Bioinformatic Prediction of Non-Coding Genes related to the Mouse FGF8, NOG, and BMP4 Ectodermal Differentiation Pathway Genes and Mapping of Related Network

Long non-coding RNAs (lncRNAs) and miRNAs belong to a class of non-coding RNAs (ncRNAs) that play important roles and functions in the regulation of the expression of genes in main biological processes, such as cell proliferation, apoptosis, and differentiation. LncRNAs can potentially affect miRNAs in the forms of cis/trans to modulate their regulatory role. In this study, mRNA, miRNA, and lncRNA gene networks were predicted by web-based programs for three ectodermal pathway markers (BMP4, NOG, FGF8) in the mouse embryonic stem cells.

In this theoretical bioinformatics study, the miRNAs of the target genes (BMP4, NOG, and FGF8) were extracted and examined by MirWalk and TARGETSCAN databases to finally obtain the common miRNAs of these three genes. Following that, the target lncRNAs for common miRNAs were then extracted from the DIANA-Tool database.

MiRs mmu-miR-92a-2-5p, mmu-miR-129b-5p, mmu-miR-130b-5p, mmu-miR-692, mmu-miR-7009-3P, mmu-miR-7116-3p, and mmu-miR-7689-3p may affect the function of lncRNAs, including Kcnq1ot1, Gm26812, Gm4117, Gm11837, 4930423MO2Rik, Malat1, Gm12594, Gm3414, 5830444B04Rik, Gm2464, and NEAT1.

Due to the mutual relationships among lncRNA, miRNA, and mRNA, our results provided a novel perspective on lncRNAs for future research and experimental studies on ectodermal differentiation pathways and molecular mechanisms.