Publication
Opposing chromatin remodelers control transcription initiation frequency and start site selection
Publications associées (42)
Context-dependent enhancer function revealed by targeted inter-TAD relocation
Denis Duboule, Lucille Delisle, Guillaume Andrey, Christopher Chase Bolt, Aurélie Hintermann
Here the authors show that a strong enhancer sequence can be controlled by the chromatin environment provided by a topologically associated domain (TAD) located nearby. An enhancer relocated by homologous recombination takes all the hallmarks of its new ne ...
NATURE PORTFOLIO2022Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance
Sebastian Maerkl, Shiyu Cheng, Ivan Istomin, Maria Lopez Malo, Amir Shahein, Evan James Olson
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 PORTFOLIO2022Computational identification and experimental characterization of preferred downstream positions in human core promoters
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 ...
PUBLIC LIBRARY SCIENCE2021Dynamic Chromatin Invasion and Remodeling by the Transcription Factor Rap1
Pioneer transcription factors (PTF) are a subset of transcription factors with nucleosome-binding properties allowing them to bind specific sequences in condensed chromatin. Although the biological functions of PTFs including target genes and epigenetic ch ...
EPFL2021Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities
Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2021High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites
Binding of mammalian transcription factors (TFs) to regulatory regions is hindered by chromatin compaction and DNA methylation of their binding sites. Nevertheless, pioneer transcription factors (PFs), a distinct class of TFs, have the ability to access nu ...
NATURE RESEARCH2021Computational study of transcription factor binding sites
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 ...
EPFL2020Transcription Factors and DNA Play Hide and Seek
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 ...
2020A complex regulatory landscape involved in the development of mammalian external genitals
Denis Duboule, Lucille Delisle, Christopher Chase Bolt
Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. ...
2020The MIDI Degradation Toolkit: Symbolic Music Augmentation and Correction
In this paper, we introduce the MIDI Degradation Toolkit (MDTK), containing functions which take as input a musical excerpt (a set of notes with pitch, onset time, and duration), and return a ``degraded'' version of that excerpt with some error (or errors) ...
2020