Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.
Base Sequence ; DNA ; DNA Copy Number Variations ; DNA Replication ; DNA Replication Timing ; Genome* ; Genome, Human ; Genomic Instability ; Humans ; Mutagenesis ; Recombination, Genetic

Eukaryotic DNA replication is tightly restricted to only once per cell cycle in order to maintain genome stability. Cells use multiple mechanisms to control the assembly of the prereplication complex (pre-RC), a process known as replication licensing. This review focuses on the regulation of replication licensing by posttranslational modifications of the licensing factors, including phosphorylation, ubiquitylation and acetylation. These modifications are critical in establishing the pre-RC complexes as well as preventing rereplication in each cell cycle. The relationship between rereplication and diseases, including cancer and virus infection, is discussed as well.
Acetylation ; Animals ; Cell Cycle ; DNA Replication ; genetics ; physiology ; DNA Replication Timing ; DNA, Neoplasm ; biosynthesis ; genetics ; Genomic Instability ; Host-Pathogen Interactions ; Humans ; Models, Biological ; Neoplasms ; drug therapy ; genetics ; metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Ubiquitination ; Virus Diseases ; genetics ; metabolism

BACKGROUND: S Phase Kinase Associated Protein 2 (Skp2), an F-box protein necessary for DNA replication, has recently been demonstrated to be an oncogene. The purpose of this study was to examine the Skp2 expression and to investigate its association with expressions of estrogen receptor (ER), androgen receptor (AR) and HER-2, as well as clinicopathological variables including tumor recurrence. METHODS: The expressions of Skp2, ER and AR were examined by immunohistochemistry and HER-2 amplification by chromogenic in situ hybridization (CISH) in 117 cases of breast carcinoma. RESULTS: Skp2 was expressed in 26 patients (22.2%) and was significantly correlated with tumor type (p=0.031), tumor grade (p=0.017) and ER expression (p=0.038). Twenty four (20.5%) of 117 patients had a tumor recurrence, and 6 patients (5.1%) died of multifocal metastases. Tumor recurrence was significantly correlated with histological grade (p=0.041) and lymph node status (p<0.001). CONCLUSIONS: Although Skp2 expression was statistically insignificant in association with tumor recurrence, it might be useful as a biologic predictor in breast cancer. The simple and reliable immunohistochemical assay presented in this study can be a routine part of breast cancer evaluation and may influence patient management.
Breast Neoplasms* ; Breast* ; DNA Replication ; Estrogens ; Humans ; Immunohistochemistry ; In Situ Hybridization ; Lymph Nodes ; Neoplasm Metastasis ; Oncogenes ; Receptors, Androgen ; Recurrence ; S Phase* ; S-Phase Kinase-Associated Proteins*

OBJECTIVETo study the pattern of DNA double-strand break (DSB) formation in S-phase cells after thermal damage and explore the mechanisms behind heat sensitivity of S-phase cells and delayed DSBs.

METHODSFlow cytometry was used to analyze the cell cycle arrest in H1299 cells exposed to thermal damage, and EdU incorporation assay was employed to evaluate the DNA replication capacity of the cells. The cells synchronized in S phase were obtained by serum starvation and DSBs were observed dynamically using neutral comet assay. Trypan blue dye exclusion technique was used to analyze the cell viability after thermal damage. Western blotting (WB) was used to detect the phosphorylation of ATM and DNA binding RAD18.

RESULTSThe percentage of S-phase cells increased significantly after exposure of the cells to 45 degrees celsius; for 1 h (P<0.01). The time-dependent variation pattern of EdU incorporation was similar to that of S-phase cell fraction. The comet tail began to appear only after incubation of the cells at 37 degrees celsius; for some time and the Olive tail moment (OTM) increased with prolonged incubation. Cell death remained low until 7.5 h after heat exposure of the S-phase cells and then increased rapidly. The phosphorylation of ATM first increased but then decreased drastically. In cells with heat exposure, DNA binding RAD18 was attenuated obviously compared that in non-exposed cells.

CONCLUSIONThermal damage causes cell cycle arrest in S phase, and delayed fatal DSBs occur in the arrested cells due to persistent replication and DNA damage repair suppression, which are the possible cause of heat sensitivity of S-phase cells.

Ataxia Telangiectasia Mutated Proteins ; metabolism ; Cell Cycle Checkpoints ; Cell Line ; Cell Survival ; Comet Assay ; DNA Breaks, Double-Stranded ; DNA Repair ; DNA Replication ; DNA-Binding Proteins ; metabolism ; Hot Temperature ; Humans ; Phosphorylation ; S Phase ; Ubiquitin-Protein Ligases

Cyclins are proteins that activate different cyclin-dependent kinases(CDKs) and promote the cell cycles. Their correlations with several human cancers have been identified. Cyclin E, as one of G1 cylins, produces DNA replication through the progression of cell cycle G1 --> S phase. In contrast, cyclin-dependent kinase inhibitors(CDKI) bound with cyclin E-cdk2 complex control the cell cycle and inhibit the cell proliferation. P21(WAF1) proteins, which are CDKIs, are transcripted by a p53 gene and participate in the cell cycle inhibition. Variant p53 proteins produced by a mutated p53 gene lose the ability to control of the cell cycle resulting in cell proliferation. This study is aimed to reveal the expressions of cyclin E, p21(WAF1) protein, p53 variant protein in colorectal adenomas and carcinomas, and also reveal their correlations in the process of carcinogenesis. Twenty-one colorectal adenomas or adenomatous polyps, and thirty colorectal carcinoma tissues were obtained by operative resections or endoscopic polypectomies. Immuno histochemical stains of the above-mentioned three proteins and a statistical analysis of their correlations were made. The results were as follows: 1. P21 proteins were expressed in the upper-one third layer of all normal colonic mucosa, but cyclin E and variant p53 protein were not identified. 2. Cyclin E was expressed in 23.8% of adenomas and 76.7% of carcinomas. Variant p53 protein was expressed in 71.4% of adenomas and 83.3% in carcinomas. The degree of positivity of variant p53 expression was correlated with cancer staging. P21 protein was expressed in all adenomas, similar to normal mucosa, but was not expressed in 43.3% of carcinomas. 3. Expression of cyclin E was increased as to the positivity of variant p53 proteins but the correlations of p21 proteins and cyclin E, and p21 proteins and variant p53 proteins were not identified. Cancer staging was not correlated with the expressions of the three proteins. In conclusion, it can be thought that the overexpression of cyclin E and variant p53 proteins, and the loss of p21 proteins are related with the colorectal carcinogenesis. We can also identify the relationship of cyclin E and variant p53 proteins.
Adenoma* ; Adenomatous Polyps ; Carcinogenesis ; Cell Cycle ; Cell Proliferation ; Colon ; Colorectal Neoplasms ; Coloring Agents ; Cyclin E* ; Cyclins* ; DNA Replication ; Genes, p53 ; Humans ; Mucous Membrane ; Neoplasm Staging ; Phosphotransferases ; S Phase

Telomeres consist of tandem guanine-thymine(G-T) repeats in most eukaryotic chromosomes. Human telomeres are predominantly linear, double stranded DNA as they ended in 30-200 nucleotides(bases,b) 3'-overhangs. In DNA replication, removal of the terminal RNA primer from the lagging strand results in a 3'-overhang of uncopied DNA. This is because of bidirectional DNA replication and specificity of unidirectional DNA polymerase. After the replication, parental and daughter DNA strands have unequal lengths due to a combination of the end- replication problem and end-processing events. The gradual chromosome shortening is observed in most somatic cells and eventually leads to cellular senescence. Telomere shortening could be a molecular clock that signals the replicative senescence. The shortening of telomeric ends of human chromosomes, leading to sudden growth arrest, triggers DNA instability as biological switches. In addition, telomere dysfunction may cause chronic allograft nephropathy or kidney cancers. The renal cell carcinoma(RCC) in women may be less aggressive and have less genomic instability than in man. Younger patients with telomere dysfunction are at a higher risk for RCC than older patients. Thus, telomeres maintain the integrity of the genome and are involved in cellular aging and cancer. By studying the telomeric DNA, we may characterize the genetic determinants in diseases and discover the tools in molecular medicine.
Aging ; Cell Aging ; Chromosomes, Human ; DNA ; DNA Replication ; Female ; Genome ; Genomic Instability ; Humans ; Kidney ; Kidney Neoplasms ; Molecular Medicine ; Nuclear Family ; Parents ; RNA ; Sensitivity and Specificity ; Telomere ; Telomere Shortening ; Transplantation, Homologous

DNA replication of human cytomegalovirus (HCMV) is a highly regulated process that requires specific interactions between cis-acting lytic origin of replication (oriLyt) and trans-acting viral proteins. Formation of the replication initiation complex is also regulated by specific interactions among viral replication proteins. HCMV replication proteins include origin-binding proteins, core proteins that work in replication forks, and regulatory proteins that modulate host cell functions. This letter describes intriguing questions regarding how HCMV origin-binding proteins interact with oriLyt to initiate DNA replication and how the regulatory UL112-113 proteins, which are found only in beta-herpesviruses, function to promote viral DNA replication.
Cytomegalovirus ; DNA ; DNA Replication ; DNA, Viral ; Humans ; Proteins ; Replication Origin ; Viral Proteins

Topoisomerases are nuclear enzymes that regulate the overwinding or underwinding of DNA helix during replication, transcription, recombination, repair, and chromatin remodeling. These enzymes perform topological transformations by providing a transient DNA break, through which the unique problems of DNA entanglement that occur owing to unwinding and rewinding of the DNA helix can be resolved. In mammals, topoisomerases are classified into two types, type I topoisomerase (Top1) and type II topoisomerase (Top2), depending on the number of strands cut in one round of action. Top1 induces single-strand breaks in DNA, and Top2 induces double-strand breaks. In cells from vertebrate species, there are two forms of Top2, designated alpha and beta. Top2α is involved in the cellular proliferation and pluripotency, while Top2β plays key roles in neurodevelopment. In this review, we cover recent advances in structural, mechanistic and functional insights into Top2.
Animals ; Cell Proliferation ; DNA Replication ; DNA Topoisomerases, Type II ; chemistry

Real-time quantitative PCR was used to characterize HearNPV DNA replication in exponential and stationary phases of HzAM1 cells. Results showed that the doubling time of HzAM1 cells was 22 h in exponential phases. Most of the exponential cells were in S phase (48.6%), and most of the stationary cells in G2/M phase (72.6%). The replication of viral DNA was completed within 60 h post infection (h p. i.) in different phases of HzAM1 cells. During 14 to 20 h p. i., the doubling time of HearNPV replica-tion was 1.8 h in exponential cells and 1.9 h in stationary cells, and no significant difference was found between them. But the amounts of BV entering and releasing, the final progeny virions and viral protein products in the infected exponential phase cells were obviously higher than that in the stationary phase cells. 25% of the total synthesized viral DNAs were released from infected exponential phase cells, but on-ly 13% from the infected stationary phase cells. Viral DNA started to be replicated from 7-8 h p. i. both in infected exponential phase and in stationary phase cells. But in infected exponential phase cells, BVs were started to release from 18-20 h p. i., and BVs were started to release from 22-25 h p. i. from infected sta-tionary phase cells. During 30-60 h p. i., the BV releasing rate was about 483 copies/cell/h in the expo-nential phase cells, but was 100 copies/cell/h in the stationary-phase cells. The initial viral DNA entering into exponential phase cells was much more than that entered into the stationary phase cells. The data of cell membrane fluidity at exponential and stationary phases suggested that the fluidity of cell membrane played an important role during virus entry.
Animals ; Cell Cycle ; Cell Line ; DNA Replication ; Membrane Fluidity ; Moths ; Nucleopolyhedrovirus ; physiology ; Virus Internalization ; Virus Replication

DNA Replication ; Epigenesis, Genetic ; Hepatitis B virus ; genetics ; physiology ; Virus Replication