ciRS-7 exonic sequence is embedded in a long non-coding RNA locus

Abstract

ciRS-7 is an intensely studied, highly expressed and conserved circRNA. Essentially nothing is known about its biogenesis, including the location of its promoter. A prevailing assumption has been that ciRS-7 is an exceptional circRNA because it is transcribed from a locus lacking any mature linear RNA transcripts of the same sense. To study the biogenesis of ciRS-7, we developed an algorithm to define its promoter and predicted that the human ciRS-7 promoter coincides with that of the long non-coding RNA, LINC00632. We validated this prediction using multiple orthogonal experimental assays. We also used computational approaches and experimental validation to establish that ciRS-7 exonic sequence is embedded in linear transcripts that are flanked by cryptic exons in both human and mouse. Together, this experimental and computational evidence generates a new model for regulation of this locus: (a) ciRS-7 is like other circRNAs, as it is spliced into linear transcripts; (b) expression of ciRS-7 is primarily determined by the chromatin state of LINC00632 promoters; (c) transcription and splicing factors sufficient for ciRS-7 biogenesis are expressed in cells that lack detectable ciRS-7 expression. These findings have significant implications for the study of the regulation and function of ciRS-7, and the analytic framework we developed to jointly analyze RNA-seq and ChIP-seq data reveal the potential for genome-wide discovery of important biological regulation missed in current reference annotations.

Biosynthesis of Circular RNA ciRS-7/CDR1as Is Mediated by Mammalian-Wide Interspersed Repeats (MIRs)

“…Recently, the genomic structure around the ciRS-7 precursor has been independently reported (Barrett et al, 2017). In agreement with our analysis, this study showed that the promoter region of ciRS-7 overlaps an upstream long non-coding transcript (LINC00632 locus), suggesting that the ciRS-7 precursor is a long non-coding RNA (Barrett et al, 2017).…”

“…Recently, the genomic structure around the ciRS-7 precursor has been independently reported (Barrett et al, 2017). In agreement with our analysis, this study showed that the promoter region of ciRS-7 overlaps an upstream long non-coding transcript (LINC00632 locus), suggesting that the ciRS-7 precursor is a long non-coding RNA (Barrett et al, 2017). The BAC clones obtained (185 and 200 kb) cover from the promoter of this non-coding transcript (LINC00632) to far downstream of the ciRS-7 exon and they were found to produce mature ciRS-7.…”

Nanopore sequencing of full-length circRNAs in human and mouse brains reveals circRNA-specific exon usage and intron retention

“…Our data also confirmed the existence of two human ciRS-7 isoforms measuring 1,485 and 1,301 bp ( Supplementary Fig. 2), caused by optional intron retention (Barrett, Parker, Horn, Mata, & Salzman, 2017;T B Hansen et al, 2011).…”

Past, present, and future of circ RNA s

“…Two studies investigated the role of CDR1as in vivo (Piwecka et al, 2017;Kleaveland et al, 2018). Although this circRNA is embedded in a long non-coding RNA locus (Barrett et al, 2017), the circularization of CDR1as is so efficient that previous studies could not detect any linear counterpart (Hansen et al, 2011(Hansen et al, , 2013Memczak et al, 2013). Also, Piwecka et al (2017) could not detect any RNAs generated from the opposite strand and concluded that CDR1as is the only gene directly affected by the deletion (Piwecka et al, 2017).…”