Publications associées à Gene structure

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

EPFL2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero, Mohan Vamsi Nallapareddy

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Daniele Tavernari, Giovanni Ciriello

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Wiley2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

A systematic CRISPR approach to understanding the role of Drosophila antimicrobial peptides in immunity in vivo

Mark Austin Hanson

Antimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading microbes. These short immune effectors are conserved in plants, animals, and fungi. Early work showed that AMPs killed bacteria in generalist fashions in vitro: i.e. AMPs that ...

EPFL2022

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

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Philipp Bucher, René Dreos

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

2021

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Giovanna Ambrosini, Philipp Bucher, Romain Fernand Pietro Groux, René Dreos, Patrick Meylan

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism

Johan Auwerx, Martin Rainer Wohlwend

Obesity and type 2 diabetes (T2D) are metabolic disorders influenced by lifestyle and genetic factors that are characterized by insulin resistance in skeletal muscle, a prominent site of glucose disposal. Numerous genetic variants have been associated with ...

Nature Research2020

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

High-throughput microfluidic platforms for characterizing and engineering cell-free gene regulatory circuits

Zoe Newell Swank

Cell-free systems have emerged as a versatile platform for constructing complex biological systems from the bottom-up. In particular, they enable the rapid engineering and characterization of gene regulatory networks, a critical cellular subsystem that all ...

EPFL2020

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Bart Deplancke, Vincent Roland Julien Gardeux, Maroun Bou Sleiman, Virginie Sandra Braman, Riccardo Dainese, Maria Litovchenko, Michael Vincent Frochaux, Dani Osman, Brian Dennis Hollis, Tommaso Andreani

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understan ...

2020

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

Suliana Manley, Elisa Oricchio, Kyle Michael Douglass, Natalya Katanayeva, Daniele Tavernari, Elena Battistello, Stephanie Jocelyne Sungalee, Maria Christine Donaldson, Timo Henry René Rey, Giovanni Ciriello, Marco Mina

Chromatin is organized into topologically associating domains (TADs) enriched in distinct histone marks. In cancer, gain-of-function mutations in the gene encoding the enhancer of zeste homolog 2 protein (EZH2) lead to a genome-wide increase in histone-3 L ...

2019

Multilevel regulation of the glass locus during Drosophila eye development

Bart Deplancke, Michael Vincent Frochaux, Abhishek Kumar Mishra

Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to contr ...

2019

Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells

Patrick Andreas Gonschorek

Optogenetic switches are emerging molecular tools for studying cellular processes as they offer higher spatiotemporal and quantitative precision than classical, chemical-based switches. Light-controllable gene expression systems designed to upregulate prot ...

Nature Research2018

Bicistronic aav vector for rna interference in als

Bernard Schneider, Julianne Bobela, Cylia Cloé Rochat

The present invention relates to a bicistronic expression vector for silencing a gene specifically in astrocytes and neurons, comprising two expression cassettes comprising a first and a second silencer sequence, respectively, wherein the expression of sai ...

2017

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Didier Trono, Giovanna Ambrosini, Bart Deplancke, Philipp Bucher, Romain Fernand Pietro Groux, Riccardo Dainese, Daniel Alpern, Michaël Imbeault, Alina Isakova, Pernille Yde Rainer

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

Giovanna Ambrosini, Philipp Bucher, René Dreos

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription ...

Public Library Science2016

Unraveling the KRAB/KAP1 control of transposable elements in pluripotent and somatic cells

Gabriela Ecco

Transposable elements (TEs) are DNA sequences able to change position in the genome, and represent more than 40% of mammalian genetic material. TEs can have positive or detrimental effects on the host, being both important motors of evolution and genomic t ...

EPFL2016