The programme of DNA replication: beyond genome duplication

The accurate duplication and transmission of genetic information is critical for cell growth and proliferation, and this is ensured in part by the multi-layered regulation of DNA synthesis. One of the key steps in this process is the selection and activation of the sites of replication initiation, or origins, across the genome. Interestingly, origin usage changes during development and in different pathologies, suggesting an integral interplay between the establishment of replication initiation along the chromosomes and cellular function. The present review discusses how the spatiotemporal organization of replication origin activation may play crucial roles in the control of biological events.

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Modeling of DNA replication in rapidly growing bacteria with one and two replication origins

10.1101/354654 ◽

2018 ◽

Cited By ~ 1

Author(s):

Renata Retkute ◽

Michelle Hawkins ◽

Christian J. Rudolph ◽

Conrad A. Nieduszynski

Keyword(s):

Dna Replication ◽

Replication Origin ◽

Genome Duplication ◽

Replication Initiation ◽

Wild Type ◽

Initiation Of Replication ◽

Initiation Of Dna Replication ◽

Time Required ◽

Double Origin ◽

Direction Opposite

AbstractIn rapidly growing bacteria initiation of DNA replication occurs at intervals shorter than the time required for completing genome duplication, leading to overlapping rounds of replication. We propose a mathematical model of DNA replication defined by the periodicity of replication initiation. Our model predicts that a steeper gradient of the replication profile is to be expected in origin proximal regions due to the overlapping rounds of synthesis. By comparing our model with experimental data from a strain with an additional replication origin, we predict defined alterations to replication parameters: (i) a reduced fork velocity when there were twice as many forks as normal; (ii) a slower fork speed if forks move in a direction opposite to normal, in line with head-on replication-transcription collisions being a major obstacle for fork progression; (iii) slower cell doubling for a double origin strain compared to wild-type cells; and (iv) potentially an earlier initiation of replication at the ectopic origin than at the natural origin, which, however, does not a˙ect the overall time required to complete synthesis.

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Nucleosomes influence multiple steps during replication initiation

eLife ◽

10.7554/elife.22512 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 27

Author(s):

Ishara F Azmi ◽

Shinya Watanabe ◽

Michael F Maloney ◽

Sukhyun Kang ◽

Jason A Belsky ◽

...

Keyword(s):

Dna Replication ◽

Chromatin Remodeling ◽

Replication Origin ◽

Replication Initiation ◽

Dna Templates ◽

Helicase Loading ◽

Origin Activation ◽

Nucleosomal Dna ◽

Origin Licensing ◽

The Impact

Eukaryotic replication origin licensing, activation and timing are influenced by chromatin but a mechanistic understanding is lacking. Using reconstituted nucleosomal DNA replication assays, we assessed the impact of nucleosomes on replication initiation. To generate distinct nucleosomal landscapes, different chromatin-remodeling enzymes (CREs) were used to remodel nucleosomes on origin-DNA templates. Nucleosomal organization influenced two steps of replication initiation: origin licensing and helicase activation. Origin licensing assays showed that local nucleosome positioning enhanced origin specificity and modulated helicase loading by influencing ORC DNA binding. Interestingly, SWI/SNF- and RSC-remodeled nucleosomes were permissive for origin licensing but showed reduced helicase activation. Specific CREs rescued replication of these templates if added prior to helicase activation, indicating a permissive chromatin state must be established during origin licensing to allow efficient origin activation. Our studies show nucleosomes directly modulate origin licensing and activation through distinct mechanisms and provide insights into the regulation of replication initiation by chromatin.

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Enhanced Myc Expression in Silkworm Silk Gland Promotes DNA Replication and Silk Production

Insects ◽

10.3390/insects12040361 ◽

2021 ◽

Vol 12 (4) ◽

pp. 361

Author(s):

Wenliang Qian ◽

Yan Yang ◽

Zheng Li ◽

Yuting Wu ◽

Xuechuan He ◽

...

Keyword(s):

Dna Replication ◽

Cell Growth ◽

Silk Gland ◽

Biological Functions ◽

Gland Cells ◽

Silk Production ◽

Myc Gene ◽

Cell Growth And Proliferation ◽

Silkworm Silk ◽

Posterior Silk Gland

Silkworm is an economically important insect that synthetizes silk proteins for silk production in silk gland, and silk gland cells undergo endoreplication during larval period. Transcription factor Myc is essential for cell growth and proliferation. Although silkworm Myc gene has been identified previously, its biological functions in silkworm silk gland are still largely unknown. In this study, we examined whether enhanced Myc expression in silk gland could facilitate cell growth and silk production. Based on a transgenic approach, Myc was driven by the promoter of the fibroin heavy chain (FibH) gene to be successfully overexpressed in posterior silk gland. Enhanced Myc expression in the PSG elevated FibH expression by about 20% compared to the control, and also increased the weight and shell rate of the cocoon shell. Further investigation confirmed that Myc overexpression increased nucleus size and DNA content of the PSG cells by promoting the transcription of the genes involved in DNA replication. Therefore, we conclude that enhanced Myc expression promotes DNA replication and silk protein expression in endoreplicating silk gland cells, which subsequently raises silk yield.

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

10.1101/2021.05.14.443897 ◽

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.

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Bombyx mori Dihydroorotate Dehydrogenase: Knockdown Inhibits Cell Growth and Proliferation via Inducing Cell Cycle Arrest

International Journal of Molecular Sciences ◽

10.3390/ijms19092581 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2581 ◽

Cited By ~ 2

Author(s):

Erhu Zhao ◽

Xiaolan Jiang ◽

Hongjuan Cui

Keyword(s):

Cell Cycle ◽

Amino Acid ◽

Dna Replication ◽

Cell Growth ◽

Cell Cycle Arrest ◽

Bombyx Mori ◽

Dihydroorotate Dehydrogenase ◽

Pyrimidine Synthesis ◽

Cycle Arrest ◽

Cell Growth And Proliferation

Dihydroorotate dehydrogenase (DHODH), in the de novo pyrimidine biosynthetic pathway, is the fourth enzyme of pyrimidine synthesis and is used to oxidize dihydroorotate and hence to orotat. We cloned and characterized here the dhod of silkworms, Bombyx mori. The full-length cDNA sequence of dhod is 1339 bp, including an open reading frame (ORF) of 1173 bp that encoded a 390 amino acid protein. And two domains were involved in the Dihydroorotate dehydrogenase amino acid sequence of silkworms, Bombyx mori (BmDHODH), namely a DHO_dh domain and a transmembrane domain in N-termina. The silkworm dhod is expressed throughout development and in nine tissues. Moreover, knockdown of the silkworm dhod gene reduced cell growth and proliferation through G2/M phase cell cycle arrest. Similarly, DHODH inhibitor (leflunomide) also reduced cell growth and proliferation, with a significant decrease of cyclin B and cdk2. DHODH is the fourth enzyme of pyrimidine synthesis, so we also found that leflunomide can inhibit, at least in part, the endomitotic DNA replication in silk glands cells. These findings demonstrate that downregulation of BmDHODH inhibits cell growth and proliferation in silkworm cells, and the endomitotic DNA replication in silk gland cells.

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Subcellular Proteomics Reveals a Role for Nucleo-cytoplasmic Trafficking at the DNA Replication Origin Activation Checkpoint

Journal of Proteome Research ◽

10.1021/pr3010919 ◽

2013 ◽

Vol 12 (3) ◽

pp. 1436-1453 ◽

Cited By ~ 11

Author(s):

Claire M. Mulvey ◽

Slavica Tudzarova ◽

Mark Crawford ◽

Gareth H. Williams ◽

Kai Stoeber ◽

...

Keyword(s):

Dna Replication ◽

Replication Origin ◽

Origin Activation ◽

Dna Replication Origin ◽

Subcellular Proteomics

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Caught in the act: structural dynamics of replication origin activation and fork progression

Biochemical Society Transactions ◽

10.1042/bst20190998 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1057-1066 ◽

Cited By ~ 4

Author(s):

Jacob S. Lewis ◽

Alessandro Costa

Keyword(s):

Dna Replication ◽

Structural Dynamics ◽

Single Molecule ◽

Single Particle ◽

Replication Origin ◽

Origin Activation ◽

Recent Advances ◽

Eukaryotic Dna ◽

New Challenges

This review discusses recent advances in single-particle cryo-EM and single-molecule approaches used to visualise eukaryotic DNA replication reactions reconstituted in vitro. We comment on the new challenges facing structural biologists, as they turn to describing the dynamic cascade of events that lead to replication origin activation and fork progression.

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