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

2011 ◽  
Vol 29 (12) ◽  
pp. 1103-1108 ◽  
Author(s):  
Subhajyoti De ◽  
Franziska Michor
Keyword(s):  
Dna Replication ◽  
Long Range ◽  
Replication Timing ◽  
Dna Interactions ◽  
Cancer Genomes ◽  
Dna Replication Timing

scholarly journals Replication timing shapes the cancer epigenome and the nature of chromosomal rearrangements

2018 ◽  
Author(s):  
Qian Du ◽  
Saul A. Bert ◽  
Nicola J. Armstrong ◽  
C. Elizabeth Caldon ◽  
Jenny Z. Song ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Prostate Cancer ◽  
Long Range ◽  
Chromosomal Rearrangements ◽  
Replication Timing ◽  
List Type ◽  
Late Replication ◽  
Facultative Heterochromatin ◽  
Cancer Genomes ◽  
Dna Replication Timing

HighlightsReplication timing alterations are conserved in cancers of different cell originsLong-range epigenetic deregulation in cancer involves altered replication timingCancer late-replicating loci are hypomethylated and acquire facultative heterochromatinReplication timing status potentiates cis and trans chromosomal rearrangementsSummaryReplication timing is known to facilitate the establishment of epigenome, however, the intimate connection between DNA replication timing and changes to the genome and epigenome in cancer remain uncharted. Here, we perform Repli-Seq and integrated epigenome analysis and show that early-replicating loci are predisposed to hypermethylation and late-replicating loci to hypomethylation, enrichment of H3K27me3 and concomitant loss of H3K9me3. We find that altered replication timing domains correspond to long-range epigenetically deregulated regions in prostate cancer, and a subset of these domains are remarkably conserved across cancers from different tissue origins. Analyses of 214 prostate and 35 breast cancer genomes reveal that late-replicating DNA is prone to cis and early-replicating DNA to trans chromosomal rearrangements. We propose that differences in epigenetic deregulation related to spatial and temporal positioning between early and late replication potentiate the landscape of chromosomal rearrangements in cancer.

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 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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