Deconstructing Somites across the Cervical-Thoracic Boundary using Advanced Genomics Approaches

Embryonic somites are paired segments that form on either side of the neural tube along the head-to-tail axis in vertebrates. They are of fundamental importance and generate cells of the musculoskeletal system, including myocytes, chondrocytes and tenocytes, as well as endothelial and dermal cells. In this thesis, I investigate the molecular profiles of somites with different axial identities by sequencing somites isolated from the chick embryo. I determined the accessible chromatin and transcriptome signatures of somites using ATACseq and RNAseq. In particular, I focus on axial positions that produce prospective cervical and thoracic somites, with anatomically discrete features such as ribs. In depth analysis of these data aims to uncover potential cis-regulatory elements and associated gene expression changes that correlate with positional identity along the cervical-thoracic boundary, as well as musculoskeletal cell fate acquisition. Classic experimental embryology combined with genomics analyses is used to validate and characterise putative enhancer elements. This provides insights into the intrinsic mechanisms that underlie morphological evolution of the vertebrate body plan