Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states.
Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around the HoxD gene cluster. This reorganization follows a global transition from one set of regulatory contacts to another, between two topologically associating domains (TADs) located on either side of the HoxD locus. Here, we use 3D DNA FISH to assess the spatial organization of chromatin at and around the HoxD gene cluster and report that although the two TADs are tightly associated, they appear as spatially distinct units. We measured the relative position of genes within the cluster and found that they segregate over long distances, suggesting that a physical elongation of the HoxD cluster can occur. We analyzed this possibility by super-resolution imaging (STORM) and found that tissues with distinct transcriptional activity exhibit differing degrees of elongation. We also observed that the morphological change of the HoxD cluster in developing digits is associated with its position at the boundary between the two TADs. Such variations in the fine-scale architecture of the gene cluster suggest causal links among its spatial configuration, transcriptional activation, and the flanking chromatin context.
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
Pierre J
PJ
Fabre
Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
Alexander
A
Benke
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
Elisabeth
E
Joye
Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland.
Thi Hanh
TH
Nguyen Huynh
Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Denis.Duboule@epfl.ch suliana.manley@epfl.ch.
Suliana
S
Manley
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland Denis.Duboule@epfl.ch suliana.manley@epfl.ch.
Denis
D
Duboule
D000818:Animals; D002843:Chromatin / Q000235:genetics / Q000648:ultrastructure*; D042002:Chromatin Assembly and Disassembly / Q000235:genetics / Q000502:physiology*; D005121:Extremities / Q000196:embryology*; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D005801:Genes, Homeobox / Q000235:genetics*; D007091:Image Processing, Computer-Assisted; D017404:In Situ Hybridization, Fluorescence; D051379:Mice; D005810:Multigene Family / Q000235:genetics*; D017434:Protein Structure, Tertiary; D018709:Statistics, Nonparametric; D015533:Transcriptional Activation / Q000235:genetics*
D002843:Chromatin
DNA FISH; HoxD; limb development; super-resolution microscopy; topologically associating domains