Transcriptomics and chromatin accessibility signatures define the cervical-thoracic boundary along the vertebrate axis

In vertebrate embryos, somite pairs form on either side of the neural tube along the main body axis. Somites generate the tissues of the musculoskeletal system, including cartilage of the vertebral column and ribs and skeletal muscles of the trunk and limbs. The detailed anatomy of somite-derived tissues varies along the axis, with unique features most easily visible in the vertebral column. Here we investigate the genetic control of this regionalization, which drives the subsequent cell differentiation programmes, focusing on the cervical to thoracic (C-T) boundary. Using ATAC-sequencing and RNA-sequencing, we establish molecular profiles of somites, in particular the chromatin landscapes and transcriptional programmes, that define this anatomical transition. Differential analysis highlights candidate cis-regulatory elements (CRE), and in silico footprints identify coverage of transcription factor (TF) binding sites associated with differentially expressed genes. Electroporation of citrine reporters in vivo validates the activity of CREs associated with key HOX genes, HOXC6 and HOXC8. HOXC6 footprints indicate its role in regulating a trio of differentially expressed SOX transcription factors, SOX5, SOX6 and SOX9, which are involved in chondrogenesis. In addition, the differential analysis identifies several lncRNAs, including one that is located within the HOXC cluster. CRISPR-on experiments suggest HOXC6 regulates its expression and therefore we name it lncRNA-HOXC6TA, however, its function in the thoracic region is currently unknown. Our study provides valuable datasets and illustrates how they can be mined to gain further insights into the regulatory mechanisms underlying the C-T transition along the vertebrate body axis.