E-GEOD-54952 - RNA-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

Released on 28 April 2014, last updated on 31 May 2014
Mus musculus
Samples (2)
Protocols (4)
Hox genes are essential regulators of embryonic development. They are activated in a temporal sequence following their topological order within their genomic clusters. Subsequently, states of activity are fine-tuned and maintained to translate into domains of progressively overlapping gene products. While the mechanisms underlying such temporal and spatial progressions begin to be understood, many of their aspects remain unclear. We have systematically analyzed the 3D chromatin organization of Hox clusters in vivo, during their activation using high-resolution circular chromosome conformation capture (4C-seq). Initially, Hox clusters are organized as single 3D chromatin compartments decorated with bivalent chromatin marks. Their progressive transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch one after the other, from an inactive to an active 3D compartment. These local 3D dynamics occur within a larger constitutive framework of interactions within the surrounding Topological Associated Domains, which confirms previous results that regulation of this process in primarily cluster intrinsic. The local step-wise progression in time can be stopped and memorized at various body levels and hence it may accounts for the various chromatin architectures previously described at different anterior to posterior body levels for the same embryo at a later stage. RNA-seq from mouse ES cells and mouse embryonic stage E10.5 forebrain. Data based on 2 biological samples.
Experiment type
RNA-seq of coding RNA 
Marion LELEU <geo@ncbi.nlm.nih.gov>, D Duboule, D Noordermeer, M Leleu
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-54952.idf.txt
Sample and data relationshipE-GEOD-54952.sdrf.txt
Processed data (1)E-GEOD-54952.processed.1.zip