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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

DNA-Liposome Hybrid Carriers for Triggered Cargo Release

Diana Kornelia Morzy

The design of simple and versatile synthetic routes to accomplish triggered-release properties in carriers is of particular interest for drug delivery purposes. In this context, the programmability and adaptability of DNA nanoarchitectures in combination w ...

AMER CHEMICAL SOC2022

Identification of broad anti-coronavirus chemical agents for repurposing against SARS-CoV-2 and variants of concern

Gerardo Turcatti, Fabien Kuttler, Michael Bauer, Liliane Yang

Endemic human coronaviruses (hCoVs) 229E and OC43 cause respiratory disease with recurrent infections, while severe acute respiratory syndrome (SARS)-CoV-2 spreads across the world with impact on health and societies. Here, we report an image-based multicy ...

2022

Circadian dynamics of RNA localisation in the mammalian liver

Clémence Yumie Syloun Hurni

Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...

EPFL2021

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Mohammadomid Oftadeh, Pierre Guy Rémy Salvy

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

Nature Portfolio2021

Enteric infection induces Lark-mediated intron retention at the 5 ' end of Drosophila genes

Bart Deplancke, Maroun Bou Sleiman, Michael Vincent Frochaux, Dani Osman, Tommaso Andreani

Background RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study ...

2020

Nucleosome Binding by the Lysine Specific Demethylase 1 (LSD1) Enzyme Enables Histone H3 Demethylation

Beat Fierz, Aurore Marie-France Delachat, Abhinav Dhall

The essential human enzyme lysine specific demethylase 1 (LSD1) silences genes by demethylating mono- and dimethylated lysine 4 in histone H3 (H3K4me1/2). Studies of the minimal requirements for LSD1 activity are complicated by the heterogeneity of histone ...

AMER CHEMICAL SOC2020

Comprehensive analysis of PM20D1 QTL in Alzheimer's disease

Johannes Gräff, Liliane Glauser, Jose Vicente Sanchez Mut

Background Alzheimer's disease (AD) is a complex disorder caused by a combination of genetic and non-genetic risk factors. In addition, an increasing evidence suggests that epigenetic mechanisms also accompany AD. Genetic and epigenetic factors are not ind ...

2020

Mitochondrial RNA granules are fluid condensates positioned by membrane dynamics

Suliana Manley, Mary-Claude Croisier-Coeytaux, Timo Henry René Rey

Phase separation concentrates mitochondrial RNA granules. Here Rey et al., show that mitochondrial RNA granules (MRGs) behaviour is consistent with liquid-liquid phase separation (LLPS) and their fusion coincides with mitochondrial remodelling. Mitochondri ...

2020

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

Fabrice Daniel Darbellay, Anamaria Necsulea

The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon l ...

OXFORD UNIV PRESS2020

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Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

Fabrice Daniel Darbellay, Anamaria Necsulea

OXFORD UNIV PRESS2020

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Mohammadomid Oftadeh, Pierre Guy Rémy Salvy

Nature Portfolio2021

Enteric infection induces Lark-mediated intron retention at the 5 ' end of Drosophila genes

Bart Deplancke, Maroun Bou Sleiman, Michael Vincent Frochaux, Dani Osman, Tommaso Andreani

2020

Mitochondrial RNA granules are fluid condensates positioned by membrane dynamics

Suliana Manley, Mary-Claude Croisier-Coeytaux, Timo Henry René Rey

2020