Circular RNA repertoires are associated with evolutionarily young transposable elements

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Abstract

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.

Data availability

Sequencing data have been deposited in GEO under accession code GSE162152

The following data sets were generated

(2020) Identification and evolutionary comparison of circular RNAs in five mammalian species and three organs.
NCBI Gene Expression Omnibus, GSE162152.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GS162152}{GSE162152

The following previously published data sets were used

(2016) Suppl. Table 4. Mouse circRNA summary.
Journal of Molecular and Cellular Cardiology, doi.org/10.1016/j.yjmcc.2016.07.007.

https://ars.els-cdn.com/content/image/1-s2.0-S0022282816302292-mmc3.txt
(2016) Suppl. Table 5. Human circRNA summary.
Journal of Molecular and Cellular Cardiology, doi.org/10.1016/j.yjmcc.2016.07.007.

https://ars.els-cdn.com/content/image/1-s2.0-S0022282816302292-mmc4.txt
1. Koren A
2. Polak P
3. Nemesh J
4. Michaelson JJ
5. Sebat J
6. Sunyaev SR
7. McCarroll SA
(2012) DNA replication time of the human genome G1 phase.
Sequence Read Archive, SRA052697.

https://www.ncbi.nlm.nih.gov/sra/SRX147697[accn]
(2012) The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
NCBI Gene Expression Omnibus, GSE37451.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37451
1. Steinberg J
2. Honti F
3. Meader S
4. Webber C
(2015) Suppl. Table S2. Haploinsufficiency predictions without study bias.
Nucleic Acids Research, https://doi.org/10.1093/nar/gkv474.

https://academic.oup.com/nar/article/43/15/e101/2414292#supplementary-data
1. Brawand D
2. Soumillon M
3. Necsulea A
4. Julien P
5. Csardi G
6. Harrigan P
7. Weier M
8. Liechti A
9. Aximu-Petri A
10. Kircher M
11. Albert FW
12. Zeller U
13. Khaitovich P
14. Grützner F
15. Bergmann S
16. Nielsen R
17. Pääbo S
18. Kaessmann H
(2011) The evolution of gene expression levels in mammalian organs
NCBI Gene Expression Omnibus, GSE30352.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30352

Article and author information

Author details

Franziska Gruhl

Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Peggy Janich

Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Henrik Kaessmann

Center for Molecular Biology of Heidelberg University, Heidelberg, Germany

For correspondence
h.kaessmann@zmbh.uni-heidelberg.de

Competing interests
The authors declare that no competing interests exist.
David Gatfield

Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

For correspondence
david.gatfield@unil.ch

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5114-2824

Funding

Swiss Institute of Bioinformatics (SIB PhD Fellowship)

Franziska Gruhl

Human Frontiers Science Program (LT000158/2013-L)

Peggy Janich

European Research Council (242597,SexGenTransEvolution)

Henrik Kaessmann

European Research Council (615253,OntoTransEvol)

Henrik Kaessmann

Swiss National Science Foundation (NCCR RNA & Disease (141735,182880))

David Gatfield

Swiss National Science Foundation (individual grant 179190)

David Gatfield

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: Mouse samples were collected by the Kaessmann lab at the Center for Integrative Genomics in Lausanne. Rat samples were kindly provided by Carmen Sandi, EPFL, Lausanne. Opossum samples were kindly provided by Peter Giere, Museum für Naturkunde, Berlin. All animal procedures were performed in compliance with national and international ethical guidelines and regulations for the care and use of laboratory animals and were approved by the local animal welfare authorities (Vaud Cantonal Veterinary office, Berlin State Office of Health and Social Affairs). The rhesus macaque samples were provided by the Suzhou Experimental Animal Center (China); the Biomedical Research Ethics Committee of Shanghai Institutes for Biological Sciences reviewed the use and care of the animals in the research project (approval ID: ER-SIBS-260802P). All rhesus macaques used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the organ sampled. The use of all samples for the work described in this study was approved by an ERC Ethics Screening panel (associated with H.K.'s ERC Consolidator Grant 615253, OntoTransEvol).

Human subjects: The human post-mortem samples were provided by the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland (USA). They originated from individuals with diverse causes of death that, given the information available, were not associated with the organ sampled. Written consent for the use of human tissues for research was obtained from all donors or their next of kin by this tissue bank. The use of these samples was approved by an ERC Ethics Screening panel (associated with H.K.'s ERC Consolidator Grant 615253, OntoTransEvol), and, in addition, by the local ethics committee in Lausanne (authorization 504/12).

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.