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 …

Epigenetic differences between naïve and primed pluripotent stem cells

S Takahashi, S Kobayashi, I Hiratani - Cellular and Molecular Life …, 2018 - Springer
It has been 8 years since the concept of naïve and primed pluripotent stem cell states was
first proposed. Both are states of pluripotency, but exhibit slightly different properties. The …

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 …

Emergence of replication timing during early mammalian development

T Nakatani, T Schauer, L Altamirano-Pacheco… - Nature, 2024 - nature.com
DNA replication enables genetic inheritance across the kingdoms of life. Replication occurs
with a defined temporal order known as the replication timing (RT) programme, leading to …

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

F Ay, TL Bailey, WS Noble - Genome research, 2014 - genome.cshlp.org
Our current understanding of how DNA is packed in the nucleus is most accurate at the fine
scale of individual nucleosomes and at the large scale of chromosome territories. However …

A comparative encyclopedia of DNA elements in the mouse genome

F Yue, Y Cheng, A Breschi, J Vierstra, W Wu, T Ryba… - Nature, 2014 - nature.com
The laboratory mouse shares the majority of its protein-coding genes with humans, making it
the premier model organism in biomedical research, yet the two mammals differ in …

Identifying cis elements for spatiotemporal control of mammalian DNA replication

J Sima, A Chakraborty, V Dileep, M Michalski, KN Klein… - Cell, 2019 - cell.com
The temporal order of DNA replication (replication timing [RT]) is highly coupled with
genome architecture, but cis-elements regulating either remain elusive. We created a series …

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
This protocol is an extension to: Nat. Protoc. 6, 870–895 (2014); doi: 10.1038/nprot.
2011.328; published online 02 June 2011 Cycling cells duplicate their DNA content during S …

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

JC Rivera-Mulia, Q Buckley, T Sasaki… - Genome …, 2015 - genome.cshlp.org
Duplication of the genome in mammalian cells occurs in a defined temporal order referred to
as its replication-timing (RT) program. RT changes dynamically during development …

[HTML][HTML] DNA replication origins—where do we begin?

MN Prioleau, DM MacAlpine - Genes & development, 2016 - genesdev.cshlp.org
For more than three decades, investigators have sought to identify the precise locations
where DNA replication initiates in mammalian genomes. The development of molecular and …