Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes.

Amelia Cervera,Marcos De La Peña

doi:10.1093/nar/gkaa187

Amelia Cervera, Marcos De La Peña

Open Access

https://doi.org/10.1093/nar/gkaa187

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Abstract

Ribozymes are catalytic RNAs present in modern genomes but regarded as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-LTR retrotransposons of the retrozyme class. These retroelements are expressed as abundant linear and circular RNAs of ∼170-400 nt in different animal tissues. Bioinformatic and in vitro analyses indicate an efficient self-cleavage of the HHRs harboured in most invertebrate retrozymes, whereas HHRs in retrozymes of vertebrates, such as the axolotl and other amphibians, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which opens the door for the development of new tools in the emerging field of study of circRNAs.

Highlights

The discovery of catalytic RNAs or ribozymes in the 80’s [1,2] strongly supported the hypothesis of a prebiotic RNA world, where the first living organisms were based on RNA as both the genetic material and as catalyst [3,4,5]
Type I hammerhead ribozyme (HHR) in cnidarian genomes occur within small DNA tandem repeats, which are expressed as linear and circular RNAs Previous studies have reported that many type I HHRs in animal genomes can be found within short tandem repeats of a few hundred base pairs (150 to 450 bp), widely but patchily distributed among most metazoan phyla [25]
In contrast to plant LTR retrozymes, which harbour type III HHRs in a dimeric arrangement (Figure 1B), metazoan repeats with type I HHRs occur in multiple copies and lack the characteristic long terminal repeats (LTRs), primer binding site (PBS), and polypurine tract (PPT) motifs

Summary

Introduction

The discovery of catalytic RNAs or ribozymes in the 80’s [1,2] strongly supported the hypothesis of a prebiotic RNA world, where the first living organisms were based on RNA as both the genetic material and as catalyst [3,4,5]. Type III HHRs detected in several flowering plants have been found to be involved in the processing of a novel family of non-autonomous LTR retrotransposons, the so-called retrozymes for retroelement with hammerhead ribozymes (Figure 1B), which spread through circRNA transposition intermediates of 600-800 nt [26]. Our results are consistent with a conserved role for most type I HHRs in the life cycle of a novel family of constitutively expressed non-autonomous non-LTR retrolements, which spread thoughout animal genomes by means of small circRNAs transposition intermediates

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Conclusion