Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development

This study explores alternative splicing's role in embryo development. Using single-cell direct isoform sequencing, we detected an abundance of 3-prime partial transcripts lacking stop codons in oocytes and zygotes, potentially influencing the maternal-to-zygote transition. Long-read sequencing identified dynamic changes in 3894 transposable element loci throughout preimplantation, impacting nearby gene expression and shedding light on early embryonic transcriptional regulation. The experiment involved 6-8-week-old female C57BL/6J and male DBA/2NCrl mice. Post-mating, embryos were collected at specific intervals post-hCG injection: 20 hours (MII oocytes, non-mated), 22-24 hours (fertilized eggs), 30-32 hours (early 2-cell stage), 46-48 hours (late 2-cell stage), 54-56 hours (4-cell), 68-70 hours (8-cell), 78-80 hours (16-32-cell), 88-90 hours (early blastocyst). Subsequently, the same amplification process as SCAN-seq was used, except a 10x gel bead was used in each single-cell embryo reaction. Following this, the PacBio sequencing library was constructed following the HIT-scISOseq process, sequenced in HiFi mode. We sequenced a total of 4 PacBio Sequel II SMRT 8M chips, each representing a different experimental replicate.