Publications related to Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Related publications (34)

CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length

Denis Duboule, Fabrice Daniel Darbellay, Lucille Delisle, Alexandre Gauthier Aurèle Mayran, Hocine Rekaik, Célia Corinne Renée Bochaton, Pierre Osteil

Mammalian tail length is controlled by several genetic determinants, among which are Hox13 genes, whose function is to terminate the body axis. Accordingly, the precise timing in the transcriptional activation of these genes may impact upon body length. Un ...

National Academy of Sciences2024

Chromosome-level organization of the regulatory genome in the Drosophila nervous system

Nicolas Jean Philippe Guex, Christian Iseli, Marion Leleu, Brian Donal McCabe, Julien Dorier, Rebecca Carolyn Smith

Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains ...

2023

Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex

Werner Alfons Hilda Van Geit

The brain consists of many cell classes yet in vivo electrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modal in vitro properties f ...

Nature Research2023

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

In vivo and ex vivo range of motion in the fire salamander Salamandra salamandra

Enrico Alexander Eberhard

Joint range of motion (RoM) analyses are fundamental to our understanding of how an animal moves throughout its ecosystem. Recent technological advances allow for more detailed quantification of this RoM (e.g. including interaction of degrees of freedom) b ...

2022

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

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

Ivan Istomin

Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechno ...

EPFL2020

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern, Antonio Carlos Alves Meireles Filho, Gerard Llimos Aubach

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molec ...

National Academy of Sciences2020

Computational study of transcription factor binding sites

Romain Fernand Pietro Groux

Any living organism contains a whole set of instructions encoded as genes on the DNA. This set of instructions contains all the necessary information that the organism will ever need, from its development to a mature individual to environment specific resp ...

EPFL2020

Transcription Factors and DNA Play Hide and Seek

David Michael Suter

Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depen ...

2020

Structural and DNA binding properties of mycobacterial integration host factor mIHF

Rajkumar Singh, Stewart Cole, Giovanni Dietler, David Lyndon Emsley, Luciano Andres Abriata, Aleksandre Japaridze, Jérémie Piton, Nina Theres Odermatt

In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted ...

Elsevier2020

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

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

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

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

Riccardo Dainese

The specific interaction between DNA and proteins constitutes one of the crucial elements in the regulation of gene expression. This thesis focuses on the development and optimization of two microfluidic-based technologies called SMiLE-seq and FloChIP that ...

EPFL2019

Exploring on Protein-DNA interactions

Alexandra Styliani Kalantzi

A variety of DNA-binding proteins organizes the chromosomal DNA and regulates gene transcription, and DNA replication and recombination. In particular, for gene regulation there is a category of DNA-binding proteins, the transcription factors, which can de ...

EPFL2019

Mitotic chromosome binding predicts transcription factor properties in interphase

Mahé Cécile Raccaud

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding affinity. How these properties affect the ability of TFs to occupy their specific binding sites in the genome and modify the epige ...

EPFL2019

Innovative Tools and in vivo Methods for Tuberculosis Drug Discovery and Development

Raphael Christopher Sommer

Worldwide, tuberculosis (TB) is the leading cause of death due to a single infectious agent, claiming 1.6 million human lives and causing >10 million new cases in 2017 alone, mostly in low-income regions. The intracellular pathogen Mycobacterium tuberculos ...

EPFL2019

Mitotic chromosome binding predicts transcription factor properties in interphase

David Michael Suter, Cédric Deluz, Andrea Brigitta Alber, Torgil Elias Friman, Mahé Cécile Raccaud

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The as ...

Nature Research2019

Beyond silence : a functional and evolutionary study of KRAB zinc finger proteins

Pierre-Yves Joseph Laurent Helleboid

Transposable elements (TEs) are genetic units capable of spreading within the genomes of their host. TEs contribute a readily recognizable 45% of the human DNA, reflecting in part their co-option for some as source of protein-coding sequences, for others a ...

EPFL2019

Subsurface ablation of tissue by ultrafast laser

Thomas Jean Victor Marie Lanvin

Laser-induced optical breakdown (LIOB) is a multiphoton process which can be used for selective removal of material. It revolves around the creation of a plasma in the focal volume of a beam, and requires very high peak intensities in the order of the GW.c ...

EPFL2017

Rapid evaluation of bioactive Ti-based surfaces using an in vitro titration method

Paul Bowen, Jacques Lemaître, Weitian Zhao

The prediction of implant behavior in vivo by the use of easy-to-perform in vitro methods is of great interest in biomaterials research. Simulated body fluids (SBFs) have been proposed and widely used to evaluate the bone-bonding ability of implant materia ...

Springer2019