Uncoupling time and space in the collinear regulation of Hox genes

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KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer

Eunji Shin

Cancer is the second leading cause of death worldwide. Cancer develops through multiple hallmark functions including apoptosis evasion, unlimited replicative potential, metastasis, and immune avoidance. Over the past few decades, researchers have reported ...

EPFL2022

Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

Didier Trono, Evaristo Jose Planet Letschert, Shaoline Sheppard, Christopher James Playfoot

Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional co ...

2022

Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance

Sebastian Maerkl, Shiyu Cheng, Amir Shahein, Maria Lopez Malo, Evan James Olson, Ivan Istomin

Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription fac ...

Nature Portfolio2022

Mitochondrial respiratory chain dysfunction disrupts intracellular cholesterol homeostasis

Christopher Tadhg James Wall

Mitochondrial diseases are rare and severe conditions with debilitating symptoms. Biochemical defects in mitochondria however are common. The difference between these two frequencies is suspected to lie in the capability of the cells to adapt to the homeos ...

EPFL2022

High-dimensional optimization under nonconvex excluded volume constraints

Antonio Sclocchi

We consider high-dimensional random optimization problems where the dynamical variables are subjected to nonconvex excluded volume constraints. We focus on the case in which the cost function is a simple quadratic cost and the excluded volume constraints a ...

AMER PHYSICAL SOC2022

Phase and microstructure selection in peritectic alloys under high G-V ratio

Wilfried Kurz

A new model for the case of a superposition of a phase transformation and a microstructure transition from columnar plane front to equiaxed dendritic growth for peritectic alloys is presented. This model is applied to Fe-Ni alloys where a phase transition ...

WALTER DE GRUYTER GMBH2022

Systematic analysis of biomolecular binding reactions using microfluidic systems

Amir Shahein

Transcription factor binding to a single binding site on DNA and its functional consequence in a promoter context are beginning to be relatively well understood. However, binding to clusters of sites has yet to be characterized in depth, and the functional ...

EPFL2022

Essential role of Cp190 in physical and regulatory boundary formation

Nicolas Jean Philippe Guex, Christian Iseli, Julien Dorier

Boundaries in animal genomes delimit contact domains with enhanced internal contact frequencies and have debated functions in limiting regulatory cross-talk between domains and guiding enhancers to target promoters. Most mammalian boundaries form by stalli ...

2022

Induction of a chromatin boundary in vivo upon insertion of a tad border

Denis Duboule, Lucille Delisle, Christopher Chase Bolt

Author summary During development, enhancer sequences tightly regulate the spatio-temporal expression of target genes often located hundreds of kilobases away. This complex process is made possible by the folding of chromatin into domains, which are separa ...

2021

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Denis Duboule, Lucille Delisle

In this study, Amandio et al. sought to understand the functions of the highly conserved CTCF sites distributed over the Hox gene clusters. The authors produced an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF b ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2021