Organization and function of the 3D genome

B Bonev, G Cavalli - Nature Reviews Genetics, 2016 - nature.com
Understanding how chromatin is organized within the nucleus and how this 3D architecture
influences gene regulation, cell fate decisions and evolution are major questions in cell …

Principles of genome folding into topologically associating domains

Q Szabo, F Bantignies, G Cavalli - Science advances, 2019 - science.org
Understanding the mechanisms that underlie chromosome folding within cell nuclei is
essential to determine the relationship between genome structure and function. The recent …

Transcriptional coupling of distant regulatory genes in living embryos

M Levo, J Raimundo, XY Bing, Z Sisco, PJ Batut… - Nature, 2022 - nature.com
The prevailing view of metazoan gene regulation is that individual genes are independently
regulated by their own dedicated sets of transcriptional enhancers. Past studies have …

Visualizing DNA folding and RNA in embryos at single-cell resolution

LJ Mateo, SE Murphy, A Hafner, IS Cinquini, CA Walker… - Nature, 2019 - nature.com
The establishment of cell types during development requires precise interactions between
genes and distal regulatory sequences. We have a limited understanding of how these …

High-resolution TADs reveal DNA sequences underlying genome organization in flies

F Ramírez, V Bhardwaj, L Arrigoni, KC Lam… - Nature …, 2018 - nature.com
Despite an abundance of new studies about topologically associating domains (TADs), the
role of genetic information in TAD formation is still not fully understood. Here we use our …

Ever-changing landscapes: transcriptional enhancers in development and evolution

HK Long, SL Prescott, J Wysocka - Cell, 2016 - cell.com
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating
spatiotemporally precise gene-expression programs during development. Consequently …

[HTML][HTML] Formation of chromosomal domains by loop extrusion

G Fudenberg, M Imakaev, C Lu, A Goloborodko… - Cell reports, 2016 - cell.com
Topologically associating domains (TADs) are fundamental structural and functional
building blocks of human interphase chromosomes, yet the mechanisms of TAD formation …

Chromatin domains: the unit of chromosome organization

JR Dixon, DU Gorkin, B Ren - Molecular cell, 2016 - cell.com
How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains
unanswered today. Early biochemical and microscopic studies revealed the existence of …

[HTML][HTML] Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions

DG Lupiáñez, K Kraft, V Heinrich, P Krawitz, F Brancati… - Cell, 2015 - cell.com
Mammalian genomes are organized into megabase-scale topologically associated domains
(TADs). We demonstrate that disruption of TADs can rewire long-range regulatory …

The role of transcription in shaping the spatial organization of the genome

B van Steensel, EEM Furlong - Nature reviews Molecular cell biology, 2019 - nature.com
The spatial organization of the genome into compartments and topologically associated
domains can have an important role in the regulation of gene expression. But could gene …