A dual enhancer-silencer element ensures transient Cdx2 expression during posterior body formation

During development, cells express precise gene expression programmes to assemble the trunk of the body plan. Appropriate control over the duration of the transcription factor Cdx2 is critical to achieve this outcome, yet, how cells control the onset, maintenance or termination of Cdx2, has remained unclear. Here, we delineate the cis-regulatory logic orchestrating dynamic Cdx2 expression in mouse caudal epiblast progenitors and their derivatives - spinal cord and presomitic mesoderm. Combining CRISPR-mediated deletion of regulatory elements with in vitro models and in vivo validation, we demonstrate that distinct enhancers, and a silencer, embedded at the Cdx2 locus, act sequentially to drive transient Cdx2 expression. We pinpoint a minimal silencer element that relies on a nuclear receptor motif to extinguish Cdx2. Changing this single motif converts the repressive element to an enhancer with opposite regulatory behaviour. Our findings elucidate design principles of developmental enhancers and silencers and establish a dual enhancer-silencer cis-regulatory logic ensuring precise spatiotemporal control over gene expression for vertebrate body patterning.