Arabidopsis thaliana cbp80, c2h2, and flk Knockout Mutants Accumulate Increased Amounts of Circular RNAs

Abstract

Circular RNAs (circRNAs) are the products of the non-canonical splicing of pre-mRNAs. In contrast to humans and animals, our knowledge of the biogenesis and function of circRNAs in plants is very scarce. To identify proteins involved in plant circRNA generation, we characterized the transcriptomes of 18 Arabidopsis thaliana knockout mutants for genes related to splicing. The vast majority (>90%) of circRNAs were formed in more than one variant; only a small fraction of circRNAs was mutant-specific. Five times more circRNA types were identified in cbp80 and three times more in c2h2 mutants than in the wild-type. We also discovered that in cbp80, c2h2 and flk mutants, the accumulation of circRNAs was significantly increased. The increased accumulation of circular transcripts was not accompanied by corresponding changes in the accumulation of linear transcripts. Our results indicate that one of the roles of CBP80, C2H2 and FLK in splicing is to ensure the proper order of the exons. In the absence of one of the above-mentioned factors, the process might be altered, leading to the production of circular transcripts. This suggests that the transition toward circRNA production can be triggered by factors sequestering these proteins. Consequently, the expression of linear transcripts might be regulated through circRNA production.

At-C-RNA database, a one-stop source for information on circRNAs inArabidopsis thalianain a unified format

“…Moreover, we compared the sources used by other plant circRNA databases and we chose those that met our criteria. In total, we utilized third-party data from eight studies (100 SRA files) and two datasets (110 SRA files) from our previous studies ( 11 , 12 ). All analyzed datasets are presented in Table 1 .…”

Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

“…In plants, the biogenesis of circRNAs has not been thoroughly investigated ( Figure 3 ). In Arabidopsis , the accumulation of circRNAs is significantly increased in the splicing-related mutants cbp80 , c2h2 , and flk ( Philips et al., 2020b ), suggesting that the biogenesis of plant circRNAs is also affected by splicing factors ( Figure 3 A).

Figure 3 Proposed model of circRNA biogenesis in plants.

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Viral Circular RNAs and Their Possible Roles in Virus-Host Interaction

“…Splicing factor proline/glutaminerich and non-POU domain-containing octamer-binding protein mediated the Alu-independent circRNA production (64). Capbinding protein 80, C2HC zinc fingers superfamily protein, and flowering locus kh domain were related to the processes of splicing and the proper order of the exons, which expression levels were negative with the circRNA production (14). Serine and Arginine Rich Splicing Factor 10 (SRSF10) promoted circ-ATXN1 production by binding to the 5′-end and 3′-end of its pre-mRNA (95).…”

“…However, increasing evidence showed that various circRNAs commonly existed in natural organisms with conservative sequences among different species. Until now, the identification of circRNAs and their possible roles have been explored in more than 20 species, including Archaea (8), plants (11,13,14), viruses (15)(16)(17)(18)(19), insects (20,21), and mammals (12,22,23). A small subset of circRNAs with different activities was confirmed to play vital roles in regulating individual growth and development, environmental stress, innate immunity, and disease occurrence (13,(24)(25)(26)(27)(28).…”