Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing

Abstract

Exon skipping by alternative splicing and circular RNA formation are proposed to be interrelated events. Since multiple patterns of alternative splicing have been demonstrated in both the 5' and 3' regions of the dystrophin gene, the dystrophin transcript in skeletal muscle cells provides a model system in which this idea is tested. Nine circular RNAs that were expected to result from known exon skipping patterns in the 5' region of this gene were in fact identified, but three other circular RNAs expected to result from other known exon skipping reactions in this region could not be detected. The identification of two unexpected circular RNAs led to the discovery of two novel alternative splicing reactions. One circular RNA originating in the 3' region of the gene was identified but it lacked one small sized exon compared with the expected exon structure. Circular RNAs from the 5' region of the dystrophin gene could not be detected in Duchenne muscular dystrophy patients who have deletions of one or more exons in this segment of the gene, even though alternative splicing products were identified. These results showed that circular RNA formation is not necessarily linked to exon skipping and suggest that an undetermined factor regulates circular RNA formation.

Duchenne and Becker Muscular Dystrophy: From Gene Diagnosis to Molecular Therapy

“…Currently PCR amplification of 19 deletion prone exons (exons 1,3,4,6,8,12,13,17,19,43,44,45,47,48,49,50, 51, 52, and 60) is commonly used to screen deletion mutations and nearly half of all cases are shown to have deletion mutations. In the remaining cases, identification of the causative mutation remains a laborious target due to the difficulty in detecting a single point mutation in the 3,000-kb gene.…”

A novel cryptic exon identified in the 3′ region of intron 2 of the human dystrophin gene

“…Though we have analyzed dystrophin mRNAs in peripheral lymphocytes obtained from more than 100 dystrophinopathy cases, exon 2b incorporation has never before been identified (Matsuo et al 1991;Hagiwara et al 1994;Surono et al 1999;Adachi et al 2003;Yagi et al 2003). In order to see whether exon 2b activation is common to all exon 2 duplication mutations, we analyzed dystrophin mRNA from lymphocytes of Between exon 2b and the branch point, a polypyrimidine tract was identified.…”

Circular RNAs: Unexpected outputs of many protein-coding genes

“…The length of the skipped exon appears to be one key determinant, 41 but other factors such as RNA secondary structures and the speed of lariat debranching are also likely to be involved. Interestingly, a correlation between exon skipping and circular RNA biogenesis has been noted at other genes 49,50,52,55 and in a global transcriptome analysis of human endothelial cells. 90 Detailed analyses are now required to determine if re-splicing truly occurs at these loci.…”

“…This was the first hint that the dominant output of a gene could, in some cases, be a circular RNA rather than a linear mRNA. 48 A handful of additional circular RNAs were identified over the ensuing years [49][50][51][52][53][54][55][56] until deep sequencing efforts combined with new computational algorithms all of a sudden revealed thousands of previously missed circular RNAs from eukaryotic cells. 13,14,27,29,31,33,40,57,58 Over 25,000 putative circular RNAs, derived from »15% of actively transcribed genes, were identified in human fibroblasts alone.…”