U2AF1 modulates alternative exon selection and guards zygotic splicing activation in mouse preimplantation embryogenesis

Gene products vary in mRNA transcript and protein isoforms. During the maternal-to-zygotic transition, massive mRNAs transcribed from either the maternal or the zygotic genome were produced, together with a combination of pre-mRNA processing progress and mRNA decay mechanism. Transcripts harbored by embryos differ from the ones contained by oocytes in an alternative exon inclusion/exclusion manner. The lengths and the compositions of polypyrimidine tracts (PPTs) are crucial in splice site definition. Exons downwards longer PPTs were preferentially included, and less pyrimidine-incorporated PPTs tended to be excluded from 2-cell embryos. The U2AF dimers, U2AF1 and U2AF2, are responsible for PPT recognition and 3' splice site determination. In oocytes, U2AF1 formed low density areas (cavities) and was positioned exclusively outside the nuclear speckles. In pre-implantation embryos, U2AF1 keeps in low abundance and disperses in the 2-cell nucleoplasm. Excessive U2AF1 expression leads to developmental arrest at the 2- to 4-cell stage, defective zygotic genome activation (ZGA), and aberrant zygotic splicing events. U2AF1 promotes exon exclusion in a PPT-dependent manner, modulates U2AF dimer's recognition of more-pyrimidine-containing PPTs, defines 3' splice sites, and selectively excludes the downstream exons. The composition of multiple gene variants, including Bclaf1, Ezh2, and several ZGA genes, is balanced by U2AF1 hypoexpression, which further assist in protein isoform maintenance, guarding proper protein positioning, and governing embryonic development.