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Publications associées (26)

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

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

Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex

Daniel Constam, Benjamin Marcel Daniel Rothé

Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examin ...

Nature Portfolio2021

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

Wnt5a promotes hippocampal postsynaptic development and GluN2B-induced expression via the eIF2 alpha HRI kinase

Eva Ramos Fernandez

Wnt signaling plays a key role in neurodevelopment and neuronal maturation. Specifically, Wnt5a stimulates postsynaptic assemblies, increases glutamatergic neurotransmission and, through calcium signaling, generates nitric oxide (NO). Trying to unveil the ...

Nature Research2021

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

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

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

The Genetics of Transcription Factor DNA Binding Variation

Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern

Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key ...

Elsevier2016

An interplay between the p38 MAPK pathway and AUBPs regulates c-fos mRNA stability during mitogenic stimulation

Diego Chiappe, Tamara Tanos

Mitogen-activated protein kinase (MAPK) pathways constitute key regulatory elements linking extracellular stimuli to nuclear gene expression. Immediate-early responsive genes (IEGs) of the activator protein 1 (AP-1) family, such as fos, achieve peak expres ...

Portland Press Ltd2015

TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation

Michele De Palma, Mario Leonardo Squadrito

Despite its importance during viral or bacterial infections, transcriptional regulation of the interferon-beta gene (Ifnb1) in activated macrophages is only partially understood. Here we report that TRIM33 deficiency results in high, sustained expression o ...

Nature Publishing Group2015

Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease

Jacques Fellay, Paul Jack Mc Laren

Variation in the 3' untranslated region (3'UTR) of the HLA-C locus determines binding of the microRNA Hsa-miR-148a, resulting in lower cell surface expression of alleles that bind miR-148a relative to those alleles that escape its binding. The HLA-C 3'UTR ...

National Academy of Sciences2013

Searching the coding region for microRNA targets

Jiri Vanicek, Ray Marcel Marin Florez, Miroslav Sulc

Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for ...

2013

High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum

Stewart Cole, Claudia Sala, Swapna Uplekar

The transcriptional regulator GlxR has been characterized as a global hub within the gene-regulatory network of Corynebacterium glutamicum. Chromatin immunoprecipitation with a specific anti-GlxR antibody and subsequent high-throughput sequencing (ChIP-seq ...

Soc General Microbiology2013

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

Slavica Dimitrieva Janeva

Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous ...

EPFL2013

Real-Time mRNA Measurement during an

Sebastian Maerkl, Henrike Marie Niederholtmeyer

In vitro transcription and translation reactions have become popular for a bottom-up approach to synthetic biology. Concentrations of the mRNA intermediate are rarely determined, although knowledge of synthesis and degradation rates could facilitate ration ...

Amer Chemical Soc2012

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

Ray Marcel Marin Florez

MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...

EPFL2012

Epigenetic Modification of the FMR1 Gene in Fragile X Syndrome Is Associated with Differential Response to the mGluR5 Antagonist AFQ056

Nouchine Hadjikhani, Fei Chen

Fragile X syndrome (FXS) is an X-linked condition associated with intellectual disability and behavioral problems. It is caused by expansion of a CGG repeat in the 5' untranslated region of the fragile X mental retardation 1 (FMR1) gene. This mutation is a ...

2011

Unique Cell-Type-Specific Distributions and Functions of Brain MicroRNAs

Ana Jovicic

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression. The first miRNA was discovered less than 20 years ago in the context of studying Caenorabditis elegans development. The discovery of the second miR ...

EPFL2011

A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing

Didier Trono, Philipp Bucher, Jacques Rougemont, Giovanna Ambrosini, Nadine Fournier, Adamantia Kapopoulou, Anna Claire Groner, Annamaria Kauzlaric

BACKGROUND: KRAB-ZFPs (Kruppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors respo ...

BioMed Central2011

Alterations of the 5 ' Untranslated Region of SLC16A12 Lead to Age-Related Cataract

PURPOSE. Knowledge of genetic factors predisposing to age-related cataract is very limited. The aim of this study was to identify DNA sequences that either lead to or predispose for this disease. ...

2010

KAP1 controls endogenous retroviruses in embryonic stem cells

Didier Trono, Jacques Rougemont, Daniel Constam, Sonia Verp, Séverine Reynard, Hillary Layard-Liesching

More than forty per cent of the mammalian genome is derived from retroelements, of which about one-quarter are endogenous retroviruses (ERVs). Some are still active, notably in mice the highly polymorphic early transposon (ETn)/MusD and intracisternal A-ty ...

Nature Publishing Group2010