Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns
- 1Johns Hopkins University
Abstract
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 study of gene expression in the human brain, using parameters corresponding to a very low false discovery rate, and found 3,022 RSSs that appear in 2,775 distinct introns from 2,407 genes. 2,891 (96%) of these RSSs are in protein-coding genes. The median length of recursively spliced introns from this set is 10,114 base pairs, which is substantially longer than the median human intron, but much shorter than average RS intron lengths reported in prior studies. Our work dramatically increases the number of known RSSs in the human genome and provides a generalizable bioinformatics pipeline for annotating RSSs from total RNA-seq data.
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BibTeX
@misc{bass2026largescale,
title = {{Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns}},
author = {D. J. Bass and S. L. Salzberg},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.10.750672},
url = {https://www.biorxiv.org/content/10.64898/2026.09.10.750672v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns
AU - D. J. Bass
AU - S. L. Salzberg
PY - 2026
DA - 2026/09/10
PB - bioRxiv
DO - 10.64898/2026.09.10.750672
UR - https://www.biorxiv.org/content/10.64898/2026.09.10.750672v1
AB - 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 study of gene expression in the human brain, using parameters corresponding to a very low false discovery rate, and found 3,022 RSSs that appear in 2,775 distinct introns from 2,407 genes. 2,891 (96%) of these RSSs are in protein-coding genes. The median length of recursively spliced introns from this set is 10,114 base pairs, which is substantially longer than the median human intron, but much shorter than average RS intron lengths reported in prior studies. Our work dramatically increases the number of known RSSs in the human genome and provides a generalizable bioinformatics pipeline for annotating RSSs from total RNA-seq data.
ER -