Lucille Lopez‐Delisle

MULTIPLE DEFECTS IN MOUSE STEM CELL BASED EMBRYO MODELS LACKING ALL HOX FUNCTION

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.

Temporal constraints on enhancer usage shape the regulation of limb gene transcription

The paper investigates how temporally restricted enhancer repertoires regulate gene expression during limb development in mice and shows that enhancer-promoter interactions dynamically change over time.

EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS

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

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

This study identifies early transcriptional targets of WNT signaling during limb bud and digit development by transiently blocking WNT signaling with small molecule inhibitors.

Fine-tuning mechanical constraints uncouples patterning and gene expression in murine pseudo-embryos

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

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

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.

CTCF-DEPENDENT INSULATION OF Hoxb13 AND THE HETEROCHRONIC CONTROL OF TAIL LENGTH

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

Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development

The paper maps chondrogenic enhancers in limb and axial skeleton development and shows their role in explaining human height heritability.

Cadherins modulate the self-organizing potential of gastruloids

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

Sequential And Directional Insulation By Conserved CTCF Sites Underlies The Hox Timer In Pseudo-Embryos

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.

CONTEXT-DEPENDENT ENHANCER FUNCTION REVEALED BYTARGETED INTER-TAD RELOCATION

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.

baredSC: Bayesian Approach to Retrieve Expression Distribution of Single-Cell

baredSC infers gene expression distributions in scRNA-seq data, revealing correlations and multimodal patterns despite sparse sampling.

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

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.

MESOMELIC DYSPLASIAS ASSOCIATED WITH THE HOXD LOCUS ARE CAUSED BY REGULATORY REALLOCATIONS

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

DEVELOPMENTAL AND EVOLUTIONARY COMPARATIVE ANALYSIS OF A HOXD REGULATORY LANDSCAPE IN MAMMALS AND BIRDS

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.

CONTEXT-INDEPENDENT FUNCTION OF A CHROMATIN BOUNDARY IN VIVO

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

HOX13-MEDIATED DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS

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

Chromatin Topology And The Timing Of Enhancer Function At The HoxD Locus

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.

SPECIFIC ECTODERMAL ENHANCERS CONTROL THE EXPRESSION OF HoxC GENES IN DEVELOPING MAMMALIAN INTEGUMENTS

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.

A Complex Regulatory Landscape Involved In The Development Of External Genitals

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.

IMPACT OF GENOME ARCHITECTURE UPON THE FUNCTIONAL ACTIVATION AND REPRESSION OF Hox REGULATORY LANDSCAPES

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.

Constrained Transcriptional Polarity In The Organization Of Mammalian Hox Gene Clusters

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

CONSERVATION AND VARIATIONS OF BIMODAL HoxD GENE REGULATION DURING TETRAPOD LIMB DEVELOPMENT

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 HoxD Cluster is a Dynamic and Resilient TAD Boundary Controling the Segregation of Antagonistic Regulatory Landscapes

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.

LARGE-SCALE GENOMIC REORGANIZATIONS OF TOPOLOGICAL DOMAINS (TADs) AT THE HoxD LOCUS

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