scholarly journals A chromatin structure‐based model accurately predicts DNA replication timing in human cells

2014 ◽  
Vol 10 (3) ◽  
pp. 722 ◽  
Author(s):  
Yevgeniy Gindin ◽  
Manuel S Valenzuela ◽  
Mirit I Aladjem ◽  
Paul S Meltzer ◽  
Sven Bilke
Keyword(s):  
Dna Replication ◽  
Chromatin Structure ◽  
Replication Timing ◽  
Human Cells ◽  
Dna Replication Timing

scholarly journals Rapid high-resolution measurement of DNA replication timing by droplet digital PCR

2017 ◽  
Author(s):  
Dzmitry G. Batrakou ◽  
Emma D. Heron ◽  
Conrad A. Nieduszynski
Keyword(s):  
Dna Replication ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Replication Timing ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Human Cells ◽  
Genome Replication ◽  
Multiple Loci ◽  
Dna Replication Timing

ABSTRACTGenomes are replicated in a reproducible temporal pattern. Current methods for assaying allele replication timing are time consuming and/or expensive. These include high-throughput sequencing which can be used to measure DNA copy number as a proxy for allele replication timing. Here, we use droplet digital PCR to study DNA replication timing at multiple loci in budding yeast and human cells. We establish that the method has temporal and spatial resolutions comparable to the high-throughput sequencing approaches, while being faster than alternative locus-specific methods. Furthermore, the approach is capable of allele discrimination. We apply this method to determine relative replication timing across timing transition zones in cultured human cells. Finally, multiple samples can be analysed in parallel, allowing us to rapidly screen kinetochore mutants for perturbation to centromere replication timing. Therefore, this approach is well suited to the study of locus-specific replication and the screening of cis- and trans-acting mutants to identify mechanisms that regulate local genome replication timing.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Asymmetrical deposition and modification of histone H3 variants are essential for zygote development

2021 ◽  
Vol 4 (8) ◽  
pp. e202101102
Author(s):  
Machika Kawamura ◽  
Satoshi Funaya ◽  
Kenta Sugie ◽  
Masataka G Suzuki ◽  
Fugaku Aoki
Keyword(s):  
Dna Replication ◽  
Mrna Expression ◽  
Detrimental Effect ◽  
Histone H3 ◽  
Replication Timing ◽  
Male And Female ◽  
Zygote Development ◽  
The One ◽  
Dna Replication Timing ◽  
Incorporation Efficiency

The pericentromeric heterochromatin of one-cell embryos forms a unique, ring-like structure around the nucleolar precursor body, which is absent in somatic cells. Here, we found that the histone H3 variants H3.1 and/or H3.2 (H3.1/H3.2) were localized asymmetrically between the male and female perinucleolar regions of the one-cell embryos; moreover, asymmetrical histone localization influenced DNA replication timing. The nuclear deposition of H3.1/3.2 in one-cell embryos was low relative to other preimplantation stages because of reduced H3.1/3.2 mRNA expression and incorporation efficiency. The forced incorporation of H3.1/3.2 into the pronuclei of one-cell embryos triggered a delay in DNA replication, leading to developmental failure. Methylation of lysine residue 27 (H3K27me3) of the deposited H3.1/3.2 in the paternal perinucleolar region caused this delay in DNA replication. These results suggest that reduced H3.1/3.2 in the paternal perinucleolar region is essential for controlled DNA replication and preimplantation development. The nuclear deposition of H3.1/3.2 is presumably maintained at a low level to avoid the detrimental effect of K27me3 methylation on DNA replication in the paternal perinucleolar region.

scholarly journals High-throughput analysis of DNA replication in single human cells reveals constrained variability in the location and timing of replication initiation

2021 ◽  
Author(s):  
Dashiell J Massey ◽  
Amnon Koren
Keyword(s):  
Dna Replication ◽  
Replication Origin ◽  
Replication Timing ◽  
S Phase ◽  
Human Cells ◽  
Replication Initiation ◽  
High Throughput Analysis ◽  
Timing Variability ◽  
Fixed Set ◽  
Fixed Order

DNA replication occurs throughout the S phase of the cell cycle, initiating from replication origin loci that fire at different times. Debate remains about whether origins are a fixed set of loci used across all cells or a loose agglomeration of potential origins used stochastically in individual cells, and about how consistent their firing time during S phase is across cells. Here, we develop an approach for profiling DNA replication in single human cells and apply it to 2,305 replicating cells spanning the entire S phase. The resolution and scale of the data enabled us to specifically analyze initiation sites and show that these sites have confined locations that are consistently used among individual cells. Further, we find that initiation sites are activated in a similar, albeit not fixed, order across cells. Taken together, our results suggest that replication timing variability is constrained both spatially and temporally, and that the degree of variation is consistent across human cell lines.

scholarly journals Rif1 Controls DNA Replication Timing in Yeast through the PP1 Phosphatase Glc7

Cell Reports ◽  
2014 ◽  
Vol 7 (1) ◽  
pp. 62-69 ◽  
Author(s):  
Stefano Mattarocci ◽  
Maksym Shyian ◽  
Laure Lemmens ◽  
Pascal Damay ◽  
Dogus Murat Altintas ◽  
...  
Keyword(s):  
Dna Replication ◽  
Replication Timing ◽  
Dna Replication Timing

scholarly journals Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

2017 ◽  
Vol 29 (9) ◽  
pp. 2126-2149 ◽  
Author(s):  
Emily E. Wear ◽  
Jawon Song ◽  
Gregory J. Zynda ◽  
Chantal LeBlanc ◽  
Tae-Jin Lee ◽  
...  
Keyword(s):  
Zea Mays ◽  
Dna Replication ◽  
Genomic Analysis ◽  
Replication Timing ◽  
S Phase ◽  
Root Tips ◽  
Dna Replication Timing

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
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