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 …

Looping the genome with SMC complexes

E Kim, R Barth, C Dekker - Annual review of biochemistry, 2023 - annualreviews.org
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily
conserved family of motor proteins that hold sister chromatids together and fold genomes …

Cohesin loss eliminates all loop domains

SSP Rao, SC Huang, BG St Hilaire, JM Engreitz… - Cell, 2017 - cell.com
The human genome folds to create thousands of intervals, called" contact domains," that
exhibit enhanced contact frequency within themselves." Loop domains" form because of …

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

EP Nora, A Goloborodko, AL Valton, JH Gibcus… - Cell, 2017 - cell.com
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly
understood. The transcription factor CTCF is a candidate regulator of chromosomal …

Complex multi-enhancer contacts captured by genome architecture mapping

RA Beagrie, A Scialdone, M Schueler, DCA Kraemer… - Nature, 2017 - nature.com
The organization of the genome in the nucleus and the interactions of genes with their
regulatory elements are key features of transcriptional control and their disruption can cause …

Chromatin architecture reorganization during stem cell differentiation

JR Dixon, I Jung, S Selvaraj, Y Shen… - Nature, 2015 - nature.com
Higher-order chromatin structure is emerging as an important regulator of gene expression.
Although dynamic chromatin structures have been identified in the genome, the full scope of …

Control of DNA replication timing in the 3D genome

C Marchal, J Sima, DM Gilbert - Nature Reviews Molecular Cell Biology, 2019 - nature.com
The 3D organization of mammalian chromatin was described more than 30 years ago by
visualizing sites of DNA synthesis at different times during the S phase of the cell cycle …

Dynamic organization of chromatin domains revealed by super-resolution live-cell imaging

T Nozaki, R Imai, M Tanbo, R Nagashima, S Tamura… - Molecular cell, 2017 - cell.com
The eukaryotic genome is organized within cells as chromatin. For proper information
output, higher-order chromatin structures can be regulated dynamically. How such structures …

Topologically associating domains are stable units of replication-timing regulation

BD Pope, T Ryba, V Dileep, F Yue, W Wu, O Denas… - Nature, 2014 - nature.com
Eukaryotic chromosomes replicate in a temporal order known as the replication-timing
program. In mammals, replication timing is cell-type-specific with at least half the genome …

DNA replication origin activation in space and time

M Fragkos, O Ganier, P Coulombe… - Nature reviews Molecular …, 2015 - nature.com
DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at
thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1–S …