Open chromatin regions of Xenopus tropicalis larval tissues

The goal of this study was to identify ubiquitous as well as osteoblast-specific open chromatin regions in the amphibian organism Xenopus tropicalis. ATAC-Seq was performed on osteoblasts extracted from the skull of Xenopus tropicalis stage NF59 tadpoles, and compared to the ATAC-Seq profiles of control tissues such as larval heart, liver and lung. Gene expression levels were also compared between bone and liver by RNA-seq. We therefore identify chromatin regions that are devoid of nucleosomes in all tissues (ubiquitously open) or only in osteoblasts, and focus our analysis on promoter elements and also on more distal transcriptional enhancers. We performed a range of analysis such as GeneOntology, TFBS enrichment, nucleotide frequency, and sequence conservation with other genomes. Our study is relevant to better understand the architectural differences between ubiquitous versus spatially and temporally restricted transcriptional regulation. It also provides a better understanding of the regulatory logic underlying osteoblastic differentiation in distinct vertebrate species. This data will also be relevant for biomedicine, as we identify osteoblast-specific enhancers that are well conserved with humans and that are located at loci involved in hereditary bone diseases. Finally, comparing the identified enhancers with the genome of distant species such as shark provides hint regarding the early evolution of the vertebrate skeleton.