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Bart Deplancke

Cette personne a quitté l’EPFL

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Publications associées (113)

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Sex-dependent and sex-independent regulatory systems of size variation in natural populations

Bart Deplancke, Vincent Roland Julien Gardeux, Ernst Hafen

Size of organs/organisms is a polygenic trait. Many of the growth-regulatory genes constitute conserved growth signaling pathways. However, how these multiple genes are orchestrated at the systems level to attain the natural variation in size including sex ...

2019

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

Bart Deplancke, Jacques Rougemont

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing geneand transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification o ...

Oxford University Press2017

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Bart Deplancke

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Nature Portfolio2022

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Matteo Dal Peraro, Bart Deplancke, Felix Naef, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Sunil Kumar Raghav, Irina Krier, Guillaume Rey, Alexandra Styliani Kalantzi, Jonathan Aryeh Sobel

Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles ...

Public Library of Science2017

GLUT3 is induced during epithelial-mesenchymal transition and promotes tumor cell proliferation in non-small cell lung cancer

Bart Deplancke, Etienne Meylan, Petra Catalina Schwalie, Svenja Johanna Groeneveld, Jessica Christine Vazquez, Natasha Ella Samson, Mark Jonathan Masin

Alterations in glucose metabolism and epithelial-mesenchymal transition (EMT) constitute two important characteristics of carcinoma progression toward invasive cancer. Despite an extensive characterization of each of them separately, the links between EMT ...

2014

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network

Didier Trono, Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Petra Catalina Schwalie, Gilles Udin, Andrea Corsinotti

Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiat ...

Elife Sciences Publications Ltd2014

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Bart Deplancke, Wouter Jozef L Saelens

The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITEseq, single-nuclei sequencing, spatial tran ...

CELL PRESS2022

Profiling of Single-Cell Transcriptomes

Bart Deplancke, Vincent Roland Julien Gardeux, Wanze Chen, Antonio Carlos Alves Meireles Filho

Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional ...

2017

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Didier Trono, Bart Deplancke, Philipp Bucher, Giovanna Ambrosini, Riccardo Dainese, Daniel Alpern, Michaël Imbeault, Alina Isakova, Romain Fernand Pietro Groux, Pernille Yde Rainer

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Vassily Hatzimanikatis, Bart Deplancke, Alina Isakova, Yves Berset

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its i ...

American Society for Biochemistry and Molecular Biology2016

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern, Antonio Carlos Alves Meireles Filho, Gerard Llimos Aubach

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molec ...

National Academy of Sciences2020

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Bart Deplancke, Jeffrey David Jensen, Sebastian Martin Waszak, Andreas Massouras

Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here ...

Public Library of Science2012

Direct In Vivo Activation of T Cells with Nanosized Immunofilaments Inhibits Tumor Growth and Metastasis

Bart Deplancke, Guido Van Mierlo, Jorieke Weiden

Adoptive T cell therapyhas successfully been implementedfor thetreatment of cancer. Nevertheless, ex vivo expansion of T cells byartificial antigen-presenting cells (aAPCs) remains cumbersome andcan compromise T cell functionality, thereby limiting their t ...

AMER CHEMICAL SOC2023

System for capture or immunoprecipitation of a protein-dna complex

Bart Deplancke, Riccardo Dainese

The present invention concerns a system for immunoprecipitation of a protein-DNA complex or for capture of a protein-DNA complex including: - a microfluidic device including a plurality of antibody units, wherein each antibody unit includes at least one mi ...

2019

Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity

Bart Deplancke, Pernille Yde Rainer, Radiana Ferrero

White adipose tissue (WAT) is a cellularly heterogeneous endocrine organ that not only serves as an energy reservoir, but also actively participates in metabolic homeostasis. Among the main constituents of adipose tissue are adipocytes, which arise from ad ...

ELSEVIER SCIENCE LONDON2020

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Alisa Yurovsky

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifac ...

Oxford University Press2014

Transcription factor proteomics - Tools, applications, and challenges

Bart Deplancke, Jovan Simicevic

Transcription factors (TFs) are a family of DNA-binding proteins whose gene regulatory capabilities are of vital importance in defining the molecular state of a cell. Despite their biological significance, our understanding of TF behavior and function is s ...

Wiley-VCH GmbH2017

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

Didier Trono, Bart Deplancke, Priscilla Turelli, Christian Axel Wandall Thorball, Julien Léonard Duc, Alexandre Coudray, Julien Paul André Pontis, Charlène Mireille Raymonde Raclot, Delphine Yvette L Grun, Christopher James Playfoot

In the first days of embryogenesis, transposable element-embedded regulatory sequences (TEeRS) are silenced by Kruppel-associated box (KRAB) zinc finger proteins (KZFPs). Many TEeRS are subsequently co-opted in transcription networks, but how KZFPs influen ...

2020

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer

Didier Trono, Bart Deplancke, Julien Léonard Duc, Riccardo Dainese, Marco Cassano, Julie Marie Russeil, Michaël Imbeault, Wanze Chen, Suk Min Jang, Carine Delattre-Gubelmann, Petra Catalina Schwalie, Sunil Kumar Raghav

Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revea ...

Nature Research2019

Dissecting the brown adipogenic regulatory network using integrative genomics

Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern, Sunil Kumar Raghav, Petra Catalina Schwalie, Julie Marie Russeil, Wanze Chen, Johannes Julius Bues, Rachana Narendra Pradhan

Brown adipocytes regulate energy expenditure via mitochondrial uncoupling, which makes them attractive therapeutic targets to tackle obesity. However, the regulatory mechanisms underlying brown adipogenesis are still poorly understood. To address this, we ...

Springer Nature2017