186/s13059-020-02039-7

Abstract

Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking. We describe SURF, Statistical Utility for RBP Functions, for integrative analysis of large collections of CLIP-seq and RNA-seq data. We demonstrate SURF’s ability to accurately detect differential alternative transcriptional regulation events and associate them to local protein-RNA interactions. We apply SURF to ENCODE RBP compendium and carry out downstream analysis with additional reference datasets. The results of this application are browsable at http://www.statlab.wisc.edu/shiny/surf/.

Highlights

RNA-binding proteins (RBPs) constitute a key class of regulators for post-transcriptional processes such as splicing, polyadenylation, transportation, translation, and degradation of RNA transcripts in eukaryotic organisms [1, 2]
SURF framework SURF is designed for large-scale analysis of RBP CLIP-seq and RNA-seq data and includes analyses and discovery modules (Fig. 2)
The relative exon usage (REU) is defined as the ratio of count of reads overlapping the event body, K1, over the count of those reads residing in the other exonic regions of the same gene, K0, and is computed as K1/K0 (Fig. 2b)

Summary

Introduction

RNA-binding proteins (RBPs) constitute a key class of regulators for post-transcriptional processes such as splicing, polyadenylation, transportation, translation, and degradation of RNA transcripts in eukaryotic organisms [1, 2]. The ENCODE (ENCyclopedia of DNA elements) project [9, 10] recently generated eCLIP-seq datasets for 120 and 104 RBPs in human cell lines K562 and HepG2 These datasets were complemented with RNA-seq datasets of the same cell lines under conditions of both wild-type and short hairpin RNA (shRNA) knockdown of the individual RBPs to identify differentially regulated AS, ATI, and APA events (Fig. 1). The discovery module of SURF queries existing reference transcriptome databases, i.e., the genotype-tissue expression (GTEx) project [13] and the Cancer Genome Atlas (TCGA) program [14], to assess differential activity of ATR-specific transcript targets of RBPs between normal tissue and the relevant tumor samples

Methods

Results

Conclusion