Figure 1

Pipeline for the identification of novel potentially functional lncRNAs in porcine pre-implantation embryos and iPSCs. The left figure is the pipeline for identification of lncRNAs from transcriptomes of porcine pre-implantation embryos and iPSCs. Transcripts were classified as known protein-coding genes and novel transcripts. The novel high-quality transcripts were subsequently filtered by sequence feature, coding potential, phylogenetic conservation as well as dissimilarity to known protein domains, and the remaining transcripts were defined as lncRNAs. The right figure is the pipeline for investigation of functional lncRNAs. To identify potentially functional lncRNAs during porcine embryo development and reprogramming to pluripotency, a co-expression network was constructed with protein coding genes and lncRNAs by WGCNA. The lncRNAs in modules that correlated with important embryonic stage and cell type were chosen to perform epigenetic modification, conservation analysis and experimental verification. Finally, the potentially functional lncRNAs in specific regulatory co-expression network were elucidated.