Developmental stage-specific TF-miRNA co-regulation during craniofacial development

Craniofacial development is regulated through dynamic and complex mechanisms that involve various signaling cascades and gene regulations. Disruption of such regulations may result in craniofacial birth defects. Here, we propose the developmental stage-specific network approach by integrating two critical regulators, transcription factor (TF) and microRNA (miRNA), to study their co-regulation during craniofacial development. Specifically, we used TFs, miRNAs, and non-TF genes to form regulatory pairs (also called composites), and then feed-forward loops (FFLs), using gene expression data covering mouse embryonic days E10.5 to E14.5. We identified TF-gene, TF-miRNA, and miRNA-gene regulation pairs at specific embryonic stages.