Publications related to Topologically associating domain

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Denis Duboule, Lucille Delisle, Jozsef Zakany, Leonardo Beccari

In this study, Amandio et al. sought to understand the functions of the highly conserved CTCF sites distributed over the Hox gene clusters. The authors produced an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF b ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2021

Induction of a chromatin boundary in vivo upon insertion of a tad border

Denis Duboule, Lucille Delisle, Christopher Chase Bolt, Edgardo Rodriguez Carballo, Marie-Laure Gadolini

Author summary During development, enhancer sequences tightly regulate the spatio-temporal expression of target genes often located hundreds of kilobases away. This complex process is made possible by the folding of chromatin into domains, which are separa ...

PUBLIC LIBRARY SCIENCE2021

Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor

Beat Fierz, Louise Catherine Bryan, Kristina Makasheva

Single-molecule measurements provide detailed mechanistic insights into molecular processes, for example in genome regulation where DNA access is controlled by nucleosomes and the chromatin machinery. However, real-time single-molecule observations of nucl ...

AMER CHEMICAL SOC2021

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

Benjamin Marcel Daniel Rothé

Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins initiates co-transcriptionally and requires the action of the assembly machinery including the Hsp90/R2TP complex, the Rsa1p:Hit1p heterodimer and the Bcd1 protein. We present genetic inte ...

NATURE RESEARCH2021

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

Felix Naef, Jake Yeung, Jérôme Mermet

The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughou ...

2021

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Marion Leleu, Ludovica Vanzan, Flavia Marzetta, Ioannis Xenarios

Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation ...

2020

A 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. ...

2020

Chromatin topology and the timing of enhancer function at the HoxD locus

Denis Duboule, Lucille Delisle, Leonardo Beccari, Edgardo Rodriguez Carballo

The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are e ...

NATL ACAD SCIENCES2020

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Topologically associating domain

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Induction of a chromatin boundary in vivo upon insertion of a tad border

Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

Dynamic Chromatin Invasion and Remodeling by the Transcription Factor Rap1

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

A complex regulatory landscape involved in the development of mammalian external genitals

Computational study of transcription factor binding sites

Chromatin topology and the timing of enhancer function at the HoxD locus

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Computational study of transcription factor binding sites

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

Dynamic Chromatin Invasion and Remodeling by the Transcription Factor Rap1

Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

A complex regulatory landscape involved in the development of mammalian external genitals

Induction of a chromatin boundary in vivo upon insertion of a tad border

Chromatin topology and the timing of enhancer function at the HoxD locus