Journal Article

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

Park, Samuel S., Vang, Søren, Yeo, Gene W., Sathe, Shashank, Okholm, Trine Line Hauge, Nielsen, Morten Muhlig, Dyrskjøt, Lars, Aigner, Stefan, Kamstrup, Andreas Bjerregaard, Damgaard, Christian Kroun, Pedersen, Jakob Skou, Rasmussen, Asta Mannstaedt, Fristrup, Niels, Shankar, Archana, Chua, Zong Ming

2020

Overview

Background Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts. Methods We conduct an extensive screen of circRNA-RBP interactions in the ENCODE cell lines HepG2 and K562. We profile circRNAs in deep-sequenced total RNA samples and analyze circRNA-RBP interactions using a large set of eCLIP data with binding sites of 150 RBPs. We validate interactions for select circRNAs and RBPs by performing RNA immunoprecipitation and functionally characterize our most interesting candidates by conducting knockdown studies followed by RNA-Seq. Results We generate a comprehensive catalog of circRNA-RBP interactions in HepG2 and K562 cells. We show that KHSRP binding sites are enriched in flanking introns of circRNAs and that KHSRP depletion affects circRNA biogenesis. We identify circRNAs that are highly covered by RBP binding sites and experimentally validate individual circRNA-RBP interactions. We show that circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, is almost completely covered with GRWD1 binding sites in HepG2 cells, and that circCDYL depletion counteracts the effect of GRWD1 depletion. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g., TP53 . Finally, we show that elevated levels of circCDYL are associated with overall survival of bladder cancer patients. Conclusions Our study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Binding proteins / Binding Sites / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Biosynthesis / Bladder cancer / Cancer / Cancer Research / Carcinogenesis - genetics / Carrier Proteins - genetics / Carrier Proteins - metabolism / Cell cycle / circCDYL / Circular RNA / Circular RNAs / Exons / Gene expression / Gene Expression Regulation, Neoplastic / Genes / Genomes / Hep G2 Cells / Human Genetics / Humans / Immunoprecipitation / Introns / K562 Cells / Medicine/Public Health / Metabolomics / MicroRNAs / Neoplasms - genetics / Oncology, Experimental / p53 Protein / Pipelines / Protein binding / Protein interaction / Proteins / RBP sponges / Ribonucleic acid / RNA / RNA - metabolism / RNA sequencing / RNA, Circular / RNA-binding protein / RNA-binding proteins / RNA-Binding Proteins - genetics / RNA-Binding Proteins - metabolism / Systems Biology / Trans-Activators - genetics / Trans-Activators - metabolism / Transcriptome / Tumor proteins / Tumorigenesis / Urinary Bladder Neoplasms - genetics