Publications de Sunil Kumar Raghav

Differential regulation of RNA polymerase III genes during liver regeneration

Olivier Martin, Bart Deplancke, Felix Naef, Jacques Rougemont, Marion Leleu, Nicolas Jean Philippe Guex, Fabrice David, Kyle Gustafson, Dominic Villeneuve, Cristian Carmeli

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Oxford University Press (OUP)2019

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

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

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

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

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

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

Dissecting the brown adipogenic regulatory network using integrative genomics

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

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

Bart Deplancke, David Hacker, Gilles Udin, Sebastian Martin Waszak, Sunil Kumar Raghav, Nouria Hernandez, Alisa Yurovsky, Sarah Thurnheer

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

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

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Nouria Hernandez, 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

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

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

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

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Bart Deplancke, Alina Isakova, Sebastian Martin Waszak, Jovan Simicevic, Sunil Kumar Raghav, Antonina Iagovitina, Carine Delattre-Gubelmann, Jean-Daniel Feuz

The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression b ...

Nature / European Molecular Biology Organization2013

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

Bart Deplancke, David Hacker, Gilles Udin, Sebastian Martin Waszak, Sunil Kumar Raghav, Nouria Hernandez, Alisa Yurovsky, Julien Bryois, Sarah Thurnheer

DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regu ...

American Association for the Advancement of Science2013

Exhaustion of tumor-specific CD8(+) T cells in metastases from melanoma patients

Bart Deplancke, Pedro Romero, Sunil Kumar Raghav, Nathalie Rufer, Lukas Baitsch

In chronic viral infections, CD8(+) T cells become functionally deficient and display multiple molecular alterations. In contrast, only little is known of self- and tumor-specific CD8(+) T cells from mice and humans. Here we determined molecular profiles o ...

American Society for Clinical Investigation2011