Publication

Chromatin organization in red triangles

Publications associées (32)

Dynamic protein-chromatin interactions in heterochromatin and during the DNA damage response on the single molecule level

Dynamic regulation of chromatin, a structure consisting of DNA and histone proteins, is mediated through histone post-translational modifications (PTMs) and effector proteins. HP1a and PRC2 are recruited to repressive PTMs (H3K9me3, H3K27me3) and enable he ...

EPFL2018

Deciphering the chromatin binding mechanisms of human HP1 variants at the single-molecule level

Louise Catherine Bryan

In eukaryotic cells, DNA is tightly packed in the form chromatin. The basic structure of chromatin is a nucleosome composed of 147 bp DNA wrapped around eight histone proteins; two copies of H2A, H2B, H3 and H4. These histone proteins are decorated with pa ...

EPFL2018

Comparison of computational methods for the identification of topologically associating domains

Marie-Pierre Zufferey, Elisa Oricchio, Giovanni Ciriello, Daniele Tavernari

BackgroundChromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiati ...

2018

Rhythmic and clock-dependent chromatin loops regulate circadian gene expression

Jérôme Mermet

In mammals the circadian clock drives daily behavioural and physiological changes that resonate with environmental cues, which can be observed, for example, in the intricate timing of rest during the night and activity during the day in humans. The circadi ...

EPFL2017

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

Vassily Hatzimanikatis, Louise Catherine Bryan, Georg Fantner, Pascal Damian Odermatt, Oliver Hantschel, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Sinan Kilic, Carolin Christine Lechner, Andreas Linus Bachmann, Daniel Robert Weilandt

Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is c ...

Oxford University Press (OUP)2017

Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation

Paul Joseph Dyson, Benjamin Samuel Murray, Tina Riedel

The 'acidic patch' is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous ...

Nature Research2017

Large scale genomic reorganization of topological domains at the HoxD locus

Denis Duboule, Daniël Noordermeer, Marion Leleu, Pierre Raymond Fabre, Leonardo Beccari, Benjamin Howard Mormann, Lucille Delisle

BACKGROUND: The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD g ...

2017

Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S-pombe

Yannis Burnier, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti

The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the vali ...

Oxford University Press (OUP)2017

Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

Denis Duboule, Fabrice Daniel Darbellay

Hox gene clusters of jaw vertebrates display a tight genomic organization, which has no equivalent in any other bilateria genomes sequenced thus far. It was previously argued that such a topological consolidation toward a condensed, metagenic structure was ...

Elsevier Academic Press Inc2016

Chromatin organization, transcription factor dynamics and gene expression in higher eukaryotes with superresolution imaging and single molecule tracking

Aleksandr Benke

Gene expression is dynamic and heterogeneous across all cell types. It serves several fundamental functions such as adaptation for changing environment and developing tissue specific phenotype and functionality during development and in adult organism. Con ...

EPFL2015

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

Denis Duboule, Suliana Manley, Aleksandr Benke, Pierre Raymond Fabre

Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around th ...

2015

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

Yannis Burnier, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide in ...

Oxford University Press2014