Benoit G. Bruneau

Neural Crest-Derived Endocardial Cells Required for Heart Valve Development

The paper identifies a rare population of neural crest-derived endocardial cells essential for heart valve development in mice and humans, showing their role in valve morphogenesis through Pthlh signaling.

Structural variants in human congenital heart disease disrupt distal genomic regulatory contacts of developmental genes

The paper develops a machine-learning model to predict how structural variants disrupt 3D chromatin structure in congenital heart disease and validates its predictions using induced pluripotent stem cells.

A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects

The paper identifies Tbx5 as a gene critical for forming a compartment boundary in the interventricular septum, and shows its disruption leads to congenital heart defects.

Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease

This study shows that reduced TBX5 dosage disrupts atrial cardiomyocyte identity, leading to cellular and molecular changes associated with atrial diseases.

MEF2C controls segment-specific gene regulatory networks that direct heart tube morphogenesis

This study identifies MEF2C-dependent gene regulatory networks in specific heart segments and shows their role in heart tube morphogenesis using multi-omics data and deep learning.

Engineering Synthetic Cell State Transitions by Harnessing Epigenetic Memory

This paper engineers synthetic epigenetic circuits that induce stable gene expression changes and drive cell state transitions through transient cell-cell interactions.

Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor

This study shows that reduced TBX5 dosage affects 3D chromatin organization in human cardiomyocytes, with cell-to-cell variation and partial protection by CTCF co-occupancy.

CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development

This study shows CDX2 dose-dependently regulates genes involved in tissue permeability, cell-cell adhesion, and cytoskeletal structure during extraembryonic mesoderm development using human induced pluripotent stem cells.

TBXT dose sensitivity and the decoupling of nascent mesoderm specification from EMT progression in 2D human gastruloids

This study shows that TBXT dose affects the timing of EMT in human gastruloids without compromising mesoderm differentiation.

A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors

The paper identifies a Mesp1-dependent developmental breakpoint in cardiac precursor cell specification using single-cell transcriptomics and chromatin accessibility analysis in mouse embryos.

A spatiotemporal gradient of mesoderm assembly governs cell fate and morphogenesis of the early mammalian heart

This study uses live embryo imaging to show how mesoderm gradients guide heart development through spatial and temporal morphodynamics.

Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis

Cell Layers provides an interactive tool to explore single-cell clustering across resolutions, linking molecular data with cluster evaluation metrics.

Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes

Modeling human TBX5 haploinsufficiency predicts regulatory networks for congenital heart disease

The paper models TBX5 haploinsufficiency in iPSC-derived cardiomyocytes to identify gene regulatory network imbalances linked to congenital heart disease.

WAPL maintains dynamic cohesin to preserve lineage specific distal gene regulation

This study shows WAPL maintains dynamic cohesin at lineage-specific regulatory regions in mouse embryonic stem cells, which is essential for gene expression and pluripotency.

Molecular basis of CTCF binding polarity in genome folding

The paper investigates how CTCF binding polarity influences chromatin loop formation by showing that CTCF positions cohesin but does not control its binding dynamics.

Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation

This study shows that Brm deletion causes identity switches in cardiac mesoderm differentiation by altering chromatin accessibility and gene expression, revealing BRM's role in safeguarding developmental canalization.

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

The paper investigates the distinct and combined roles of CTCF and CTCFL in chromosome organization and transcription by analyzing their binding sites and functional domains.

Developmental co-emergence of cardiac and gut tissues modeled by human iPSC-derived organoids

This study shows that human iPSC-derived organoids can model the cooperative development of cardiac and gut tissues through paracrine signaling.

Minimal in vivo requirements for developmentally regulated cardiac long intergenic non-coding RNAs

The paper investigates the role of developmentally regulated cardiac lincRNAs in heart development and function, finding that their deletion does not cause severe cardiac phenotypes.

CTCF confers local nucleosome resiliency after DNA replication and during mitosis

The paper shows that CTCF and Esrrb maintain nucleosome positioning at gene regulatory regions during DNA replication and mitosis in mouse ES cells.

A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards

The paper presents a high-resolution chromosome-assigned genome of the Komodo dragon, identifying adaptations in cardiovascular, muscular, and chemosensory systems through comparative genomics.

RNA interactions with CTCF are essential for its proper function

The paper shows that CTCF's RNA-binding ability is crucial for its chromatin association and insulation function.

Identification of cis elements for spatio-temporal control of DNA replication

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

Heart enhancers with deeply conserved regulatory activity are established early in development

The paper identifies conserved enhancers active early in zebrafish heart development that recapitulate human expression patterns, suggesting ancient regulatory mechanisms.

BAF chromatin remodeling complex subunit diversity promotes temporally distinct gene expression programs in cardiogenes

The paper identifies BAF complex subunit dynamics during cardiac differentiation, showing how BAF60c and BAF170 regulate gene expression programs in cardiac precursors and cardiomyocytes.

A Novel Reporter Allele For Monitoring Dll4 Expression Within The Embryonic And Adult Mouse

The paper develops a novel Dll4 reporter allele to accurately monitor Dll4 expression in embryonic and adult mice, overcoming limitations of previous reporter lines.

Transcription Factors Recognize DNA Shape Without Nucleotide Recognition

The paper shows that transcription factors recognize DNA shape rather than sequence, using ShapeMF to identify shape-motifs that drive binding independent of sequence motifs.

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization

This study shows CTCF is essential for TAD organization but not for genome compartmentalization, revealing distinct mechanisms for chromatin folding and insulation.

Cardiac enriched BAF chromatin remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function

This study shows that Baf60c regulates gene expression programs critical for heart development and function by interacting with Myocardin and controlling contractile proteins and metabolic genes.