CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs

Abstract

Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.

Extracellular RNA profiles with human age

“…These circRNAs were the most abundant and/or were also present in ≥2 individuals in our sequencing. Divergent primers for each circRNA were designed using CircInteractome (Dudekula et al., 2016). Each primer set was validated initially by examining RNA isolated from PBMCs, HUVECs, and serum.…”

“…Divergent primers for circRNAs were designed using the CircInteractome web tool (https://circinteractome.nia.nih.gov/Divergent_Primers/divergent_primers.html) (Dudekula et al., 2016). cDNA used to validate linear transcripts (see above) was used for RT‐qPCR reactions.…”

Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1

“…21,22 Here, we identified HuR-associated circRNAs using RIP-chip and RIP-RT-qPCR analyses, bioinformatic prediction, and in vitro binding assays (Figs. 1-3, Table S2).…”

The emerging role and clinical implication of human exonic circular RNA

“…33 CircInteractome is a web-tool for exploring circular RNAs and their interacting proteins and miRNAs. 34 The design of divergent primers and specific siRNA for circRNA was also provided by circInteractome. CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines.…”