High Resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Zhao, Peiyao A.; Sasaki, Takayo; Gilbert, David M.

doi:10.1101/755629

Cited by 29 publications

(68 citation statements)

References 41 publications

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“…CFSs are reported to share a number of structural characteristics: the presence of long genes, AT-rich sequences and late replication timing ( Arlt et al., 2009 ; Fungtammasan et al., 2012 ; Wilson et al., 2015 ). The genomic features of the sites we identified were consistent with these trends, although CFSs do not contain the most guanine cytosine (GC)-poor regions in the genome, the longest genes ( Figures 1 C and 1D), or the latest replicating regions ( Zhao et al., 2020 ) ( Table S1 ). Among the most-fragile locations in our study, 9 of 11 overlapped with genes larger than 0.3 Mb, including FRA3B (FHIT), FRA4F (GRID2, CCSER), 4q32.2 (MARCH1, 0.85 Mb; FSTL5, 0.78 Mb), and FRA7E, which span MAGI2 (1.4 Mb).…”

Section: Resultssupporting

confidence: 64%

Common Fragile Sites Are Characterized by Faulty Condensin Loading after Replication Stress

et al. 2020

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Summary Cells coordinate interphase-to-mitosis transition, but recurrent cytogenetic lesions appear at common fragile sites (CFSs), termed CFS expression, in a tissue-specific manner after replication stress, marking regions of instability in cancer. Despite such a distinct defect, no model fully provides a molecular explanation for CFSs. We show that CFSs are characterized by impaired chromatin folding, manifesting as disrupted mitotic structures visible with molecular fluorescence in situ hybridization (FISH) probes in the presence and absence of replication stress. Chromosome condensation assays reveal that compaction-resistant chromatin lesions persist at CFSs throughout the cell cycle and mitosis. Cytogenetic and molecular lesions are marked by faulty condensin loading at CFSs, a defect in condensin-I-mediated compaction, and are coincident with mitotic DNA synthesis (MIDAS). This model suggests that, in conditions of exogenous replication stress, aberrant condensin loading leads to molecular defects and CFS expression, concomitantly providing an environment for MIDAS, which, if not resolved, results in chromosome instability.

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Section: Resultssupporting

confidence: 64%

Common Fragile Sites Are Characterized by Faulty Condensin Loading after Replication Stress

et al. 2020

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“…Accession codes for all datasets used in the paper can be found in Additional file 2: Table S2. All data generated in this study have been deposited to the GEO depository (GSE137764) [55]. The python code for data processing can be found on https://github.com/oliviacamel/High-Resolution-RepliSeq [56] and is released under Apache License 2.0.…”

Section: Acknowledgementsmentioning

confidence: 99%

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

2020

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Background: DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here, we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116, and mouse embryonic stem cells and their neural progenitor derivatives. Results: Fine temporal windows revealed a remarkable degree of cell-to-cell conservation in RT, particularly at the very beginning and ends of S phase, and identified 5 temporal patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation (IZs) were detected throughout S phase and interacted in 3D space preferentially with other IZs of similar firing time. Temporal transition regions were resolved into segments of uni-directional replication punctuated at specific sites by small, inefficient IZs. Sites of convergent replication were divided into sites of termination or large constant timing regions consisting of many synchronous IZs in tandem. Developmental transitions in RT occured mainly by activating or inactivating individual IZs or occasionally by altering IZ firing time, demonstrating that IZs, rather than individual origins, are the units of developmental regulation. Finally, haplotype phasing revealed numerous regions of allele-specific and alleleindependent asynchronous replication. Allele-independent asynchronous replication was correlated with the presence of previously mapped common fragile sites. Conclusions: Altogether, these data provide a detailed temporal choreography of DNA replication in mammalian cells.

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“…These RT profiles were generated by aggregating the Repli-seq read densities for each S-phase sample in 3-kb static windows, scaling the reads to 1× genome coverage, and then dividing by the scaled read counts from the unlabeled 2C reference data and smoothing by Haar wavelet transform (see Methods and [ 24 ]). Normalizing with the pre-replicative 2C reference provided a uniform 2C copy number and corrected for differences in sequence mappability and collapsed repeats that caused “spikes” in the data (illustrated for late replication in the endocycle in S3 Fig ) while preserving replication signal [ 24 , 48 ]. The 3-kb windows identified as having no or extremely low read coverage in the 2C reference sample (see Methods ) were excluded from all analyses.…”

Section: Resultsmentioning

confidence: 99%

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

Wear

Song²,

Zynda³

et al. 2020

PLoS Genet

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Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize ( Zea mays ) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.

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High Resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Cited by 29 publications

References 41 publications

Common Fragile Sites Are Characterized by Faulty Condensin Loading after Replication Stress

Common Fragile Sites Are Characterized by Faulty Condensin Loading after Replication Stress

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

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