Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Methods for mapping 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

Cohesin and CTCF control the dynamics of chromosome folding

P Mach, PI Kos, Y Zhan, J Cramard, S Gaudin… - Nature …, 2022 - nature.com
In mammals, interactions between sequences within topologically associating domains
enable control of gene expression across large genomic distances. Yet it is unknown how …

Nonlinear control of transcription through enhancer–promoter interactions

J Zuin, G Roth, Y Zhan, J Cramard, J Redolfi… - Nature, 2022 - nature.com
Chromosome structure in mammals is thought to regulate transcription by modulating three-
dimensional interactions between enhancers and promoters, notably through CTCF …

Enhancer–promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

S Chakraborty, N Kopitchinski, Z Zuo, A Eraso… - Nature …, 2023 - nature.com
How enhancers activate their distal target promoters remains incompletely understood. Here
we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions …

The relationship between genome structure and function

AM Oudelaar, DR Higgs - Nature Reviews Genetics, 2021 - nature.com
Precise patterns of gene expression in metazoans are controlled by three classes of
regulatory elements: promoters, enhancers and boundary elements. During differentiation …

Computational methods for analysing multiscale 3D genome organization

Y Zhang, L Boninsegna, M Yang, T Misteli… - Nature Reviews …, 2024 - nature.com
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

CTCF shapes chromatin structure and gene expression in health and disease

B Dehingia, M Milewska, M Janowski, A Pękowska - EMBO reports, 2022 - embopress.org
CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional
regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations …

[HTML][HTML] Chromosome conformation capture and beyond: toward an integrative view of chromosome structure and function

RP McCord, N Kaplan, L Giorgetti - Molecular cell, 2020 - cell.com
Rapidly developing technologies have recently fueled an exciting era of discovery in the
field of chromosome structure and nuclear organization. In addition to chromosome …

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

NJ Rinzema, K Sofiadis, SJD Tjalsma… - Nature Structural & …, 2022 - nature.com
Developmental gene expression is often controlled by distal regulatory DNA elements called
enhancers. Distant enhancer action is restricted to structural chromosomal domains that are …