Denis Duboule

This study shows that mouse gastruloids lacking all HOX function can elongate but fail to form endoderm and properly segment mesoderm, suggesting HOX proteins are needed to posteriorize anterior structures.

The paper shows that the regulatory landscape controlling Hoxd gene expression in limbs was co-opted from an ancestral cloacal program in tetrapods.

This study shows that mechanical constraints can separately affect patterning and gene expression in murine gastruloids, revealing distinct cellular responses to external forces.

This study shows that physical size affects morphogenetic timing and outcomes in gastruloids, while transcriptional programs remain stable, with extreme sizes showing distinct gene expression patterns.

The paper investigates how CTCF sites in a DNA spacer delay Hoxb13 activation, affecting tail length by modulating its heterochronic expression.

This study identifies a Cadherin switch mechanism that regulates self-organization in gastruloids by linking pluripotency exit and cell differentiation.

The paper shows that conserved CTCF sites create sequential insulation, controlling the timing of Hox gene activation in pseudo-embryos through chromatin extrusion and cohesin loading.

The paper shows that enhancer function depends on their chromatin context by relocating a distal limb enhancer into a proximal limb TAD, where it loses its distal specificity.

The paper uses in-cis mutations to study CTCF site functions in the mouse HoxD cluster, showing their roles in insulation, enhancer-promoter interactions, and TAD border formation.

The paper shows that mesomelic dysplasia caused by HOXD locus rearrangements results from ectopic HOXD13 expression due to regulatory reallocations.

The paper compares Hoxd gene regulation in mammalian vibrissae and avian feather primordia with trunk elongation in mice and chickens, showing lineage-specific enhancer usage and functional divergence in conserved CREs.

The paper shows that a chromatin boundary from the HoxD gene cluster can function independently of its genomic context when relocated in mouse development.

The paper identifies POLYCERATE alleles in sheep and goats linked to defective HOXD1 function, showing haploinsufficiency causes horn bud splitting and highlights HOXD1's role in headgear patterning in Bovidae.

The paper identifies HOX13-mediated regulation of DBX2 in limb development and shows enhancers can cross TAD boundaries to regulate genes in different domains.

The paper investigates how chromatin topology affects the timing of enhancer function at the HoxD locus, finding that enhancer sequences can overcome adverse chromatin architecture to activate genes.

This study identifies two mammalian-specific enhancers upstream of the HoxC gene cluster that regulate Hoxc gene expression in ectodermal organs like hair and nails.

The paper investigates how regulatory landscapes around the HoxD gene cluster are formed and function, finding that individual sequence deletions have minimal impact on transcription.

The paper investigates how chromatin domain structure affects Hox gene regulation, showing that enhancer activity and silencing marks are influenced by TAD boundaries and Polycomb complex recruitment.

The paper investigates the role of uniform transcriptional orientation in mammalian Hox gene clusters by engineering inversions and observing their impact on gene regulation.

The paper compares bimodal HoxD gene regulation in chicken and mouse limb development, finding conserved mechanisms with species-specific differences in enhancer activity and TAD boundaries.

The paper analyzes single-cell transcriptomes of developing mammalian limb buds to show that Hoxd genes are expressed in specific combinations linked to cell types and follow a pseudotime trajectory during digit development.

The paper investigates the HoxD cluster's role as a dynamic TAD boundary in limb development, showing its resilience and ability to maintain regulatory segregation.

The paper investigates how genomic rearrangements affect TAD structures at the HoxD locus by analyzing long-range chromatin interactions and boundary selection mechanisms.