Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns
Recursive splicing (RS) is a process in which an intron is removed from a nascent RNA molecule in two or more splicing events rather than one. We introduce a novel approach for detecting recursive splice sites (RSSs), the intronic loci at which RS events occur, based on alignment of total RNA-seq data to short, customized "target" sequences. We applied this approach to a data set from a recent…
Recursive splicing (RS) is a process where an intron is excised from a nascent RNA molecule through two or more splicing events instead of a single event. Researchers have now developed a new method to identify recursive splice sites (RSSs), the intronic locations where RS events take place, by aligning complete RNA-seq data to brief, custom-designed target sequences.
This technique was applied to a recent dataset of human brain gene expression, employing settings that resulted in a very low rate of false discoveries. The analysis uncovered 3,022 RSSs, present in 2,775 separate introns from 2,407 genes. Remarkably, 96% of these RSSs are located within protein-coding genes. Among the RSSs identified, 2,891 (96%) are situated in protein-coding genes.
The average length of these recursively spliced introns in this dataset is 10,114 base pairs, notably longer than the typical human intron, but shorter than the average lengths of RS introns reported in previous research. This study significantly expands the catalog of known RSSs in the human genome and presents a versatile computational pipeline for pinpointing RSSs from total RNA-seq data.
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