Cis-regulatory architecture and functions of a gene desert controlling pleiotropic expression and cardiac pacemaker development

Abstract Gene deserts are extensive genomic regions spanning more than 500 kilobases and enriched near developmental genes. Despite their proposed critical roles in development, the enhancer architecture, biological functions of most gene mammalian genomes remain unknown. The Shox2 transcription factor is a key regulator cardiac pacemaker differentiation at level flanked by centromeric desert harboring multitude predicted cis-regulatory modules (CRMs). Using CRISPR-Cas9 we demonstrate requirement this for pleiotropic expression embryonic survival through full control sinoatrial node (SAN). To decode underlying chromatin architecture CRM logic, performed region-specific conformation capture, epigenomic analysis transgenic vivo reporter assays. While regulatory landscape was found partitioned into largely tissue-invariant loops, identified surprising cardiac-specific contact domain within desert. Subsequent revealed clustering non-cardiac enhancers with activities limb, craniofacial or neuronal populations domain, pointing to potential tissue-specific 3D-mechanism attenuation. In addition, SAN-chromatin assessment H3K27ac profiling from human fetal compartments enabled identification unique located outside essential robust levels during development. summary, our results serve as blueprint investigate function context defects identify hub indispensable patterning, survival. Funding Acknowledgement Type funding sources: Public grant(s) – National budget only. Main source(s): Swiss Science Foundation (SNSF),National Institutes Health (NIH)