Loss of U11/U12 spliceosome gene ZCRB1 leads to aberrant ciliogenesis and WNT signaling

The U12-dependent, or minor, spliceosome processes only 0.5% of human introns, and yet, it is known to profoundly influence gene expression and cellular signaling. The ZCRB1 protein is a core component of the U12 mono-snRNP, but its functional significance to minor splicing, gene regulation, and biological signaling cascades remains poorly understood. Using CRISPR-Cas9 and siRNA-targeted knockout and knockdown strategies, we show that human cell lines with a partial reduction in ZCRB1 expression exhibit significant abnormal splicing events and altered expression of minor intron–containing genes. RNA-sequencing and targeted analyses of minor intron–containing genes indicate direct mis-splicing and expression of genes involved in ciliogenesis, with a coinciding up-regulation of WNT signaling pathway components. CRISPR-Cas12a knockdown of zcrb1 in zebrafish embryos leads to developmental patterning and body axis abnormalities, disrupted ciliogenesis, and up-regulated WNT signaling, complementing our human cell studies. This work highlights a conserved and essential biological role of the minor spliceosome, via ZCRB1, in cellular and developmental processes across species, shedding light on the molecular crosstalk that integrates splicing regulation, ciliogenesis, and WNT signaling.