scholarly journals DNA Replication Timing Enters the Single-Cell Era

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 221 ◽  
Author(s):  
Ichiro Hiratani ◽  
Saori Takahashi
Keyword(s):  
Dna Replication ◽  
Single Cell ◽  
Cell Population ◽  
Mammalian Cells ◽  
Current Knowledge ◽  
Three Dimensional ◽  
Replication Timing ◽  
3D Genome ◽  
Population Analyses ◽  
Dna Replication Timing

In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome regulation at various levels and a variety of studies have been carried out over the years. However, DNA replication timing studies traditionally required at least tens of thousands of cells, and it was unclear whether the replication domains detected by cell population analyses were preserved at the single-cell level. Recently, single-cell DNA replication profiling methods became available, which revealed that the Mb-sized replication domains detected by cell population analyses were actually well preserved in individual cells. In this article, we provide a brief overview of our current knowledge on DNA replication timing regulation in mammals based on cell population studies, outline the findings from single-cell DNA replication profiling, and discuss future directions and challenges.

scholarly journals Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 196 ◽  
Author(s):  
Phoebe Oldach ◽  
Conrad A. Nieduszynski
Keyword(s):  
Dna Replication ◽  
Genome Organization ◽  
Mammalian Cells ◽  
Replication Timing ◽  
S Phase ◽  
Genome Architecture ◽  
3D Genome ◽  
Synchronized Cells ◽  
Dna Replication Timing ◽  
Phase Entry

3D genome organization is strongly predictive of DNA replication timing in mammalian cells. This work tested the extent to which loop-based genome architecture acts as a regulatory unit of replication timing by using an auxin-inducible system for acute cohesin ablation. Cohesin ablation in a population of cells in asynchronous culture was shown not to disrupt patterns of replication timing as assayed by replication sequencing (RepliSeq) or BrdU-focus microscopy. Furthermore, cohesin ablation prior to S phase entry in synchronized cells was similarly shown to not impact replication timing patterns. These results suggest that cohesin-mediated genome architecture is not required for the execution of replication timing patterns in S phase, nor for the establishment of replication timing domains in G1.

scholarly journals Cohesin-mediated genome architecture does not define DNA replication timing domains

2019 ◽  
Author(s):  
Phoebe Oldach ◽  
Conrad A Nieduszynski
Keyword(s):  
Dna Replication ◽  
Genome Organization ◽  
Mammalian Cells ◽  
Replication Timing ◽  
S Phase ◽  
Genome Architecture ◽  
3D Genome ◽  
Synchronized Cells ◽  
Dna Replication Timing ◽  
Phase Entry

3D genome organization is strongly predictive of DNA replication timing in mammalian cells. This work tested the extent to which loop-based genome architecture acts as a regulatory unit of replication timing by using an auxin-inducible system for acute cohesin ablation. Cohesin ablation in a population of cells in asynchronous culture was shown not to disrupt patterns of replication timing as assayed by replication sequencing (RepliSeq) or BrdU-focus microscopy. Furthermore, cohesin ablation prior to S phase entry in synchronized cells was similarly shown to not impact replication timing patterns. These results suggest that cohesin-mediated genome architecture is not required for the execution of replication timing patterns in S phase, nor for the establishment of replication timing domains in G1.

Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing

2020 ◽  
Vol 15 (12) ◽  
pp. 4058-4100
Author(s):  
Hisashi Miura ◽  
Saori Takahashi ◽  
Takahiro Shibata ◽  
Koji Nagao ◽  
Chikashi Obuse ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Cell ◽  
Mammalian Cells ◽  
Replication Timing ◽  
Genome Wide

Control of DNA replication timing in the 3D genome

2019 ◽  
Vol 20 (12) ◽  
pp. 721-737 ◽  
Author(s):  
Claire Marchal ◽  
Jiao Sima ◽  
David M. Gilbert
Keyword(s):  
Dna Replication ◽  
Replication Timing ◽  
3D Genome ◽  
Dna Replication Timing

scholarly journals Genome-wide stability of the DNA replication program in single mammalian cells

2017 ◽  
Author(s):  
Saori Takahashi ◽  
Hisashi Miura ◽  
Takahiro Shibata ◽  
Koji Nagao ◽  
Katsuzumi Okumura ◽  
...  
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Developmental Plasticity ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Small Degree ◽  
3D Genome ◽  
Inactive X Chromosome ◽  
Genome Wide ◽  
Individual Mouse

ABSTRACTHere, we report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

scholarly journals DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

2020 ◽  
Author(s):  
Qian Du ◽  
Grady C. Smith ◽  
Phuc Loi Luu ◽  
James M. Ferguson ◽  
Nicola J. Armstrong ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Replication ◽  
Replication Timing ◽  
Genome Architecture ◽  
Genome Organisation ◽  
Dna Hypomethylation ◽  
3D Genome ◽  
Timing Precision ◽  
The Impact ◽  
Dna Replication Timing

AbstractDNA replication timing and three-dimensional (3D) genome organisation occur across large domains associated with distinct epigenome patterns to functionally compartmentalise genome regulation. However, it is still unclear if alternations in the epigenome, in particular cancer-related DNA hypomethylation, can directly result in alterations to cancer higher order genome architecture. Here, we use Hi-C and single cell Repli-Seq, in the colorectal cancer DNMT1 and DNMT3B DNA methyltransferases double knockout model, to determine the impact of DNA hypomethylation on replication timing and 3D genome organisation. First, we find that the hypomethylated cells show a striking loss of replication timing precision with gain of cell-to-cell replication timing heterogeneity and loss of 3D genome compartmentalisation. Second, hypomethylated regions that undergo a large change in replication timing also show loss of allelic replication timing, including at cancer-related genes. Finally, we observe the formation of broad ectopic H3K4me3-H3K9me3 domains across hypomethylated regions where late replication is maintained, that potentially prevent aberrant transcription and loss of genome organisation after DNA demethylation. Together, our results highlight a previously underappreciated role for DNA methylation in maintenance of 3D genome architecture.

scholarly journals DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

Cell Reports ◽  
2021 ◽  
Vol 36 (12) ◽  
pp. 109722
Author(s):  
Qian Du ◽  
Grady C. Smith ◽  
Phuc Loi Luu ◽  
James M. Ferguson ◽  
Nicola J. Armstrong ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Replication ◽  
Genome Organization ◽  
Replication Timing ◽  
3D Genome ◽  
Timing Precision ◽  
Dna Replication Timing
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