title: Visualizing the HoxD Gene Cluster at the Nanoscale Level.
abstract: Transcription of HoxD cluster genes in limbs is coordinated by two topologically associating domains (TADs), neighboring the cluster and containing various enhancers. Here, we use a combination of microscopy approaches and chromosome conformation capture to assess the structural changes occurring in this global architecture in various functional states. We observed that despite their spatial juxtaposition, the TADs are consistently kept as distinct three-dimensional units. Hox genes located at their boundary can show significant spatial segregation over long distances, suggesting that physical elongation of the HoxD cluster occurs. The use of superresolution imaging (STORM [stochastic optical reconstruction microscopy]) revealed that the gene cluster can be in an either compact or elongated shape. The latter configuration is observed in transcriptionally active tissue and in embryonic stem cells, consistent with chromosome conformation capture results. Such morphological changes at HoxD in developing digits seem to be associated with its position at the boundary between two TADs and support the idea that chromatin dynamics is important in the establishment of transcriptional activity.
authors.affiliation: School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
authors.forename: Pierre J
authors.initials: PJ
authors.lastname: Fabre
authors.affiliation: Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Benke
authors.affiliation: Laboratory of Experimental Biophysics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Suliana
authors.initials: S
authors.lastname: Manley
authors.affiliation: School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland.
authors.forename: Denis
authors.initials: D
authors.lastname: Duboule
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism*; D053595:Embryonic Stem Cells; D005121:Extremities / Q000196:embryology; D018507:Gene Expression Regulation, Developmental; D005801:Genes, Homeobox / Q000235:genetics*; D008853:Microscopy; D005810:Multigene Family; D061848:Optical Imaging
chemical_list: D002843:Chromatin