A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation

• Published in: Nature plants Vol. 3; no. 5; p. 17053
• Main Authors: Conn, Vanessa M., Hugouvieux, Véronique, Nayak, Aditya, Conos, Stephanie A., Capovilla, Giovanna, Cildir, Gökhan, Jourdain, Agnès, Tergaonkar, Vinay, Schmid, Markus, Zubieta, Chloe, Conn, Simon J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.04.2017; Nature Publishing Group
• Subjects: 38/39; 38/77; 38/90; 42; 45/22; 45/29; 631/449/2491/2046; 631/80; 64; 82; Alternative splicing; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Biochemistry, Molecular Biology; Biology; Biomarkers; Biomedical and Life Sciences; Biosynthesis; Deoxyribonucleic acid; DNA; DNA, Circular - genetics; DNA, Circular - metabolism; DNA, Plant - genetics; DNA, Plant - metabolism; Flowers & plants; Genes; Genetic engineering; Genotype & phenotype; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; letter; Life Sciences; Phenotypes; Plant Sciences; Proteins; Ribonucleic acid; RNA; RNA Splicing - genetics; RNA, Messenger - genetics; RNA, Messenger - metabolism; Splicing; Splicing factors; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Plant; SEP3; Gene regulation; Circular RNA; Flowering; SEPALLATA3; Transcription factor
• ISSN: 2055-0278; 2055-026X; 2055-0278
• DOI: 10.1038/nplants.2017.53

Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life 1 , yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis , including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 ( SEP3 ) gene increase abundance of the cognate exon-skipped AS variant ( SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS 2 – 4 . This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation. While circular RNAs (circRNAs) have been identified in all eukaryotic kingdoms of life, their functions have remained elusive. Now, a study shows that circRNAs can promote alternative splicing of their cognate mRNA, thus driving homeotic phenotypes.