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Genes Aug 2020DNA replication is the fundamental process for accurate duplication and transfer of genetic information. Its fidelity is under constant stress from endogenous and... (Review)
Review
DNA replication is the fundamental process for accurate duplication and transfer of genetic information. Its fidelity is under constant stress from endogenous and exogenous factors which can cause perturbations that lead to DNA damage and defective replication. This can compromise genomic stability and integrity. Genomic instability is considered as one of the hallmarks of cancer. In normal cells, various checkpoints could either activate DNA repair or induce cell death/senescence. Cancer cells on the other hand potentiate DNA replicative stress, due to defective DNA damage repair mechanism and unchecked growth signaling. Though replicative stress can lead to mutagenesis and tumorigenesis, it can be harnessed paradoxically for cancer treatment. Herein, we review the mechanism and rationale to exploit replication stress for cancer therapy. We discuss both established and new approaches targeting DNA replication stress including chemotherapy, radiation, and small molecule inhibitors targeting pathways including ATR, Chk1, PARP, WEE1, MELK, NAE, TLK etc. Finally, we review combination treatments, biomarkers, and we suggest potential novel methods to target DNA replication stress to treat cancer.
Topics: Animals; DNA Damage; DNA Repair; DNA Replication; Genomic Instability; Humans; Neoplasms; Signal Transduction
PubMed: 32854236
DOI: 10.3390/genes11090990 -
Genes Dec 2021Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle-dependent manner. The assembly of the pre-replicative complex...
Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle-dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characterized; however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. To investigate the dynamic changes in chromatin organization at and surrounding replication origins, we used micrococcal nuclease (MNase) to generate genome-wide chromatin occupancy profiles of nucleosomes, transcription factors, and replication proteins through consecutive cell cycles in . During each G1 phase of two consecutive cell cycles, we observed the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence (ACS) indicative of pre-RC assembly. We also found that the strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the Cdc45-Mcm2-7-GINS (CMG) complex being a determinant of origin activity. Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. These results provide insights into cell-cycle-regulated chromatin dynamics and how they relate to the regulation of origin activity.
Topics: Cell Cycle; Cell Cycle Proteins; Cell Division; Chromatin; DNA Replication; G1 Phase; Nucleosomes; Replication Origin; S Phase; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 34946946
DOI: 10.3390/genes12121998 -
International Journal of Molecular... Oct 2021Replication timing (RT) is a cellular program to coordinate initiation of DNA replication in all origins within the genome. RIF1 (replication timing regulatory factor 1)... (Review)
Review
Replication timing (RT) is a cellular program to coordinate initiation of DNA replication in all origins within the genome. RIF1 (replication timing regulatory factor 1) is a master regulator of RT in human cells. This role of RIF1 is associated with binding G4-quadruplexes and changes in 3D chromatin that may suppress origin activation over a long distance. Many effects of RIF1 in fork reactivation and DNA double-strand (DSB) repair (DSBR) are underlined by its interaction with TP53BP1 (tumor protein p53 binding protein). In G1, RIF1 acts antagonistically to BRCA1 (BRCA1 DNA repair associated), suppressing end resection and homologous recombination repair (HRR) and promoting non-homologous end joining (NHEJ), contributing to DSBR pathway choice. RIF1 is an important element of intra-S-checkpoints to recover damaged replication fork with the involvement of HRR. High-resolution microscopic studies show that RIF1 cooperates with TP53BP1 to preserve 3D structure and epigenetic markers of genomic loci disrupted by DSBs. Apart from TP53BP1, RIF1 interact with many other proteins, including proteins involved in DNA damage response, cell cycle regulation, and chromatin remodeling. As impaired RT, DSBR and fork reactivation are associated with genomic instability, a hallmark of malignant transformation, RIF1 has a diagnostic, prognostic, and therapeutic potential in cancer. Further studies may reveal other aspects of common regulation of RT, DSBR, and fork reactivation by RIF1.
Topics: BRCA1 Protein; Chromatin; DNA; DNA Breaks, Double-Stranded; DNA End-Joining Repair; DNA Repair; DNA Replication; DNA Replication Timing; Genomic Instability; Humans; Recombinational DNA Repair; Telomere-Binding Proteins; Tumor Suppressor p53-Binding Protein 1
PubMed: 34768871
DOI: 10.3390/ijms222111440 -
Trends in Cell Biology Jul 2021Accurate duplication of chromosomal DNA is vital for faithful transmission of the genome during cell division. However, DNA replication integrity is frequently... (Review)
Review
Accurate duplication of chromosomal DNA is vital for faithful transmission of the genome during cell division. However, DNA replication integrity is frequently challenged by genotoxic insults that compromise the progression and stability of replication forks, posing a threat to genome stability. It is becoming clear that the organization of the replisome displays remarkable flexibility in responding to and overcoming a wide spectrum of fork-stalling insults, and that these transactions are dynamically orchestrated and regulated by protein post-translational modifications (PTMs) including ubiquitylation. In this review, we highlight and discuss important recent advances on how ubiquitin-mediated signaling at the replication fork plays a crucial multifaceted role in regulating replisome composition and remodeling its configuration upon replication stress, thereby ensuring high-fidelity duplication of the genome.
Topics: DNA Damage; DNA Repair; DNA Replication; Genomic Instability; Humans; Ubiquitination
PubMed: 33612353
DOI: 10.1016/j.tcb.2021.01.008 -
STAR Protocols Dec 2023Single-molecule analysis of replicated DNA (SMARD) is a unique technique that enables visualization of DNA replication at specific genomic regions at single-molecule...
Single-molecule analysis of replicated DNA (SMARD) is a unique technique that enables visualization of DNA replication at specific genomic regions at single-molecule resolution. Here, we present a protocol for visualizing DNA replication by SMARD. We describe steps for pulse labeling DNA, followed by isolating and stretching of genomic DNA. We then detail the detection of the replication at chromosomal regions through immunostaining and fluorescence in situ hybridization. Using SMARD, we can visualize replication initiation, progression, termination, and fork stalling. For complete details on the use and execution of this protocol, please refer to Norio et al. (2001) and Gerhardt et al. (2014)..
Topics: In Situ Hybridization, Fluorescence; DNA; DNA Replication; Single Molecule Imaging; Genomics
PubMed: 38048218
DOI: 10.1016/j.xpro.2023.102721 -
Cell Cycle (Georgetown, Tex.) Aug 2016
Topics: DNA Damage; DNA Repair; DNA Replication; Sirtuin 2
PubMed: 27153288
DOI: 10.1080/15384101.2016.1184517 -
Nature Reviews. Neuroscience Nov 2016Topoisomerases are unique enzymes that regulate torsional stress in DNA to enable essential genome functions, including DNA replication and transcription. Although all... (Review)
Review
Topoisomerases are unique enzymes that regulate torsional stress in DNA to enable essential genome functions, including DNA replication and transcription. Although all cells in an organism require topoisomerases to maintain normal function, the nervous system in particular shows a vital need for these enzymes. Indeed, a range of inherited human neurologic syndromes, including neurodegeneration, schizophrenia and intellectual impairment, are associated with aberrant topoisomerase function. Much remains unknown regarding the tissue-specific function of neural topoisomerases or the connections between these enzymes and disease aetiology. Precisely how topoisomerases regulate genome dynamics within the nervous system is therefore a crucial research question.
Topics: Animals; DNA Damage; DNA Replication; DNA Topoisomerases; Humans; Nervous System Diseases; Neurons; Transcription, Genetic
PubMed: 27630045
DOI: 10.1038/nrn.2016.101 -
Development (Cambridge, England) Jul 2018Polyploid cells, which contain multiple copies of the typically diploid genome, are widespread in plants and animals. Polyploidization can be developmentally programmed... (Review)
Review
Polyploid cells, which contain multiple copies of the typically diploid genome, are widespread in plants and animals. Polyploidization can be developmentally programmed or stress induced, and arises from either cell-cell fusion or a process known as endoreplication, in which cells replicate their DNA but either fail to complete cytokinesis or to progress through M phase entirely. Polyploidization offers cells several potential fitness benefits, including the ability to increase cell size and biomass production without disrupting cell and tissue structure, and allowing improved cell longevity through higher tolerance to genomic stress and apoptotic signals. Accordingly, recent studies have uncovered crucial roles for polyploidization in compensatory cell growth during tissue regeneration in the heart, liver, epidermis and intestine. Here, we review current knowledge of the molecular pathways that generate polyploidy and discuss how polyploidization is used in tissue repair and regeneration.
Topics: Animals; Cell Division; DNA Replication; Humans; Organ Specificity; Polyploidy; Regeneration; Stress, Physiological
PubMed: 30021843
DOI: 10.1242/dev.156034 -
Current Opinion in Cell Biology Jun 2016DNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a... (Review)
Review
DNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a defined temporal order known as the replication-timing (RT) program, which is regulated during the cell cycle and development in discrete units referred to as replication domains (RDs). RDs correspond to topologically-associating domains (TADs) and are spatio-temporally compartmentalized in the nucleus. While improvements in experimental tools have begun to reveal glimpses of causality, they have also unveiled complex context-dependent relationships that challenge long recognized correlations of RT to chromatin organization and gene regulation. In particular, RDs/TADs that switch RT during development march to the beat of a different drummer.
Topics: Animals; Cell Cycle; Cell Nucleus; DNA Replication; DNA Replication Timing; Gene Expression Regulation; Genome; Humans; Transcription, Genetic
PubMed: 27115331
DOI: 10.1016/j.ceb.2016.03.022 -
Viruses Mar 2017Transposable elements subvert host cellular functions to ensure their survival. Their interaction with the host DNA replication machinery indicates that selective... (Review)
Review
Transposable elements subvert host cellular functions to ensure their survival. Their interaction with the host DNA replication machinery indicates that selective pressures lead them to develop ancestral and convergent evolutionary adaptations aimed at conserved features of this fundamental process. These interactions can shape the co-evolution of the transposons and their hosts.
Topics: Biological Evolution; DNA Replication; DNA Transposable Elements; Gene Expression Regulation; Humans
PubMed: 28335567
DOI: 10.3390/v9030057