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Analysis of Circular RNAs Using the Web Tool CircInteractome

  • Amaresh C. Panda
  • Dawood B. Dudekula
  • Kotb AbdelmohsenEmail author
  • Myriam Gorospe
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1724)

Abstract

Circular RNAs (circRNAs) are generated through nonlinear back splicing, during which the 5′ and 3′ ends are covalently joined. Consequently, the lack of free ends makes them very stable compared to their counterpart linear RNAs. By selectively interacting with microRNAs and RNA-binding proteins (RBPs), circRNAs have been shown to influence gene expression programs. We designed a web tool, CircInteractome, in order to (1) explore potential interactions of circRNAs with RBPs, (2) design specific divergent primers to detect circRNAs, (3) study tissue- and cell-specific circRNAs, (4) identify gene-specific circRNAs, (5) explore potential miRNAs interacting with circRNAs, and (6) design specific siRNAs to silence circRNAs. Here, we review the CircInteractome tool and explain recent updates to the site. The database is freely accessible at http://circinteractome.nia.nih.gov.

Key words

RNA-binding proteins Gene-specific circRNAs Divergent primer design Cell- and tissue-specific circRNAs Transcriptome CLIP-seq 

Notes

Acknowledgments

This work was supported in full by the National Institute on Aging Intramural Research Program, National Institutes of Health.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Amaresh C. Panda
    • 1
  • Dawood B. Dudekula
    • 1
  • Kotb Abdelmohsen
    • 1
    Email author
  • Myriam Gorospe
    • 1
  1. 1.Laboratory of Genetics and GenomicsNational Institute on Aging-Intramural Research Program, National Institutes of HealthBaltimoreUSA

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