Publications by Lucille Delisle

WNT signaling coordinately controls mouse limb bud outgrowth and establishment of the digit-interdigit pattern

Lucille Delisle, Alexandre Gauthier Aurèle Mayran

Self-organization, such as the emergence of a pattern from a homogenous state, is a fascinating property of biological systems. Early limb bud outgrowth and patterning in mice are controlled by a robust and self-regulatory signaling system, and initiation ...

The Company of Biologists2025

Size-dependent temporal decoupling of morphogenesis and transcriptional programs in pseudoembryos

Denis Duboule, Lucille Delisle, Alexandre Gauthier Aurèle Mayran

Understanding the interplay between cell fate specification and morphogenetic changes remains a challenge in developmental biology. Gastruloids, stem cell models of postimplantation mammalian development, provide a platform to address this question. Here, ...

American Association for the Advancement of Science (AAAS)2025

Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development

Lucille Delisle

Chondrocyte differentiation controls skeleton development and stature. Here we provide a comprehensive map of chondrocyte-specific enhancers and show that they provide a mechanistic framework through which non-coding genetic variants can influence skeletal ...

Nature Research2024

CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length

Denis Duboule, Célia Corinne Renée Bochaton, Fabrice Daniel Darbellay, Lucille Delisle, Hocine Rekaik, Alexandre Gauthier Aurèle Mayran, Pierre Osteil

Mammalian tail length is controlled by several genetic determinants, among which are Hox13 genes, whose function is to terminate the body axis. Accordingly, the precise timing in the transcriptional activation of these genes may impact upon body length. Un ...

National Academy of Sciences2024

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

Denis Duboule, Célia Corinne Renée Bochaton, Lucille Delisle, Hocine Rekaik, Aurélie Hintermann, Alexandre Gauthier Aurèle Mayran

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 ...

NATURE PORTFOLIO2023

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

Denis Duboule, Guillaume Andrey, Christopher Chase Bolt, Lucille Delisle, Aurélie Hintermann

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 ...

Nature Portfolio2022

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Lucille Delisle

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to th ...

2022

Induction of a chromatin boundary in vivo upon insertion of a tad border

Denis Duboule, Marie-Laure Gadolini, Christopher Chase Bolt, Lucille Delisle, Edgardo Rodriguez Carballo

Author summary During development, enhancer sequences tightly regulate the spatio-temporal expression of target genes often located hundreds of kilobases away. This complex process is made possible by the folding of chromatin into domains, which are separa ...

2021

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Denis Duboule, Leonardo Beccari, Lucille Delisle, Jozsef Zakany

In this study, Amandio et al. sought to understand the functions of the highly conserved CTCF sites distributed over the Hox gene clusters. The authors produced an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF b ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2021

Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations

Denis Duboule, Christopher Chase Bolt, Lucille Delisle

Mesomelic dysplasia, a severe shortening and bending of the limb, has been linked to rearrangements in the HoxD cluster in humans and mice. Here the authors engineer a 1 Mb inversion including the HoxD gene cluster and use this model to provide a mechanist ...

Nature Portfolio2021

Chromatin topology and the timing of enhancer function at the HoxD locus

Denis Duboule, Leonardo Beccari, Lucille Delisle, Edgardo Rodriguez Carballo

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 e ...

National Academy of Sciences2020

Teaching Transversal Skills in the Engineering Curriculum: the Need to Raise the Temperature

Pascal Vuilliomenet, Roland John Tormey, Jessica Elke Dehler Zufferey, Lucille Delisle, Mirjam Mekhaiel, Helena Kovacs

Engineers and architects today are dealing with great social, technical and environmental complexities, and the demand for having broadly educated holistic engineers will only continue to grow in the future. Being able to manage and lead diverse teams, und ...

University of Twente2020

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

Denis Duboule, Christopher Chase Bolt, Lucille Delisle

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. ...

2020

pyGenomeTracks: reproducible plots for multivariate genomic datasets

Lucille Delisle

Motivation Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures requires considerable effort. This is usually done by hand or using a vector graphic software. ...

2020

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

Denis Duboule, Nayuta Yakushiji, Lucille Delisle, Edgardo Rodriguez Carballo

Background The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match wi ...

2019

Constrained Transcriptional Polarity In The Organization Of Mammalian Hox Gene Clusters

Denis Duboule, Saskia Joëlle Delpretti Anex, Célia Corinne Renée Bochaton, Fabrice Daniel Darbellay, Lucille Delisle, Jozsef Zakany

2019

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

Denis Duboule, Guillaume Andrey, Leonardo Beccari, Nayuta Yakushiji, Christopher Chase Bolt, Lucille Delisle

In all tetrapods examined thus far, the development and patterning of limbs require the activation of gene members of the HoxD cluster. In mammals, they are regulated by a complex bimodal process that controls first the proximal patterning and then the dis ...

PUBLIC LIBRARY SCIENCE2018

The ALK receptor in sympathetic neuron development and neuroblastoma

Lucille Delisle

The ALK gene encodes a tyrosine kinase receptor characterized by an expression pattern mainly restricted to the developing central and peripheral nervous systems. In 2008, the discovery of ALK activating mutations in neuroblastoma, a tumor of the sympathet ...

2018

Large scale genomic reorganization of topological domains at the HoxD locus

Denis Duboule, Daniël Noordermeer, Marion Leleu, Pierre Raymond Fabre, Leonardo Beccari, Benjamin Howard Mormann, Lucille Delisle

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 ...

2017

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

Denis Duboule, Pierre Raymond Fabre, Leonardo Beccari, Lucille Delisle, Edgardo Rodriguez Carballo

The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas ...

2017