Origins of DNA replication in eukaryotes

Y Hu, B Stillman - Molecular cell, 2023 - cell.com
Errors occurring during DNA replication can result in inaccurate replication, incomplete
replication, or re-replication, resulting in genome instability that can lead to diseases such as …

[HTML][HTML] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

J Dekker, F Alber, S Aufmkolk, BJ Beliveau… - Molecular cell, 2023 - cell.com
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …

Integrated spatial genomics reveals global architecture of single nuclei

Y Takei, J Yun, S Zheng, N Ollikainen, N Pierson… - Nature, 2021 - nature.com
Identifying the relationships between chromosome structures, nuclear bodies, chromatin
states and gene expression is an overarching goal of nuclear-organization studies …

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 …

Biological phase separation: cell biology meets biophysics

T Yoshizawa, RS Nozawa, TZ Jia, T Saio, E Mori - Biophysical reviews, 2020 - Springer
Progress in development of biophysical analytic approaches has recently crossed paths with
macromolecule condensates in cells. These cell condensates, typically termed liquid-like …

Replication timing maintains the global epigenetic state in human cells

KN Klein, PA Zhao, X Lyu, T Sasaki, DA Bartlett… - Science, 2021 - science.org
The temporal order of DNA replication [replication timing (RT)] is correlated with chromatin
modifications and three-dimensional genome architecture; however, causal links have not …

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

PA Zhao, T Sasaki, DM Gilbert - Genome biology, 2020 - Springer
Background DNA replication in mammalian cells occurs in a defined temporal order during
S phase, known as the replication timing (RT) programme. Replication timing is …

Mechanisms and functions of chromosome compartmentalization

EM Hildebrand, J Dekker - Trends in biochemical sciences, 2020 - cell.com
Active and inactive chromatin are spatially separated in the nucleus. In Hi-C data, this is
reflected by the formation of compartments, whose interactions form a characteristic …

Replication dynamics identifies the folding principles of the inactive X chromosome

R Poonperm, S Ichihara, H Miura, A Tanigawa… - Nature Structural & …, 2023 - nature.com
Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome
(Xi). How it is established and what it represents remains obscure. By single-cell DNA …

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

C Marchal, T Sasaki, D Vera, K Wilson, J Sima… - Nature protocols, 2018 - nature.com
Cycling cells duplicate their DNA content during S phase, following a defined program
called replication timing (RT). Early-and late-replicating regions differ in terms of mutation …