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

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.

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Faculty Opinions recommendation of Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727380810.793535287 ◽

2017 ◽

Author(s):

Catherine Fox

Keyword(s):

Dna Replication ◽

Spatial Organization ◽

Replication Timing ◽

Dna Replication Timing

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Faculty Opinions recommendation of Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727545410.793549651 ◽

2018 ◽

Author(s):

Domenico Maiorano

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Dna Replication ◽

Lymphoblastic Leukemia ◽

Replication Timing ◽

Patient Specific ◽

Dna Replication Timing ◽

Human Acute Lymphoblastic Leukemia

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

Bioinformatics ◽

10.1093/bioinformatics/btab166 ◽

2021 ◽

Cited By ~ 1

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

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

Cell Reports ◽

10.1016/j.celrep.2014.03.010 ◽

2014 ◽

Vol 7 (1) ◽

pp. 62-69 ◽

Cited By ~ 102

Author(s):

Stefano Mattarocci ◽

Maksym Shyian ◽

Laure Lemmens ◽

Pascal Damay ◽

Dogus Murat Altintas ◽

...

Keyword(s):

Dna Replication ◽

Replication Timing ◽

Dna Replication Timing

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

The Plant Cell ◽

10.1105/tpc.17.00037 ◽

2017 ◽

Vol 29 (9) ◽

pp. 2126-2149 ◽

Cited By ~ 11

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

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Control of DNA replication timing in the 3D genome

Nature Reviews Molecular Cell Biology ◽

10.1038/s41580-019-0162-y ◽

2019 ◽

Vol 20 (12) ◽

pp. 721-737 ◽

Cited By ~ 48

Author(s):

Claire Marchal ◽

Jiao Sima ◽

David M. Gilbert

Keyword(s):

Dna Replication ◽

Replication Timing ◽

3D Genome ◽

Dna Replication Timing

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DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes

Nature Biotechnology ◽

10.1038/nbt.2030 ◽

2011 ◽

Vol 29 (12) ◽

pp. 1103-1108 ◽

Cited By ~ 113

Author(s):

Subhajyoti De ◽

Franziska Michor

Keyword(s):

Dna Replication ◽

Long Range ◽

Replication Timing ◽

Dna Interactions ◽

Cancer Genomes ◽

Dna Replication Timing

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Abstract 5150: What is in control of DNA replication timing.

10.1158/1538-7445.am2013-5150 ◽

2013 ◽

Author(s):

Yevgeniy Gindin ◽

Paul S. Meltzer ◽

Sven Bilke

Keyword(s):

Dna Replication ◽

Replication Timing ◽

Dna Replication Timing

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Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa045 ◽

2020 ◽

Vol 2 (2) ◽

Cited By ~ 1

Author(s):

Djihad Hadjadj ◽

Thomas Denecker ◽

Eva Guérin ◽

Su-Jung Kim ◽

Fabien Fauchereau ◽

...

Keyword(s):

Dna Replication ◽

Cell Fate ◽

Web Application ◽

Timing Analysis ◽

Mutant Cell ◽

Replication Timing ◽

Experimental Conditions ◽

Replication Process ◽

Time Required ◽

Dna Replication Timing

Abstract DNA replication must be faithful and follow a well-defined spatiotemporal program closely linked to transcriptional activity, epigenomic marks, intranuclear structures, mutation rate and cell fate determination. Among the readouts of the spatiotemporal program of DNA replication, replication timing analyses require not only complex and time-consuming experimental procedures, but also skills in bioinformatics. We developed a dedicated Shiny interactive web application, the START-R (Simple Tool for the Analysis of the Replication Timing based on R) suite, which analyzes DNA replication timing in a given organism with high-throughput data. It reduces the time required for generating and analyzing simultaneously data from several samples. It automatically detects different types of timing regions and identifies significant differences between two experimental conditions in ∼15 min. In conclusion, START-R suite allows quick, efficient and easier analyses of DNA replication timing for all organisms. This novel approach can be used by every biologist. It is now simpler to use this method in order to understand, for example, whether ‘a favorite gene or protein’ has an impact on replication process or, indirectly, on genomic organization (as Hi-C experiments), by comparing the replication timing profiles between wild-type and mutant cell lines.

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