| Summary: | Abstract Background Preimplantation embryo development is a highly ordered sequence of processes and it requires a precise temporal and spatial control of gene expression. Alternative splicing (AS) is a crucial process that changes the genomic instructions into functional proteins, playing a critical role in the regulation of gene expression. Therefore, studies of AS can significantly improve our understanding of transcription and splicing events in preimplantation embryo development. Results To study signatures of AS in embryo development, we firstly identified the critical stage for gene transcription during the preimplantation embryo development. By analyzing single cells RNA-seq (scRNA-seq) data, we found that the two-cell stage is a critical stage for gene transcription in preimplantation embryo development. Further study showed that AS was widespread in preimplantation embryo development, especially at the two-cell stage. In combination with high-throughput chromosome conformation (Hi-C) data, we demonstrated that AS genes were highly enriched in TAD boundaries, while they had no relationship with the A/B compartment and TAD. Conclusion Our results provide new insight into the relationship among AS, gene transcription and chromatin structure in preimplantation embryo development.
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