PT  - JOURNAL ARTICLE
AU  - Joseph, Brian
AU  - Scala, Chaz
AU  - Kondo, Shu
AU  - Lai, Eric C
TI  - Molecular and genetic dissection of recursive splicing
AID  - 10.26508/lsa.202101063
DP  - 2022 Jan 01
TA  - Life Science Alliance
PG  - e202101063
VI  - 5
IP  - 1
4099  - http://www.life-science-alliance.org/content/5/1/e202101063.short
4100  - http://www.life-science-alliance.org/content/5/1/e202101063.full
SO  - Life Sci. Alliance2022 Jan 01; 5
AB  - Intronic ratchet points (RPs) are abundant within long introns in the Drosophila genome and consist of juxtaposed splice acceptor and splice donor (SD) sites. Although they appear to encompass zero-nucleotide exons, we recently clarified that intronic recursive splicing (RS) requires a cryptic exon at the RP (an RS-exon), which is subsequently always skipped and thus absent from mRNA. In addition, Drosophila encodes a smaller set of expressed exons bearing features of RS. Here, we investigate mechanisms that regulate the choice between RP and RS-exon SDs. First, analysis of Drosophila RP SD mutants demonstrates that SD competition suppresses inclusion of cryptic exons in endogenous contexts. Second, characterization of RS-exon reporters implicates exonic sequences as influencing choice of RS-exon usage. Using RS-exon swap and mutagenesis assays, we show exonic sequences can determine RS-exon inclusion. Finally, we provide evidence that splicing can suppress utilization of RP SDs to enable RS-exon expression. Overall, multiple factors can influence splicing of Drosophila RS-exons, which usually result in their complete suppression as zero-nucleotide RPs, but occasionally yield translated RS-exons.