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 …

[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 …

Mammalian DNA replication timing

AE Vouzas, DM Gilbert - Cold Spring Harbor …, 2021 - cshperspectives.cshlp.org
Immediately following the discovery of the structure of DNA and the semi-conservative
replication of the parental DNA sequence into two new DNA strands, it became apparent …

[HTML][HTML] Three-dimensional nuclear organisation and the DNA replication timing program

N Chen, SCB Buonomo - Current opinion in structural biology, 2023 - Elsevier
In eukaryotic cells, genome duplication is temporally organised according to a program
referred to as the replication-timing (RT) program. The RT of individual genomic domains …

Replication timing and transcriptional control: beyond cause and effect—part IV

AE Vouzas, DM Gilbert - Current opinion in genetics & development, 2023 - Elsevier
Decades of work on the spatiotemporal organization of mammalian DNA replication timing
(RT) continues to unveil novel correlations with aspects of transcription and chromatin …

[HTML][HTML] Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction

S Gnan, IM Flyamer, KN Klein, E Castelli… - Nature …, 2021 - nature.com
Three-dimensional genome organisation and replication timing are known to be correlated,
however, it remains unknown whether nuclear architecture overall plays an instructive role …

[HTML][HTML] Computational stem cell biology: open questions and guiding principles

P Cahan, D Cacchiarelli, SJ Dunn, M Hemberg… - Cell Stem Cell, 2021 - cell.com
Computational biology is enabling an explosive growth in our understanding of stem cells
and our ability to use them for disease modeling, regenerative medicine, and drug …

Quantifying chromosome structural reorganizations during differentiation, reprogramming, and transdifferentiation

X Chu, J Wang - Physical Review Letters, 2022 - APS
We developed a nonequilibrium model to study chromosome structural reorganizations
within a simplified cell developmental system. From the chromosome structural perspective …

[HTML][HTML] A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships

R Lohia, N Fox, J Gillis - Genome biology, 2022 - Springer
Background Chromatin contacts are essential for gene-expression regulation; however,
obtaining a high-resolution genome-wide chromatin contact map is still prohibitively …

Chromosome compartmentalization: causes, changes, consequences, and conundrums

H Li, C Playter, P Das, RP McCord - Trends in Cell Biology, 2024 - cell.com
The spatial segregation of the genome into compartments is a major feature of 3D genome
organization. New data on mammalian chromosome organization across different conditions …