Chromatin topology and the timing of enhancer function at the HoxD locus.
The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate from two distinct topologically associating domains (TADs) flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory submodules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites, or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrate the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts was eventually resumed, showing that the presence of enhancer sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavorable orientation of CTCF sites.
['Rodríguez-Carballo|Eddie|E|0000-0003-4321-508X', 'Lopez-Delisle|Lucille|L|0000-0002-1964-4960', 'Willemin|Andréa|A|0000-0002-4370-6914', 'Beccari|Leonardo|L|0000-0001-6472-5105', 'Gitto|Sandra|S|', 'Mascrez|Bénédicte|B|', 'Duboule|Denis|D|0000-0001-9961-2960']
D000818:Animals D000076246:CCCTC-Binding Factor D002843:Chromatin D042002:Chromatin Assembly and Disassembly D047108:Embryonic Development D004742:Enhancer Elements, Genetic D005121:Extremities D018507:Gene Expression Regulation, Developmental D005801:Genes, Homeobox D018878:Limb Buds D051379:Mice
enhancers chromatin architecture Hox clusters TAD boundary gene regulation