TADs: Dynamic structures to create stable regulatory functions
JA da Costa-Nunes, D Noordermeer - Current Opinion in Structural Biology, 2023 - Elsevier
Mammalian chromosomes are organized at different length scales within the cell nucleus.
Topologically Associating Domains (TADs) are structural units of 3D genome organization …
Topologically Associating Domains (TADs) are structural units of 3D genome organization …
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments
Although enhancers are central regulators of mammalian gene expression, the mechanisms
underlying enhancer–promoter (EP) interactions remain unclear. Chromosome …
underlying enhancer–promoter (EP) interactions remain unclear. Chromosome …
[HTML][HTML] Topology regulatory elements: From shaping genome architecture to gene regulation
The importance of 3D genome topology in the control of gene expression is becoming
increasingly apparent, while regulatory mechanisms remain incompletely understood …
increasingly apparent, while regulatory mechanisms remain incompletely understood …
[HTML][HTML] Topologically associating domain boundaries are required for normal genome function
Topologically associating domain (TAD) boundaries partition the genome into distinct
regulatory territories. Anecdotal evidence suggests that their disruption may interfere with …
regulatory territories. Anecdotal evidence suggests that their disruption may interfere with …
Loop stacking organizes genome folding from TADs to chromosomes
Although population-level analyses revealed significant roles for CTCF and cohesin in
mammalian genome organization, their contributions at the single-cell level remain …
mammalian genome organization, their contributions at the single-cell level remain …
[HTML][HTML] Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries
Abstract Topologically Associating Domains (TADs) separate vertebrate genomes into
insulated regulatory neighborhoods that focus genome-associated processes. TADs are …
insulated regulatory neighborhoods that focus genome-associated processes. TADs are …
Increased enhancer–promoter interactions during developmental enhancer activation in mammals
Remote enhancers are thought to interact with their target promoters via physical proximity,
yet the importance of this proximity for enhancer function remains unclear. Here we …
yet the importance of this proximity for enhancer function remains unclear. Here we …
Modeling epigenetic lesions that cause gliomas
Epigenetic lesions that disrupt regulatory elements represent potential cancer drivers.
However, we lack experimental models for validating their tumorigenic impact. Here, we …
However, we lack experimental models for validating their tumorigenic impact. Here, we …
[HTML][HTML] Enhancer–promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation
T Pollex, A Rabinowitz, MC Gambetta… - Nature Genetics, 2024 - nature.com
To regulate expression, enhancers must come in proximity to their target gene. However, the
relationship between the timing of enhancer–promoter (E–P) proximity and activity remains …
relationship between the timing of enhancer–promoter (E–P) proximity and activity remains …
[HTML][HTML] Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
The inability to scalably and precisely measure the activity of developmental cis-regulatory
elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a …
elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a …