Hox genes are essential regulators of embryonic development. Their step-wise 
transcriptional activation follows their genomic topology and the various states 
of activation are subsequently memorized into domains of progressively 
overlapping gene products. We have analyzed the 3D chromatin organization of Hox 
clusters during their early activation in vivo, using high-resolution circular 
chromosome conformation capture. Initially, Hox clusters are organized as single 
chromatin compartments containing all genes and bivalent chromatin marks. 
Transcriptional activation is associated with a dynamic bi-modal 3D 
organization, whereby the genes switch autonomously from an inactive to an 
active compartment. These local 3D dynamics occur within a framework of 
constitutive interactions within the surrounding Topological Associated Domains, 
indicating that this regulation process is mostly cluster intrinsic. The 
step-wise progression in time is fixed at various body levels and thus can 
account for the chromatin architectures previously described at a later stage 
for different anterior to posterior levels.DOI: 
http://dx.doi.org/10.7554/eLife.02557.001.