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Bart Deplancke

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Related publications (113)

Page 1 of 6

Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress

Michael Vincent Frochaux, Bart Deplancke, Maroun Bou Sleiman, Virginie Sandra Braman, Maria Litovchenko

Eukaryotic genomes encode several buffering mechanisms that robustly maintain invariant phenotypic outcome despite fluctuating environmental conditions. Here we show that the Drosophila gut-associated commensals, represented by a single facultative symbion ...

2019

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Bart Deplancke

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, a ...

2020

An evolutionarily conserved role for the aryl hydrocarbon receptor in the regulation of movement

Michael Vincent Frochaux, Bart Deplancke, Johan Auwerx, Pénélope Andreux, Evan Graehl Williams, Laurent Mouchiroud

The BXD genetic reference population is a recombinant inbred panel descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains of mice, which segregate for about 5 million sequence variants. Recently, some of these variants have been established ...

Public Library of Science2014

Live-seq enables temporal transcriptomic recording of single cells

Bart Deplancke, Pernille Yde Rainer, Riccardo Dainese, Wanze Chen, Magda Zachara, Vincent Roland Julien Gardeux, Wouter Jozef L Saelens, Orane Josiane Guillaume-Gentil

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity(1). However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Liv ...

NATURE PORTFOLIO2022

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

Michael Vincent Frochaux, Bart Deplancke, Vincent Roland Julien Gardeux

Background The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum ...

2020

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Bart Deplancke, Andreas Massouras

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used a ...

Cold Spring Harbor Laboratory Press2014

Transcriptomic profiling of murine GnRH neurons reveals developmental trajectories linked to human reproduction and infertility

Bart Deplancke, Julie Marie Russeil, Daniel Alpern, Vincent Roland Julien Gardeux

Rationale: Neurons producing Gonadotropin-Releasing Hormone (GnRH) are essential for human reproduction and have to migrate from nose to brain during prenatal life. Impaired GnRH neuron biology results in alterations of the reproductive axis, including del ...

2025

Current challenges in understanding the role of enhancers in disease

Bart Deplancke

Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing eviden ...

Nature Research2022

Single-cell transcriptional profiling of splenic fibroblasts reveals subset-specific innate immune signatures in homeostasis and during viral infection

Bart Deplancke

Our understanding of the composition and functions of splenic stromal cells remains incomplete. Here, based on analysis of over 20,000 single cell transcriptomes of splenic fibroblasts, we characterized the phenotypic and functional heterogeneity of these ...

NATURE PORTFOLIO2021

Hippo, TGF-beta, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection

Bart Deplancke

Cytokine signaling is responsible for coordinating conserved epithelial regeneration and immune responses in the digestive tract. In the Drosophila midgut, Upd3 is a major cytokine, which is induced in enterocytes (EC) and enteroblasts (EB) upon oral infec ...

Public Library of Science2017

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior

Michael Vincent Frochaux, Bart Deplancke, Matteo Dal Peraro, Antonio Carlos Alves Meireles Filho, Roel Paulus Josephus Bevers, Alessio Prunotto, Julie Marie Russeil, Virginie Sandra Braman, Vincent Roland Julien Gardeux, Maria Litovchenko, Brian Dennis Hollis

Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transc ...

2021

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

Carine Delattre-Gubelmann, Bart Deplancke, Jacques Rougemont, Fabrice David, Andreas Massouras

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and ...

2011

Pseudomonas aeruginosa type IV pili actively induce mucus contraction to form biofilms in tissue-engineered human airways

Bart Deplancke, Lorenzo Anton-Louis Talà, Tamara Rossy, Alexandre Louis André Persat, Jörn Pezoldt, Tania Distler, Lucas Andrade Meirelles

The opportunistic pathogen Pseudomonas aeruginosa causes antibiotic-recalcitrant pneumonia by forming biofilms in the respiratory tract. Despite extensive in vitro experimentation, how P. aeruginosa forms biofilms at the airway mucosa is unresolved. To inv ...

PUBLIC LIBRARY SCIENCE2023

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Bart Deplancke, Vincent Roland Julien Gardeux, Olga Pushkarev, Judith Franziska Kribelbauer, Wouter Jozef L Saelens, Guido Van Mierlo

Background: Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify ...

2024

Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence

Bruno Lemaitre, Bart Deplancke, Andreas Massouras, Dani Osman, Maroun Bou Sleiman

Gut immunocompetence involves immune, stress and regenerative processes. To investigate the determinants underlying inter-individual variation in gut immunocompetence, we perform enteric infection of 140 Drosophila lines with the entomopathogenic bacterium ...

Nature Publishing Group2015

Gene regulatory mechanisms underlying the intestinal innate immune response

Bart Deplancke, Antonio Carlos Alves Meireles Filho

In the mammalian gastrointestinal tract, distinct types of cells, including epithelial cells and macrophages, collaborate to eliminate ingested pathogens while striving to preserve the commensal microbiota. The underlying innate immune response is driven b ...

Elsevier2017

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

David Hacker, Gilles Udin, Bart Deplancke, Alisa Yurovsky, Sunil Kumar Raghav, Sebastian Martin Waszak

Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase ...

Elsevier2015

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development

Bart Deplancke

Transcription factors (TFs) are key regulators of cell fate. The estimated 755 genes that encode DNA binding domain-containing proteins comprise similar to 5% of all Drosophila genes. However, the majority has remained uncharacterized so far due to the lac ...

Cold Spring Harbor Laboratory Press2015

Automated protein-DNA interaction screening of Drosophila regulatory elements

Antonina Iagovitina, Bart Deplancke, Alina Isakova, Andreas Massouras

Drosophila melanogaster has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. To explore how these elements contribute to gene regulation, we need convenient tools to identify the proteins that bind to t ...

Nature Publishing Group2011

The NAD-Booster Nicotinamide Riboside Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance

Matthias Lütolf, Vincent Trachsel, Bart Deplancke, Nicola Vannini, Johan Auwerx, Pedro Romero, Carlos Canto Alvarez, Mukul Girotra, Aurélien Laurent Jean-Charles Oggier, Dongryeol Ryu, Eija Riitta Pirinen, Olaia Maria Naveiras Torres-Quiroga, Pernille Yde Rainer, Gennady Nikitin, Vasco Ledebur de Antas de Campos, Joanna Ratajczak, Josefine Catharina Pedersen Tratwal, George Coukos, Sonja Giger, Shanti Rojas-Sutterlin, Yang Li

It has been recently shown that increased oxidative phosphorylation, as reflected by increased mitochondrial activity, together with impairment of the mitochondrial stress response, can severely compromise hematopoietic stem cell (HSC) regeneration. Here w ...

CELL PRESS2019