CircPrime: a web-based platform for design of specific circular RNA primers

Fedor Sharko; Golam Rbbani; Prabhugouda Siriyappagouder; Joost A M Raeymaekers; Jorge Galindo-Villegas; Artem Nedoluzhko; Jorge M O Fernandes

doi:10.1186/s12859-023-05331-y

CircPrime: a web-based platform for design of specific circular RNA primers

BMC Bioinformatics. 2023 May 19;24(1):205. doi: 10.1186/s12859-023-05331-y.

Authors

Fedor Sharko^#^{1

2

3}, Golam Rbbani^#⁴, Prabhugouda Siriyappagouder⁴, Joost A M Raeymaekers⁴, Jorge Galindo-Villegas⁴, Artem Nedoluzhko^{5

6}, Jorge M O Fernandes⁷

Affiliations

¹ Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33/2, 119071, Moscow, Russia.
² Limited Liability Company ELGENE, Malaya Kalitnikovskaya 16, 109029, Moscow, Russia.
³ National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, 123182, Moscow, Russia.
⁴ Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway.
⁵ Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway. nedoluzhko@gmail.com.
⁶ Paleogenomics Laboratory, European University at Saint Petersburg, 6/1A Gagarinskaya st., 191187, Saint Petersburg, Russia. nedoluzhko@gmail.com.
⁷ Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, PB 1490, 8049, Bodø, Norway. jorge.m.fernandes@nord.no.

^# Contributed equally.

Abstract

Background: Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication.

Results: Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods.

Conclusions: User-friendly CircPrime web platform ( http://circprime.elgene.net/ ) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database).

Keywords: Circular RNAs; PCR; Prediction; Primer design; RNA-sequencing; RT-PCR; Validation; Web platform; circRNAs; qPCR.

MeSH terms

Computational Biology / methods
Internet
Polymerase Chain Reaction
RNA* / genetics
RNA, Circular* / genetics
Sequence Analysis, RNA / methods

Substances

RNA, Circular
RNA

Grants and funding

683210/ERC_/European Research Council/International