Publications related to Control of growth and gut maturation by &ITHoxD&IT genes and the associated lncRNA &ITHaglr&IT

A CTCF-dependent mechanism underlies the Hox timer relation to a segmented body plan

During gastrulation, Hox genes are activated in a timesequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated wit ...

Current Biology Ltd2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

Genetic features and genomic targets of human KRAB-zinc finger proteins

Didier Trono, Priscilla Turelli, Julien Léonard Duc, Sandra Eloise Kjeldsen, Jonas Caspar De Tribolet-Hardy, Bara Khubieh, Jacques Fellay, Michaël Imbeault, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Evaristo Jose Planet Letschert, Christian Axel Wandall Thorball, Romain Forey

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

2023

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Denis Duboule, Célia Corinne Renée Bochaton, Lucille Delisle, Hocine Rekaik, Aurélie Hintermann, Alexandre Gauthier Aurèle Mayran

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

NATURE PORTFOLIO2023

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

Screening for drivers of SARS-CoV-2 uptake

Christoph Merten, Alexis Louis Autour

Genetic and cellular drivers of the cellular uptake of SARS-CoV-2 can be screened at high throughput via droplet microfluidics and size-exclusion methods for the analysis of the formation of fusions between cells expressing the virus's spike protein and ce ...

Nature Portfolio2023

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

Maria del Carmen Sandi Perez, Mandy Meijer

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

PERGAMON-ELSEVIER SCIENCE LTD2023

How are cells instructed to form somite boundaries by the zebrafish segmentation clock?

Olivier François Venzin

In vertebrate embryos, the elongating body axis is patterned via the sequential and rhyth-mic production of segments from a posterior unsegmented tissue called the presomitic mesoderm (PSM). This process is controlled by a population of cellular oscillator ...

EPFL2023

Predicting type 2 diabetes risk before and after solid organ transplantation using polygenic scores in a Danish cohort

Jacques Fellay, Christian Axel Wandall Thorball

Type 2 diabetes mellitus (T2DM) can be multifactorial where both genetics and environmental factors play a role. We aimed to investigate the use of polygenic risk scores (PRS) in the prediction of pre-transplant T2DM and post-transplant diabetes mellitus ( ...

Frontiers Media Sa2023

Targeted search for scaling genes reveals matrix metalloproteinase 3 as a scaler of the dorsal-ventral pattern in Xenopus laevis embryos

Daria Korotkova

How embryos scale patterning according to size is still not fully understood. Through in silico screening and analysis of reaction-diffusion systems that could be responsible for scaling, we predicted the existence of genes whose expression is sensitive to ...

Cell Press - Elsevier2022

Context-dependent enhancer function revealed by targeted inter-TAD relocation

Denis Duboule, Guillaume Andrey, Christopher Chase Bolt, Lucille Delisle, Aurélie Hintermann

Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...

Nature Portfolio2022

Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation

Matthias Rüegg, Mahmut Selman Sakar, Erik Mailand, Ece Özelçi, Andrew Charles Oates

Classic microsurgical techniques, such as those used in the early 1900s by Mangold and Spemann, have been instrumental in advancing our understanding of embryonic development. However, these techniques are highly specialized, leading to issues of inter-ope ...

Nature Research2022

Generation of a Gal4-dependent gene recombination and illuminating mouse

Freddy Radtke

Cell labeling technologies, including the Cre/loxP system, are powerful tools in developmental biology. Although the conventional Cre/loxP system has been extensively used to label the expression of specific genes, it is less frequently used for labeling p ...

INT PRESS EDITING CENTRE INC2022

Engineering of chitosan-based derivatives for non-viral gene delivery

Laura Camille Louise Nicolle

Gene therapy offers the possibility to treat or even cure diseases originating from genetic defects by introducing a therapeutic gene in target cells or correcting the initial defective gene. Amongst different options, non-viral vectors rely on the deliver ...

EPFL2022

Towards mouse genetic-specific RNA-sequencing read mapping

Maxime Jan, Ioannis Xenarios

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Laure Marie Colette Leynaud-Kieffer Curran

Many challenges are faced in the conversion of biomass into advanced biofuels, one of which is finding the correct organism for the job. The filamentous fungus Aspergillus niger has been chosen as a biocatalyst for cellulose, hemicellulose, and lignin degr ...

EPFL2021

Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Denis Duboule, Aurélie Hintermann, Jozsef Zakany

In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as "headgear," which likely share the same origin and genetic basis. However, the nature and function of ...

OXFORD UNIV PRESS2021

Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mouse

Alexis Maximilien Bachmann

Overweight and obesity are increasingly common public health issues worldwide, leading to a wide range of diseases from metabolic syndrome to steatohepatitis and cardiovascular diseases. While the increase in the prevalence of obesity is partly attributabl ...

EPFL2021

Toward a mechanistic understanding of variable chromatin modules

Gerard Llimos Aubach

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is a ...

EPFL2021