circRNA_paperScripts

last update: 10 January 2022

This repository contains the scripts used to generate the main figures and tables of the paper "Circular RNA repertoires are associated with evolutionarily young transposable elements".

The paper was accepted in eLife on 19 September 2021: https://elifesciences.org/articles/67991

Each figure/table has its own folder with the perspective scripts and a readme-file describing how to use them. The corresponidng data files can be downloaded via this link (zipped file, same folder structure as described in the readme-files). For all old files corresponding to the initial submission, please use this link.

Circular RNA repertoires are associated with evolutionarily young transposable elements

Franziska Gruhl^1,2, Peggy Janich^2,3, Henrik Kaessmann^4*, David Gatfield^2*

1. SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
2. Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
3. Krebsliga Schweiz, CH-3001 Bern, Switzerland
4. Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany

* corresponding authors: h.kaessmann@zmbh.uni-heidelberg.de; david.gatfield@unil.ch

Circular RNAs (circRNAs) are found across eukaryotes and can function in post-transcriptional gene regulation. Their biogenesis through a circle-forming backsplicing reaction is facilitated by reverse-complementary repetitive sequences promoting pre-mRNA folding. Orthologous genes from which circRNAs arise, overall contain more strongly conserved splice sites and exons than other genes, yet it remains unclear to what extent this conservation reflects purifying selection acting on the circRNAs themselves. Our analyses of circRNA repertoires from five species representing three mammalian lineages (marsupials, eutherians: rodents, primates) reveal that surprisingly few circRNAs arise from orthologous exonic loci across all species. Even the circRNAs from orthologous loci are associated with young, recently active and species-specific transposable elements, rather than with common, ancient transposon integration events. These observations suggest that many circRNAs emerged convergently during evolution – as a byproduct of splicing in orthologs prone to transposon insertion. Overall, our findings argue against widespread functional circRNA conservation.

Preprint: https://www.biorxiv.org/content/10.1101/2021.03.01.433421v1
doi: https://doi.org/10.1101/2021.03.01.433421
Paper status: accepted (eLife) https://elifesciences.org/articles/67991