73 Comparative analysis of gene expression and transposable elements dynamics in bovine early embryos across different conditions

Dairy cows are important farm animals worldwide due to their nutritional and economic benefits. However, producing high-quality bovine embryos remains challenging. Previous studies have mainly focused on protein-coding genes, with limited understanding of other genomic elements among embryos derived from various conditions. Transposable elements, which can move to new positions in the genome, often influence gene expression and genome stability. This study aimed to compare the transcriptome features and expression dynamics of transposable elements in bovine early embryos generated by different methods. We combined publicly available RNA-seq data sets with our data, which yielded 163 samples from 14 studies. The analysis included embryos produced in vivo (IVV, n = 16), in vitro (IVT, n = 89), and by somatic cell nuclear transfer (SCNT, n = 58), covering oocytes and all preimplantation stages. Gene expression was normalized by transcripts per million to account for sequencing platform differences. Principal component analysis found embryos were clustered by stages rather than by study. Only highly expressed genes were considered for downstream analysis. Using DEseq2, we identified the differential expression genes (|log2FC| > 1 and padj <0.05) between stages and observed delayed genome activation in IVT and SCNT (at 8-cell stage) compared with IVV embryos (at 4-cell stage). Notably, SCNT embryos exhibited significant gene downregulation at the 4-cell stage compared with the 2-cell stage, a pattern not observed in IVV or IVT. Pseudotime analysis revealed gene expression patterns along the pseudotime path in early embryos. Both IVV and IVT showed a smooth transition of gene expression across early development, while SCNT displayed disrupted pseudotime patterns. Pluripotent genes and lineage markers exhibited similar expression patterns in IVV and IVT, whereas DPPA4, GATA4, GNL3, HAND1, POU5F1, SOX2, and TEAD4 were abnormally activated in SCNT from the 8-cell stage onward. We further defined the self-expressed transposable elements (located in intergenic regions or introns of non-expressed genes) loci in the bovine genome to avoid the co-expression effect of nearby genes using all samples, and stage-wise comparison obtained 4043, 14 545, and 13 111 significant transposable element loci in IVV, IVT and SCNT, respectively. Through enrichment analysis of self-expressed transposable element loci clusters, we found that ERVK loci were reactivated at the 16-cell stage in IVV but at the blastocyst stage of IVT and SCNT embryos. Compared with IVT, ERVL loci were activated before the 8-cell stage in SCNT. Additionally, 8-cell specifically expressed transposable element loci showed higher enrichment of H3K27ac instead of H3K4me3, suggesting that transposable elements may function as enhancers in bovine embryos. Overall, this study is the first to comprehensively compare the transcriptome features of both coding genes and transposable elements among three bovine embryo types. Our results revealed dysregulated genes and transposable elements associated with IVT and SCNT, which can be targeted for improving bovine embryo quality and reproductive technologies. This study highlighted the significance and potential applications of understanding the roles of transposable elements in embryogenesis.