Publications by Denis Duboule | EPFL Graph Search

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Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. ...

Collinear expression of 5′ Hoxd genes during mammalian limb development is required to properly determine digits number and identity. We recently proposed a two-step model to account for the underlying regulatory mechanism, which involves an initial loopin ...

BACKGROUND: The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD g ...

The HoxD cluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxD genes. In rare patients, duplications, balanced translocations or inv ...

During gastrulation, Hox genes are activated in a timesequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated wit ...

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 th ...

The emergence of multiple axes is an essential element in the establishment of the mammalian body plan. This process takes place shortly after implantation of the embryo within the uterus and relies on the activity of gene regulatory networks that coordina ...

Lentivector-mediated transgenesis is increasingly used, whether for basic studies as an alternative to pronuclear injection of naked DNA or to test candidate gene therapy vectors. In an effort to characterize the genetic features of this approach, we first ...

Despite the crucial importance of Hox genes functions during animal development, the mechanisms that control their transcription in time and space are not yet fully understood. In this context, it was proposed that Hotair, a lncRNA transcribed from within ...

The extent to which the nuclear organisation of a gene impacts on its ability to be expressed, or whether nuclear organisation merely reflects gene expression states, remains an important but unresolved issue. A model system that has been instrumental in i ...

Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated wi ...

During development of the vertebrate body axis, Hox genes are transcribed sequentially, in both time and space, following their relative positions within their genomic clusters. Analyses of animal genomes support the idea that Hox gene clustering is essent ...

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical a ...

Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...

During embryonic development, fields of progenitor cells form complex structures through dynamic interactions with external signaling molecules. How complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood ...

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

During the development of mammalian digits, clustered Hoxd genes are expressed following a collinear regulatory strategy, leading to both the growth of digits and their morphological identities. Because gene dosage is a key parameter in this system, we use ...

Developmentally regulated genes are often controlled by distant enhancers, silencers and insulators, to implement their correct transcriptional programs. In recent years, the development of 3C and derived techniques (4C, 5C, HiC, ChIA- PET, etc.) has confi ...

In particular, this sequence is found in the 39 members of the amniote Hox gene family, a series of genes activated in mid-gastrulation and involved in organizing morphologies along the extending anterior to posterior (AP) body axis. Over the past 30 years ...

During vertebrate limb development, Hoxd genes are regulated following a bimodal strategy involving two topologically associating domains (TADs) located on either side of the gene cluster. These regulatory landscapes alternatively control different subsets ...

Denis Duboule

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A complex regulatory landscape involved in the development of mammalian external genitals

Long-range enhancer-promoter interactions in the HoxD complex

Large scale genomic reorganization of topological domains at the HoxD locus

Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster

A CTCF-dependent mechanism underlies the Hox timer relation to a segmented body plan

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

Genotypic features of lentivirus transgenic mice

Hotair Is Dispensible for Mouse Development

Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

Uncoupling time and space in the collinear regulation of Hox genes

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

Context-dependent enhancer function revealed by targeted inter-TAD relocation

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness

Chromatin looping and organization at developmentally regulated gene loci

Comments on the Hox timer and related issues

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus