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. 2016;13(1):34-42.
doi: 10.1080/15476286.2015.1128065.

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

Dawood B Dudekula  1 , Amaresh C Panda  1 , Ioannis Grammatikakis  1 , Supriyo De  1 , Kotb Abdelmohsen  1 , Myriam Gorospe  1
Affiliations

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

Dawood B Dudekula et al. RNA Biol. 2016.

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.

Keywords: CLIP-Seq; CircRNA-miRNA; RNA-binding proteins; circRNA IRES; circRNA siRNA; divergent primer design; sponge circRNAs; transcriptome.

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Figures

Figure 1.
Figure 1.
Workflow of the web tool Circular RNA Interactome or ‘CircInteractome’.
Figure 2.
Figure 2.
View of CircInteractome input and output pages. A. Example the ‘Circular RNA’ page exhibiting the input parameters needed for a CircInteractome run. B. Screenshot of ‘Circular RNA search’ for has_circ_0000020, showing RBPs binding in different regions of this circRNA. C. Schematic representation of the potential binding sites of different RBPs to mature and pre-hsa_circ_0000020.
Figure 3.
Figure 3.
Predicted IRES possibly mediating circRNA translation. A. Schematic representation of hsa_circ_0041407, which contains the MNT 36-160 IRES that may potentially drive translation. B. The sequence of hsa_circ_0041407 highlighted can potentially be translated via the IRES underlined.
Figure 4.
Figure 4.
Potential miRNA-circRNA interactions. For a given circRNA ID entered, the miRNAs potentially targeting that circRNA are identified.
Figure 5.
Figure 5.
CircRNA primer design. A. Schematic representation of the design of divergent primers for circRNA detection by RT-qPCR analysis. B. Input webpage for divergent primer design. C. Screenshot of the output page showing the junction sequence of circRNA and links of primer design tools (Primer3 and NCBI).
Figure 6.
Figure 6.
CircRNA siRNA design. Screenshot of the CircInteractome siRNA design page, including an example of output siRNAs targeting the junction sequence of a given circRNA.
See this image and copyright information in PMC

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