Transcriptomic analysis of long non coding RNAs and their association with TET family genes in Sus scrofa embryo

Noncoding RNAs play diverse and crucial roles across various cell types, with many long noncoding RNAs (lncRNAs) implicated in germ cell development. Although lncRNAs remain largely uncharacterized, they play essential roles in key biological processes, including X-inactivation, pluripotency, genomic imprinting, and cell differentiation. In this study, we conducted a comprehensive bioinformatics analysis using publicly accessible single-cell RNA sequencing data (scRNA-seq) from Gene Expression Omnibus repository. The dataset includes four distinct cell types from different stages of porcine embryonic development: E11 derived epiblast cells, E14 derived somatic and primordial germ cells, E31 derived primordial germ cells. Our analysis identified a large number of lncRNAs and assessed their expression patterns, highlighting their critical roles in embryonic development. We also explored the relationship between lncRNAs and protein-coding genes, particularly focusing on the ten eleven translocation (TET) family genes, which are known for their role in DNA demethylation during early embryogenesis. We identified approximately 0.15 million lncRNA transcripts in porcine early embryos. Additionally, we investigated the differential expression profiles of both lncRNAs and protein-coding genes across different cell types, observing both similarities and differences in gene expression as the embryo differentiates. Finally, we used LncTar to predict potential interactions between co-expressed TET family genes and differentially expressed lncRNAs, providing further insight into their functional relationships in early embryonic development.