GSE110051
GRNs driving cartilage and bone formation interact via averaging and synergism during cartilage maturation
Transcriptional control of any biological process occurs through the action of one to many gene regulatory networks (GRNs), but studies analyzing GRN interaction are lacking.  To address this, we tested for the first time in vivo the hypothesis that two independent GRNs, which are active during formation of two discrete skeletal cell types (immature chondrocytes and osteoblasts), interact during differentiation of a third skeletal cell type (mature chondrocytes).  These three cell types were isolated from the mouse embryo specifically using laser capture microdissection, and then RNA was extracted.  Multiple analyses of corresponding RNA-seq data supported the hypothesis.  Gene co-expression network analyses of differentially expressed genes suggested that one GRN containing the chondrogenic transcription factor Sox9 characterizes immature chondrocytes, one GRN containing the osteogenic transcription factor Runx2 characterizes osteoblasts, and both GRNs operate in mature chondrocytes.  Indeed, mature chondrocytes differentially expressed fewer genes than the other cell types, consistent with the idea that overlapping actions of the immature chondrocyte and osteoblast GRNs regulate mature chondrocytes.  Clustering analyses provided molecular insights into potential GRN interactions.  Several genes in mature chondrocytes had expression levels that represented an averaging between levels in the immature chondrocyte and osteoblast.  Interestingly, expression levels of one gene cluster, containing the hallmark mature chondrocyte genes Collagen type 10a1 and Indian hedgehog, suggested a synergistic interaction between immature chondrocyte and osteoblast GRNs.  In addition to identifying novel genes expressed in mature chondrocytes, these results outline a novel in vivo experimental system through which to understand GRN organization and interaction. Overall design: Skeletal tissue mRNA profiles of C57BL/6J mice were generated by RNA sequencing, in triplicate, using Illumina HiSeq 2500.