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 …

Nuclear compartments: an incomplete primer to nuclear compartments, bodies, and genome organization relative to nuclear architecture

AS Belmont - Cold Spring Harbor perspectives in biology, 2022 - cshperspectives.cshlp.org
This work reviews nuclear compartments, defined broadly to include distinct nuclear
structures, bodies, and chromosome domains. It first summarizes original cytological …

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Management Group Liefer Laura A. 51 Wetterstrand … - nature, 2007 - nature.com
We report the generation and analysis of functional data from multiple, diverse experiments
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …

Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes

A Helmrich, M Ballarino, L Tora - Molecular cell, 2011 - cell.com
We show that the time required to transcribe human genes larger than 800 kb spans more
than one complete cell cycle, while their transcription speed equals that of smaller genes …

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

M Weber, JJ Davies, D Wittig, EJ Oakeley, M Haase… - Nature …, 2005 - nature.com
Cytosine methylation is required for mammalian development and is often perturbed in
human cancer. To determine how this epigenetic modification is distributed in the genomes …

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

E Besnard, A Babled, L Lapasset, O Milhavet… - Nature structural & …, 2012 - nature.com
DNA replication is highly regulated, ensuring faithful inheritance of genetic information
through each cell cycle. In metazoans, this process is initiated at many thousands of DNA …

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

RS Hansen, S Thomas, R Sandstrom… - Proceedings of the …, 2010 - National Acad Sciences
Faithful transmission of genetic material to daughter cells involves a characteristic temporal
order of DNA replication, which may play a significant role in the inheritance of epigenetic …

Eukaryotic chromosome DNA replication: where, when, and how?

H Masai, S Matsumoto, Z You… - Annual review of …, 2010 - annualreviews.org
DNA replication is central to cell proliferation. Studies in the past six decades since the
proposal of a semiconservative mode of DNA replication have confirmed the high degree of …

Eukaryotic DNA replication origins: many choices for appropriate answers

M Méchali - Nature reviews Molecular cell biology, 2010 - nature.com
At each cell division in humans, 30,000–50,000 DNA replication origins are activated, and it
remains unclear how they are selected and recognized by replication factors. DNA …

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

C Cayrou, P Coulombe, A Vigneron… - Genome …, 2011 - genome.cshlp.org
In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle.
Their genomic organization and their genetic nature remain elusive. Here, we characterized …