query: which molecule initiates the halt of the cycle when damaged dna is detected in g1

pos: Cell cycle checkpoint the cell cycle in G1, arrest occurs through several mechanisms. The rapid response involves phosphorylation events that initiate with either kinase ATM (Ataxia telangiectasia mutated) or ATR (Ataxia Telangiectasia and Rad3 related), which act as sensors, depending on the type of damage. These kinases phosphorylate and activate the effector kinases Chk2 and Chk1, respectively, which in turn phosphorylate the phosphatase Cdc25A, thus marking it for ubiquitination and degradation. As Cdc25A activates the previously mentioned cyclin E-CDK2 complex by removing inhibitory phosphates from CDK2, in the absence of Cdc25A, cyclin E-CDK2 remains inactive, and the cell remains in G1. To maintain

pos: G1/S transition cycle until DNA damage can be corrected. Of the four DNA damage checkpoints, two have an additional process for monitoring DNA damage other than activating p53. Before entry into S phase and during S phase, ATM/R also activates Chk1/2 that inhibits Cdc25A, a protein responsible for activating cyclin-Cdk dimers. Without cyclin dimer activation, the cell cannot transition through the cycle. These two checkpoints have additional processes for regulation because replicating damaged DNA in S phase can be deleterious to the cell and more importantly, the organism. G1/S transition The G1/S transition is a stage in the cell cycle at the

neg: G1/S transition highly regulated check point can lead to cellular transformation and disease states such as cancer During this transition, G1 cyclin D-Cdk4/6 dimer phosphorylates retinoblastoma releasing transcription factor E2F, which then drives the transition from G1 to S phase. The G1/S transition is highly regulated by transcription factor p53 in order to halt the cell cycle when DNA is damaged. It is a "point of no return" beyond which the cell is committed to dividing; in yeast this is called START and in multicellular eukaryotes it is termed the restriction point (R-Point). If a cell passes through the G1/S transition the

neg: G1/S transition phase. Retinoblastoma (Rb) is a cancer of the eye due to a mutant pRb protein. When pRb is mutated it becomes nonfunctional and is not able to inhibit the expression of transcription factor E2F. Therefore, E2F is always active and driving the cell cycle to progress from G1 to S phase. As a result, cell growth and division is unregulated causing tumor formation in the eye. To ensure proper cell division, the cell cycle utilizes numerous checkpoints to monitor cell progression and halt the cycle when processes go awry. These checkpoints include four DNA damage checkpoints, one unreplicated DNA checkpoint

neg: Cell cycle checkpoint inhibit p27. The G1 phase cyclin-dependent kinase works together with S phase cyclin-dependent kinase target p27 for degradation. In turn, this allows for full activation of Cyclin A:Cdk2, a complex which phosphorylates E2F1-3 initiating their disassociation from the DNA promoter sites. This allows E2F 6-8 to bind to the DNA and inhibit transcription. The negative feedback loop used to successfully inhibit the inhibitor, p27, is another essential process used by cells to ensure mono-directional movement and no backtrack through the cell cycle. When DNA damage occurs, or when the cell detects any defects which necessitate it to delay or halt

neg: Sister chromatid exchange in Bernstein and Bernstein, pp 220–221). In order for yeast cells to repair damage by homologous recombination, there must be present, in the same nucleus, a second DNA molecule containing sequence homology with the region to be repaired. In a diploid cell in G1 phase of the cell cycle, such a molecule is present in the form of the homologous chromosome. However, in the G2 phase of the cell cycle (following DNA replication), a second homologous DNA molecule is also present: the sister chromatid. Evidence indicates that, due to the special nearby relationship they share, sister chromatids are not only

neg: DNA damage (naturally occurring) to progress to mitosis. The three main checkpoints are at G1/s, G2/m, and at the spindle assembly checkpoint regulating progression through anaphase. G1 and G2 checkpoints involve scanning for damaged DNA. During S phase the cell is more vulnerable to DNA damage than any other part of the cell cycle. G2 checkpoint checks for damaged DNA and DNA replication completeness. DNA damage is an alteration in the chemical structure of DNA, such as a break in a strand of DNA, a base missing from the backbone of DNA, or a chemically changed base as 8-OHdG. DNA damage can occur naturally

neg: Homology directed repair region to be repaired. In a diploid cell in G1 phase of the cell cycle, such a molecule is present in the form of the homologous chromosome. However, in the G2 stage of the cell cycle (following DNA replication), a second homologous DNA molecule is also present: the sister chromatid. Evidence indicates that, due to the special nearby relationship they share, sister chromatids are not only preferred over distant homologous chromatids as substrates for recombinational repair, but have the capacity to repair more DNA damage than do homologs. During meiosis up to one-third of all homology directed repair events occur

neg: Cyclin A2 localizes to the nucleus, where the cyclin A2-CDK2 complex is implicated in the initiation and progression of DNA synthesis. Phosphorylation of CDC6 and MCM4 by the cyclin A2-CDK2 complex prevents re-replication of DNA during the cell cycle. Cyclin A2 is involved in the G2/M transition but it cannot independently form a maturation promoting factor (MPF). Recent studies have shown that the cyclin A2-CDK1 complex triggers cyclin B1-CDK1 activation which results in chromatin condensation and the breakdown of the nuclear envelope. The levels of cyclin A2 are tightly synchronized with the progression of the cell cycle. Transcription initiates in late G1,

neg: G1/S transition G1/S transition The G1/S transition is a stage in the cell cycle at the boundary between the G1 phase, in which the cell grows, and the S phase, during which DNA is replicated. It is a cell cycle check point where DNA integrity is assessed and the cell cycle can pause in response to improperly or partially replicated DNA. During this transition the cell makes decisions to become quiescent (enter G0), differentiate, make DNA repairs, or proliferate based on environmental cues and molecular signaling inputs. The G1/S transition occurs late in G1 and the absence or improper application of this

neg: Neuronal cell cycle the kinases (Fisher, 2012). During G1, cyclin D is synthesized and binds to Cdk4/6, which in turn phosphorylates retinoblastoma (Rb) protein and induces the release of the transcription factor E2F1 which is necessary for DNA replication (Liu et al., 1998). The G1/S transition is regulated by cyclin E binding to Cdk2 which phosphorylates Rb as well (Merrick and Fisher, 2011). S phase is then driven by the binding of cyclin A with Cdk2. In late S phase, cyclin A binds with Cdk1 to promote late replication origins and also initiates the condensation of the chromatin in the late G2 phase.

neg: DNA repair downstream proteins. DNA damage checkpoint is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows down the rate of S phase progression when DNA is damaged. It leads to a pause in cell cycle allowing the cell time to repair the damage before continuing to divide. Checkpoint Proteins can be separated into four groups: phosphatidylinositol 3-kinase (PI3K)-like protein kinase, proliferating cell nuclear antigen (PCNA)-like group, two serine/threonine(S/T) kinases and their adaptors. Central to all DNA damage induced checkpoints responses is a pair of large protein kinases belonging to the first group of PI3K-like

neg: Hydroxycarbamide other antimetabolite anti-cancer drugs, it acts by disrupting the DNA replication process of dividing cancer cells in the body. Hydroxyurea selectively inhibits ribonucleoside diphosphate reductase, an enzyme required to convert ribonucleoside diphosphates into deoxyribonucleoside diphosphates, thereby preventing cells from leaving the G1/S phase of the cell cycle. This agent also exhibits radiosensitizing activity by maintaining cells in the radiation-sensitive G1 phase and interfering with DNA repair. Biochemical research has explored its role as a DNA replication inhibitor which causes deoxyribonucleotide depletion and results in DNA double strand breaks near replication forks (see DNA repair). Repair of DNA damaged by chemicals

neg: Protein phosphorylation systems including the skin, lung, heart, and brain. Excessive signaling through the EGFR pathway is found in many human cancers. Cyclin-dependent kinases (CDKs) are serine-threonine kinases which regulate progression through the eukaryotic cell cycle. CDKs are catalytically active only when bound to a regulatory cyclin. Animal cells contain at least nine distinct CDKs which bind to various cyclins with considerable specificity. CDK inhibitors (CKIs) block kinase activity in the cyclin-CDK complex to halt the cell cycle in G1 or in response to environmental signals or DNA damage. The activity of different CDKs activate cell signaling pathways and transcription factors that

neg: DNA re-replication decline of CDK activity at the end of mitosis. Thus, CDKs serve a dual role in the regulation of eukaryotic DNA replication: elevated CDK activity initiates replication at the origins and prevents rereplication by inhibiting origin re-licensing. This ensures that no replication origin fires twice in the same cell cycle. Early experimental evidence on the regulation of DNA replication suggests that replication origins exist in one of two states during the cell cycle: a prereplicative state in G1 and a postreplicative state from the moment of initiation until passage through mitosis. Origins of replication alternate between these two distinct states

neg: G1/S transition at the end of G2, one spindle assembly checkpoint in mitosis, and a chromosome segregation checkpoint during mitosis. Between G1 and S phase, three DNA damage checkpoints occur to ensure proper growth and synthesis of DNA prior to cell division. Damaged DNA during G1, before entry into S phase, and during S phase result in the expression of ATM/R protein. ATM/R protein then stabilizes and activates transcription factor p53 so that it can bind to upstream regions of genes, inducing the expression of proteins including p21CIP. p21CIP binds to and inhibits any cyclin-cdk present in the cell cycle, halting the

neg: POLD1 CTD domain of Polζ, and the iron clusters within each CTD mediate interactions involving binding to POLD2 that permit polymerase switching during TLS. Some recent studies suggest that a switch from Polδ to Pol lambda (λ) also supports the TLS and repair of oxidative DNA damage like 7,8-Dihydro-8-oxoguanine lesions. Depletion of "POLD1" can halt cell cycle at G1 and G2/M phases in human cells. Cell cycle block in these phases typically indicates presence of DNA damage and activation of DNA damage checkpoints. "POLD1" depleted cells are sensitive to inhibition of DNA damage checkpoint kinases ATR and CHK1. In "S. pombe",

neg: Whi5 to enter the cell cycle. For example if the cell is starving, or if there is nutrient depletion, then it will halt progression in the cell cycle. However, if the Start checkpoint is satisfied then the cell can begin DNA replication and the cell will halt growing. In the cascade of events that leads to transcription of G1-specific genes, Whi5 is involved in the regulation of transcription. According to David Morgan, SCB-binding factor (SBF) and MCB-binding factor (MBF) are transcription factors that bind to SCBs and MCBs respectively. SCBs and MCBs are in promoter regions upstream of key genes expressing

neg: Single-molecule real-time sequencing single molecule level. The signal from a phospho-linked nucleotide incorporated by the DNA polymerase is detected as the DNA synthesis proceeds which results in the DNA sequencing in real time. For each of the nucleotide bases, there is a corresponding fluorescent dye molecule that enables the detector to identify the base being incorporated by the DNA polymerase as it performs the DNA synthesis. The fluorescent dye molecule is attached to the phosphate chain of the nucleotide. When the nucleotide is incorporated by the DNA polymerase, the fluorescent dye is cleaved off with the phosphate chain as a part of a

neg: Nuclear DNA DNA. The original polynucleotide strand of DNA serves as a template to guide the synthesis of the new complementary polynucleotide of DNA. The DNA single strand template serves to guide the synthesis of a complementary strand of DNA. DNA replication begins at a specific site in the DNA molecule called the origin of replication. The enzyme helicase unwinds and separates a portion of the DNA molecule after which single-strand binding proteins react with and stabilize the separated, single-stranded sections of the DNA molecule. The enzyme complex DNA polymerase engages the separated portion of the molecule and initiates the process of

neg: Neuronal cell cycle Kozminski, K.G. (2013). Cell cycle checkpoint regulators reach a zillion. Cell Cycle 12, 1501–1509. Neuronal cell cycle The Cell Cycle represents the life cycle of the biological cell, its creation, reproduction and eventual death. The process by which cells divide into two daughter cells is called mitosis. Once these cells are formed they enter G1, the phase in which many of the proteins needed to replicate DNA are made. After G1, the cells enter S phase during which the DNA is replicated. After S, the cell will enter G2 where the proteins required for mitosis to occur are synthesized. Unlike

neg: Cell cycle checkpoint which the cell becomes committed to entering the cell cycle. As the cell progresses through G1, depending on internal and external conditions, it can either delay G1, enter a quiescent state known as G0, or proceed past the restriction point. DNA damage is the main indication for a cell to "restrict"and not enter the cell cycle. The decision to commit to a new round of cell division occurs when the cell activates cyclin-CDK-dependent transcription which promotes entry into S phase. During early G1, there are three transcriptional repressors, known as pocket proteins, that bind to E2F transcription factors. The E2F

neg: Neuronal cell cycle Neuronal cell cycle The Cell Cycle represents the life cycle of the biological cell, its creation, reproduction and eventual death. The process by which cells divide into two daughter cells is called mitosis. Once these cells are formed they enter G1, the phase in which many of the proteins needed to replicate DNA are made. After G1, the cells enter S phase during which the DNA is replicated. After S, the cell will enter G2 where the proteins required for mitosis to occur are synthesized. Unlike most cell types however, neurons are generally considered incapable of proliferating once they are

neg: P14arf functions are not likely to be overlapping. An important cyclin-dependent substrate is the retinoblastoma protein Rb, which is phosphorylated in late gap 1 phase (G1 phase), allowing G1 exit. The Rb protein limits cell proliferation by blocking the activity of E2F transcription factors, which activate the transcription of genes needed for DNA replication. When Rb is phosphorylated by cyclin D and E-dependent kinases during the G1 phase of the cell cycle, Rb can not block E2F-dependent transcription, and the cell can progress to the DNA synthetic phase(S phase). Therefore, INK4a and INK4b serve as tumor suppressors by restricting proliferation though

neg: DNA damage (naturally occurring) the cell cycle control system to delay the progression of the cell cycle. Chk1 leads to the production of DNA repair enzymes. Chk2 leads to reversible cell cycle arrest. Chk2, as well as ATR/ATM, can activate p53, which leads to permanent cell cycle arrest or apoptosis. When there is too much damage, apoptosis is triggered in order to protect the organism from potentially harmful cells.7 p53, also known as a tumor suppressor gene, is a major regulatory protein in the DNA damage response system which binds directly to the promoters of its target genes. p53 acts primarily at the G1

neg: Cyclin on their behavior in the cell cycle of vertebrate somatic cells and yeast cells: G1 cyclins, G1/S cyclins, S cyclins, and M cyclins. This division is useful when talking about most cell cycles, but it is not universal as some cyclins have different functions or timing in different cell types. G1/S Cyclins rise in late G1 and fall in early S phase. The Cdk- G1/S cyclin complex begins to induce the initial processes of DNA replication, primarily by arresting systems that prevent S phase Cdk activity in G1. The cyclins also promote other activities to progress the cell cycle, such

neg: G1/S transition cell will continue through the cell cycle regardless of incoming mitogenic factors due to the positive feed-back loop of G1-S transcription. Positive feed-back loops include G1 cyclins and accumulation of E2F. The cell cycle is a process in which an ordered set of events leads to the growth and division into two daughter cells. The cell cycle is a cycle rather than a linear process because the two daughter cells produced repeat the cycle. This process contains two main phases, interphase, in which the cell grows and synthesizes a copy of its DNA, and the mitotic (M) phase, during which

neg: Estradiol receptor β (ERβ). One of the functions of these estrogen receptors is the modulation of gene expression. Once estradiol binds to the ERs, the receptor complexes then bind to specific DNA sequences, possibly causing damage to the DNA and an increase in cell division and DNA replication. Eukaryotic cells respond to damaged DNA by stimulating or impairing G1, S, or G2 phases of the cell cycle to initiate DNA repair. As a result, cellular transformation and cancer cell proliferation occurs. Estradiol has complex effects on the liver. It affects the production of multiple proteins, including lipoproteins, binding proteins, and proteins

neg: G1 and G1/S cyclins- budding yeast and Clb6 in budding yeast), which form S cyclin-Cdk complexes that are directly responsible for stimulating DNA replication. Cln1 and Cln2 are involved in regulation of the cell cycle. Cln1 is closely related to Cln2 and has overlapping functions with Cln2. For instance, Cln1 and Cln2 repress the mating factor response pathway at Start. Additionally, both Cln1 and Cln2 are expressed in late G1 phase when they associate with Cdc28p to activate its kinase activity. Lastly, late G1-specific expression for both of them depends on transcription factor complexes, MBF and SBF. G1 and G1/S cyclins- budding yeast Cln1, Cln2, and

neg: P21 exposed to DNA damaging agents, have shown that DNA damage occurring in mother cell S-phase can induce p21 accumulation over both mother G2 and daughter G1 phases which subsequently induces cell cycle arrest; this responsible for the bifurcation in CDK2 activity observed in Spencer "et al.". p21 is negatively regulated by ubiquitin ligases both over the course of the cell cycle and in response to DNA damage. Specifically, over the G1/S transition it has been demonstrated that the E3 ubiquitin ligase complex SCF induces degradation of p21. Studies have also demonstrated that the E3 ubiquitin ligase complex CRL4 degrades p21

neg: Neuronal cell cycle differentiated, as they are in the adult nervous system. Nevertheless, it remains plausible that neurons may re-enter the cell cycle under certain circumstances. Sympathetic and cortical neurons, for example, try to reactivate the cell cycle when subjected to acute insults such as DNA damage, oxidative stress, and excitotoxicity. This process is referred to as “abortive cell cycle re-entry” because the cells usually die in the G1/S checkpoint before DNA has been replicated. Cell Cycle Regulation Transitions through the cell cycle from one phase to the next are regulated by cyclins binding their respective cyclin dependent kinases (Cdks) which then activate

neg: G1 phase not move into the S phase include insufficient cell growth, damaged DNA, or other preparations have not been completed. At the G/S checkpoint, formation of the G/S cyclin with Cdk to form a complex commits the cell to a new division cycle. These complexes then activate S-Cdk complexes that move forward with DNA replication in the S phase. Concurrently, anaphase-promoting complex (APC) activity decreases significantly, allowing S and M cyclins to become activated. If a cell does not clear to pass through to the S phase, it enters the dormant G phase in which there is no cellular growth or

neg: DNA damage (naturally occurring) been analyzed. A mutant rad52 rad9 strain—which is both defective in DNA repair and G2 arrest—fails to undergo cell cycle arrest when exposed to x-irradiation. This suggests that even if DNA damage cannot be repaired, if RAD9 is not present, the cell cycle will not delay. Thus, unrepaired DNA damage is the signal that tells RAD9 to halt division and arrest the cell cycle in G2. Furthermore, there is a dose-dependent response; as the levels of x-irradiation—and subsequent DNA damage—increase, more cells, regardless of the mutations they have, become arrested in G2. Another, and perhaps more helpful way to visualize

neg: Oncovirus the site of integration. After integration, the host’s cell cycle loses regulation from Rb and p53, and the cell begins cloning to form a tumor. Rb and p53 regulate the transition between G1 and S phase, arresting the cell cycle before DNA replication until the appropriate checkpoint inputs, such as DNA damage repair, are completed. p53 regulates the p21 gene, which produces a protein which binds to the Cyclin D-Cdk4/6 complex. This prevents Rb phosphorylation and prevents the cell from entering S phase. In mammals, when Rb is active (unphosphorylated), it inhibits the E2F family of transcription factors, which regulate

neg: Tax gene product processes by protein-protein interaction (binding with proteins), transcriptional activation (promoting the production of proteins) and transcriptional repression (inhibiting the production of proteins). Cellular processes that Tax dysregulates to produce cancerous cells include the cell cycle and the maintenance of genomic integrity. The cell cycle has four stages (G1, S, G2 and M) and Tax is known to accelerate the transition between G1 and S phase. Two DNA repair pathways (base excision repair and nucleotide excision repair) are affected by Tax, leading to mutations in DNA; a classical hallmark of cancer. Tax also causes aneuploidy (abnormal chromosome numbers), which is a

neg: P53 down-stream genes. p21 (WAF1) binds to the G1-S/CDK (CDK4/CDK6, CDK2, and CDK1) complexes (molecules important for the G1/S transition in the cell cycle) inhibiting their activity. When p21(WAF1) is complexed with CDK2, the cell cannot continue to the next stage of cell division. A mutant p53 will no longer bind DNA in an effective way, and, as a consequence, the p21 protein will not be available to act as the "stop signal" for cell division. Studies of human embryonic stem cells (hESCs) commonly describe the nonfunctional p53-p21 axis of the G1/S checkpoint pathway with subsequent relevance for cell cycle regulation

neg: Therapeutic index radical, hydronium and electron. Then, hydroxyl radical transfers its radical to DNA. Or together with hydronium and electron, a free hydroxyl radical can damage base region of DNA. Cancer cells have imbalance of signals in cell cycle. G1 and G2/M arrest are found to be major checkpoints by irradiation in human cells. G1 arrest delays repair mechanism before synthesis of DNA in S phase and mitosis in M phase, suggesting key checkpoint to lead survival of cells. G2/M arrest occurs when cells need to repair after S phase before the mitotic entry. It was also known that S phase is

neg: DNA damage (naturally occurring) checkpoint (controlling the G1 to S transition), where it blocks cell cycle progression. Activation of p53 can trigger cell death or permanent cell cycle arrest. p53 can also activate certain repair pathways such was NER. In the absence of DNA damage, p53 is regulated by Mdm2 and constantly degraded. When there is DNA damage, Mdm2 is phosphorylated, most likely caused by ATM. The phosphorylation of Mdm2 leads to a reduction in the activity of Mdm2, thus preventing the degradation of p53. Normal, undamaged cell, usually has low levels of p53 while cells under stress and DNA damage, will have high

neg: DNA damage (naturally occurring) or via environmental factors. The DNA damage response (DDR) is a complex signal transduction pathway which recognizes when DNA is damaged and initiates the cellular response to the damage. Damage to DNA that occurs naturally can result from metabolic or hydrolytic processes. Metabolism releases compounds that damage DNA including reactive oxygen species, reactive nitrogen species, reactive carbonyl species, lipid peroxidation products and alkylating agents, among others, while hydrolysis cleaves chemical bonds in DNA. Naturally occurring oxidative DNA damages arise at least 10,000 times per cell per day in humans and 50,000 times or more per cell per day in rats,

neg: Single-molecule real-time sequencing natural DNA synthesis process during which a phosphodiester bond is created to elongate the DNA chain. The cleaved fluorescent dye molecule then diffuses out of the detection volume so that the fluorescent signal is no longer detected. The zero-mode waveguide (ZMW) is a nanophotonic confinement structure that consists of a circular hole in an aluminum cladding film deposited on a clear silica substrate. The ZMW holes are ~70 nm in diameter and ~100 nm in depth. Due to the behavior of light when it travels through a small aperture, the optical field decays exponentially inside the chamber. The observation volume

neg: Staphylococcus phage G1 content requires host cell DNA polymerases and, hence, the process is highly dependent on the cell cycle. The phage contains a genome of 138,715 base pairs with a 30.4% of GC content and 214 predicted genes; this means that the 88.5% of the DNA is coding open reading frames, and therefore the gene density (the number of genes per kilobase) is 1.54. Staphylococcus phage G1 Staphylococcus phage G1 is a virus of the family Myoviridae, genus "Twortlikevirus". As a member of the group I of the Baltimore classification, "Staphylococcus phage G1" is a dsDNA viruses. All the family Myoviridae members

neg: TP53-inducible glycolysis and apoptosis regulator under low levels of cellular stress, p53 initiates cell cycle arrest to allow the cell time for repair. Under high levels of cellular stress, p53 initiates apoptosis instead. In non-resting cells, the cell cycle consists of G0 -> G1 -> S -> G2 -> M phases, and is tightly regulated at checkpoints between the phases. If the cell has undergone stress, certain proteins are expressed that will prevent the specific sequence of macromolecular interactions at the checkpoint required for progression to the next phase. TIGAR activity can prevent cells progressing into S phase through a checkpoint known in humans as

neg: Cell division cycle 7-related protein kinase transformation for some tumors. Additional transcript sizes have been detected, suggesting the presence of alternative splicing. The gene, CDC7, is involved in the regulation of cell cycle because of the gene product Cdc7 kinase. The protein is expressed at constant levels throughout the cell cycle. The gene coding for the Dbf4 or ASK protein is regulated during the different phases of cell cycle. The concentration of Dbf4 at the G1/S transition of the cell cycle is higher than the concentration at the M/G1 transition. This tells us that Dbf4 is expressed around the time for replication; right after replication is

neg: DNA replication factor CDT1 DNA replication factor CDT1 CDT1 (Chromatin licensing and DNA replication factor 1) is a protein that in humans is encoded by the "CDT1" gene. It is a licensing factor that functions to limit DNA from replicating more than once per cell cycle. The protein encoded by this gene is a key licensing factor in the assembly of pre-replication complexes (pre-RC), which occurs during the G1 phase of the cell cycle. In the assembly of pre-RCs, origin recognition complexes (ORC1-6) recognize and bind to DNA replication origins. CDT1, along with the protein CDC6, are then recruited to the forming pre-RC, followed

neg: RecBCD reflecting the Chi-dependent disassembly of RecBCD observed in vitro under conditions of excess ATP and nicking of DNA at Chi. Under both reaction conditions, the 3' strand remains intact downstream of Chi. The RecA protein is then actively loaded onto the 3' tail by RecBCD. At some undetermined point RecBCD dissociates from the DNA, although RecBCD can unwind at least 60 kb of DNA without falling off. RecA initiates exchange of the DNA strand to which it is bound with the identical, or nearly identical, strand in an intact DNA duplex; this strand exchange generates a joint DNA molecule, such

neg: UHRF1 UHRF1 Ubiquitin-like, containing PHD and RING finger domains, 1, also known as UHRF1, is a protein which in humans is encoded by the "UHRF1" gene. This gene encodes a member of a subfamily of RING-finger type E3 ubiquitin ligases. The protein binds to hemi-methylated DNA during S-phase and recruits the main DNA methyltransferase gene, DNMT1, to regulate chromatin structure and gene expression. Its expression peaks at late G1 phase and continues during G2 and M phases of the cell cycle. It plays a major role in the G1/S transition, and functions in the p53-dependent DNA damage checkpoint. Multiple transcript variants

neg: Cell cycle checkpoint p130 act as co-repressors for E2F4 and E2F5, which work to repress transcription of G1-to-S promoting factors. The third pocket protein, Rb, binds to and represses E2F1, E2F2, and E2F3, which are the E2F proteins with activating abilities . Positive feedback plays an essential role in regulating the progression from G1 to S phase, particularly involving the phosphorylation of Rb by a Cyclin/CDK protein complex. Rb without a phosphate, or unphosphorylated Rb, regulates G0 cell cycle exit and differentiation. During the beginning of the G1 phase, growth factors and DNA damage signal for the rise of cyclin D levels, which

neg: Cyclin D/Cdk4 cycle, for the Start or G1/S checkpoint. Under non-dividing conditions (when the cell is in the G0 phase of the cell cycle), Retinoblastoma protein (Rb) is bound with the E2F transcription factor. Once Cdk4 is activated and is bound with Cyclin D, the Cyclin D/Cdk4 complex phosphorylates Retinoblastoma protein (pRb). Once the Retinoblastoma protein has been phosphorylated, E2F is released. The released E2F is then free to act as a transcription factor and it subsequently binds to DNA promoter regions and activates the expression of proteins required in the next stages of the cell cycle and in DNA replication. Specifically,

neg: DNA replication independently of the cell cycle, through the process of D-loop replication. In vertebrate cells, replication sites concentrate into positions called replication foci. Replication sites can be detected by immunostaining daughter strands and replication enzymes and monitoring GFP-tagged replication factors. By these methods it is found that replication foci of varying size and positions appear in S phase of cell division and their number per nucleus is far smaller than the number of genomic replication forks. P. Heun et al.(2001) tracked GFP-tagged replication foci in budding yeast cells and revealed that replication origins move constantly in G1 and S phase and

neg: Angelika Amon continues until reactivation of CDC28 toward the end of G1. The Amon lab primarily investigates yeast ("Saccharomyces cerevisiae") as a model for understanding the controls that govern cell-cycle progression. As a Whitehead Fellow, her team discovered that CDC20 plays a crucial role in cell division. Her Whitehead team identified an interaction between phosphatase and CDC14 which initiates the exit of cells from mitosis to the G1 phase. Amon's team demonstrated that CDC20 is the target protein in the spindle checkpoint during mitosis. Amon's more recent work has investigated the regulation of chromosome segregation and how chromosomes are accurately transmitted to

neg: Methyltransferase interaction is also an example of a protein-DNA interaction, as another domain of RCC1 interacts directly with DNA when this protein is methylated. When RCC1 is not methylated, dividing cells have multiple spindle poles and usually cannot survive. p53 methylated on lysine to regulate its activation and interaction with other proteins in the DNA damage response. This is an example of regulation of protein-protein interactions and protein activation. p53 is a known tumor suppressor that activates DNA repair pathways, initiates apoptosis, and pauses the cell cycle. Overall, it responds to mutations in DNA, signaling to the cell to fix them

neg: RecBCD molecule fluorescence as an experimental technique used to better understand the function of protein-DNA interactions. The enzyme is also useful in removing linear DNA, either single- or double-stranded, from preparations of circular double-stranded DNA, since it requires a DNA end for activity. RecBCD RecBCD (, "Exonuclease V", "Escherichia coli exonuclease V", "E. coli exonuclease V", "gene recBC endoenzyme", "RecBC deoxyribonuclease", "gene recBC DNase", "gene recBCD enzymes") is an enzyme of the "E. coli" bacterium that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host

neg: Meiotic recombination checkpoint repair process that removes damages from the DNA passed on to gametes. Generally speaking, the cell cycle regulation of meiosis is similar to that of mitosis. As in the mitotic cycle, these transitions are regulated by combinations of gene regulatory factors, cyclin-Cdk complex and the APC. The first major regulatory transition occurs in late G1, when the Start of meiotic cycle is activated by Ime1 instead of Cln3/Cdk1 in mitosis. The second major transition occurs at the entry into metaphase I. The main purpose of this step is to make sure that DNA replication has completed without error so that

neg: Control of chromosome duplication DNA polymerases and the rest of the replicative machinery have to load onto the DNA. These events depend on the assembly of a several proteins to form the pre-initiation complex at the replication origins loaded with pre-replicative complexes. Assembly of the pre-initiation complex depends on the activities of S-Cdks and the protein kinase Cdc7. The pre-initiation complex activates the Mcm helicase and recruits DNA polymerase. When the cell commits to a new cell cycle, after passing through the Start checkpoint, G1 and G1/S cyclin CDK complexes are activated. These activate the expression of the replicative machinery and of S-Cdk cylin

neg: DNA damage (naturally occurring) extent of pyrimidine dimerization (which is indicative of DNA damage) was assessed using sensitive primer extension techniques. It was found that the removal of DNA photolesions was much less efficient in rad9 mutant cells than normal cells, providing evidence that RAD9 is involved in DNA repair. Thus, the role of RAD9 in repairing DNA damage remains unclear. Regardless, it is clear that RAD9 is necessary to sense DNA damage and halt cell division. RAD9 has been suggested to possess 3’ to 5’ exonuclease activity, which is perhaps why it plays a role in detecting DNA damage. When DNA is damaged,

neg: Origin recognition complex Cdc6, Tah11 (a.k.a. Cdt1), and the Mcm2-Mcm7 complex. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase. The ORC is present throughout the cell cycle bound to replication origins, but is only active in late mitosis and early G1. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR). ORC

neg: Neuronal cell cycle However, it is also possible that, under certain conditions, these factors can induce cell cycle re-entry. Under conditions such as DNA damage, oxidative stress, and activity withdrawal these factors have been shown to be upregulated. However the cells usually die in the G1/S checkpoint before DNA has been replicated (Park et al., 1998). The process by which the cell re-enters the cell cycle and dies is called “abortive cell cycle re-entry” and is characterized by the upregulation of cyclin D-cdk4/6 and downregulation of E2F, followed by cell death (Frade and Ovejero-Benito, 2015). In cerebellar granule cells and cortical neurons, E2F1

neg: Pre-replication complex MCM10. MCM10 cooperates with MCM2-7 in the recruitment of Cdc45. Cdc45 then recruits key components of the replisome; the replicative DNA polymerase α and its primase. DNA replication can then begin. During each cell cycle, it is important that the genome be completely replicated once and only once. Formation of the pre-replication complex during late M and early G1 phase is required for genome replication, but after the genome has been replicated the pre-RC must not form again until the next cell cycle. In S. cerevisiae, CDKs prevent formation of the replication complex during late G1, S, and G2 phases

neg: ATM serine/threonine kinase different DNA damage checkpoints, which inhibit the next or maintain the current cell cycle step. There are two main checkpoints, the G1/S and the G2/M, during the cell cycle, which preserve correct progression. ATM plays a role in cell cycle delay after DNA damage, especially after double-strand breaks (DSBs). ATM together with NBS1 act as primary DSB sensor proteins. Different mediators, such as Mre11 and MDC1, acquire post-translational modifications which are generated by the sensor proteins. These modified mediator proteins then amplify the DNA damage signal, and transduce the signals to downstream effectors such as CHK2 and p53. The ATM

neg: DNA replication the cell cycle; DNA replication takes place during the S phase (synthesis phase). The progress of the eukaryotic cell through the cycle is controlled by cell cycle checkpoints. Progression through checkpoints is controlled through complex interactions between various proteins, including cyclins and cyclin-dependent kinases. Unlike bacteria, eukaryotic DNA replicates in the confines of the nucleus. The G1/S checkpoint (or restriction checkpoint) regulates whether eukaryotic cells enter the process of DNA replication and subsequent division. Cells that do not proceed through this checkpoint remain in the G0 stage and do not replicate their DNA. Replication of chloroplast and mitochondrial genomes occurs

neg: Oncovirus head and neck cancer. These three viruses have parallel mechanisms of action, forming an archetype for DNA oncoviruses. All three of these DNA oncoviruses are able to integrate their DNA into the host cell, and use this to transcribe it and transform cells by bypassing the G1/S checkpoint of the cell cycle. DNA oncoviruses transform infected cells by integrating their DNA into the host cell’s genome. The DNA is believed to be inserted during transcription or replication, when the two annealed strands are separated. This event is relatively rare and generally unpredictable; there seems to be no deterministic predictor of

neg: Biochemical switches in the cell cycle this positive feedback does indeed occur. A small amount of Cln3 induces Cln1/2 expression and then the feedback loop takes over, leading to rapid and abrupt exit of Whi5 from the nucleus and consequently coherent expression of G1/S regulon genes. In the absence of coherent gene expression, cells take longer to exit G1 and a significant fraction even arrest before S phase, highlighting the importance of positive feedback in sharpening the G1/S switch. The G1/S cell cycle checkpoint controls the passage of eukaryotic cells from the first gap phase, G1, into the DNA synthesis phase, S. In this switch in

neg: Cotton leaf curl virus the helper begomovirus to support one or more stages of their infection cycle (movement and insect transmission for both molecules and, additionally, replication in the case of DNA β). DNA β is symptom-modulating and typical cotton leaf curl disease symptoms only develop when this molecule is present: in the absence of DNA β, the concentration of viral DNA (DNA A) is low and the symptoms of infection very mild. DNA β has a single open reading frame (βC1 ORF), which encodes a suppressor of RNA silencing. DNA 1 is homologous to the DNA-R component of the nanoviruses and encodes a

neg: E2F vivo footprinting experiments obtained on Cdc2 and B-myb promoters demonstrated E2F DNA binding site occupation during G0 and early G1, when E2F is in transcriptional repressive complexes with the pocket proteins. pRb is one of the targets of the oncogenic human papilloma virus protein E7, and human adenovirus protein E1A. By binding to pRB, they stop the regulation of E2F transcription factors and drive the cell cycle to enable virus genome replication. Activators are maximally expressed late in G1 and can be found in association with E2F regulated promoters during the G1/S transition. The activation of E2F-3a genes follows upon

neg: Reverse Transcription Loop-mediated Isothermal Amplification it binds to itself. The FIP primer binds to the 5’ end of this single strand and accompanied by DNA polymerase, synthesizes a complementary strand. The F3 primer, with DNA polymerase, binds to this end and generates a new double stranded DNA molecule while displacing the previously made single strand. This new single strand that has been released will act as the starting point for the LAMP cycling amplification. The DNA has a dumbbell-like structure as the ends fold in and self anneal. This structure becomes a stem-loop when the FIP or BIP primer once again initiates DNA synthesis at

neg: Epitranscriptome the alternative splicing of certain mRNAs and lncRNAs. mA is not only found on mRNAs, various non-coding RNAs also contain this mark. For instance, XIST, the lncRNA that initiates X-inactivation, is enriched in mA. These mA are recognized and bound by the YTH domain protein YTHDC1. XIST mediated silencing of the X chromosome is negatively affected when XIST is not modified with mA. RNA molecules containing mA are involved in UV-induced DNA damage repair mechanisms. When DNA is damaged, poly(A)+ transcripts containing numerous mA residues accumulate in the region. This facilitates the accessibility of DNA-repairing proteins, such as DNA polymerase

neg: G1 and G1/S cyclins- budding yeast activation by Cln3 in mid-G1, bind Cdk1 (Cdc28) to complete progression through "Start". These cyclins oscillate during the cell cycle - rise in late G1 and fall in early S phase. The primary function of G1/S cyclin-Cdk complexes is to trigger progression through Start and initiate the processes leading to DNA replication, principally by shutting down the various braking systems that suppress S-phase Cdk activity in G1. G1/S cyclins also initiate other early cell-cycles events such as duplication of the spindle pole body in yeast. The rise of G1/S cyclins is accompanied by the appearance of the S cyclins (Clb5

neg: DNA repair damage to DNA. This relaxation allows other proteins in the nucleotide excision repair pathway to enter the chromatin and repair UV-induced cyclobutane pyrimidine dimer damages. After rapid chromatin remodeling, cell cycle checkpoints are activated to allow DNA repair to occur before the cell cycle progresses. First, two kinases, ATM and ATR are activated within 5 or 6 minutes after DNA is damaged. This is followed by phosphorylation of the cell cycle checkpoint protein Chk1, initiating its function, about 10 minutes after DNA is damaged. After DNA damage, cell cycle checkpoints are activated. Checkpoint activation pauses the cell cycle and gives

neg: Ubiquitin their rate of ubiquitination and internalisation. Like monoubiquitination, lysine 63-linked polyubiquitin chains also has a role in the trafficking some membrane proteins. Proliferating cell nuclear antigen (PCNA) is a protein involved in DNA synthesis. Under normal physiological conditions PCNA is sumoylated (a similar post-translational modification to ubiquitination). When DNA is damaged by ultra-violet radiation or chemicals, the SUMO molecule that is attached to a lysine residue is replaced by ubiquitin. Monoubiquitinated PCNA recruits polymerases that can carry out DNA synthesis with damaged DNA; but this is very error-prone, possibly resulting in the synthesis of mutated DNA. Lysine 63-linked polyubiquitination of

neg: DNA base flipping DNA, enzymes need to repair any damage. There are many types of DNA repair. Base excision repair utilizes base flipping to flip the damaged base out of the double helix and into the specificity pocket of a glycosylase which hydrolyzes the glycosidic bond and removes the base. DNA glycosylases interact with DNA, flipping bases to determine a mismatch. An example of base excision repair occurs when a cytosine base is deaminated and becomes a uracil base. This causes a U:G mispair which is detected by Uracil DNA glycosylase. The uracil base is flipped out into the glycosylase active pocket where

neg: Start point (yeast) mutant, cdc28, which arrests in very early stages of the cell cycle, but he also recognised that the presence of mating factors could result in similar phenotypes of inhibited bud formation and lack of DNA synthesis. Notably, cells that were exposed to mating factors at later stages of the cycle continued division, and only arrested when the resulting daughter cells reached the “early stages” (or more technically, the G1 phase) of the cell cycle. These results suggest that both cdc28 and mating pheromones mediate such early events, and further suggest that there exists a point in the cell cycle where

neg: Indole-3-carbinol a natural anticarcinogen (indole-3-carbinol) found in human diet was claimed by Dashwood, et al., in 1989. Indole-3-carbinol induces a G1 growth arrest of human reproductive cancer cells. This is potentially relevant to the prevention and treatment of cancer, as the G1 phase of cell growth occurs early in the cell life cycle, and, for most cells, is the major period of cell cycle during its lifespan. The G1 phase is marked by synthesis of various enzymes that are required in the next ("S") phase, including those needed for DNA replication. Overuse of indole-3-carbinol supplements in the hope of preventing cancer

neg: Midblastula replication of cells. At this stage, the zygote starts producing its own mRNAs that are made from its own DNA, and no longer uses the maternal mRNA. This can also be called the maternal to zygotic transition. The maternal mRNAs are then degraded. Since the cells are now transcribing their own DNA, this stage is where expression of paternal genes is first observed. When the zygote begins to produce its own mRNA, the cell cycle begins to slow down and the G1 and G2 phases are added to the cell cycle. The addition of these phases allows the cell to

neg: Lytic cycle Lytic cycle The lytic cycle ( ) is one of the two cycles of viral reproduction (referring to bacterial viruses or bacteriophages), the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteriophages that only use the lytic cycle are called virulent phages (in contrast to temperate phages). In the lytic cycle, the viral DNA exists as a separate free floating molecule within the bacterial cell, and replicates separately from the host bacterial DNA, whereas in the lysogenic cycle, the viral DNA is located within the host DNA. This is

neg: Pre-replication complex to bind the AT-rich portion of the origin of replication in "S. pombe" using AT hook motifs. The mechanism of origin recognition in higher eukaryotes is not well understood but it is thought that the ORC1-6 proteins depend on unusual DNA topology for binding. Assembly of the pre-replication complex only occurs during late M phase and early G1 phase of the cell cycle when cyclin-dependent kinase (CDK) activity is low. This timing and other regulatory mechanisms ensure that DNA replication will only occur once per cell cycle. Assembly of the pre-RC relies on prior origin recognition, either by DnaA in

neg: Philadelphia chromosome apoptosis downstream of BCR-ABL (Cortez et al). Interactions with the IL-3 receptor also induce the Ras/RAF/MEK/ERK pathway to phosphorylate transcription factors which play a role in driving the G1/S transition of the cell cycle. The c-Abl gene in wild-type cells is implicated in DNA binding, which affects such processes as DNA transcription, repair, apoptosis, and other processes underlying the cell cycle. While the nature of this interaction has been debated, evidence exists to suggest that c-Abl phosphorylates HIPK2, a serine/threonine kinase, in response to DNA damage and promotes apoptosis in normal cells. The BCR-ABL fusion, in contrast, has been shown

neg: Proliferative index thymidine-labeling indexing, incubates cells with radiolabeled bromodeoxyuridine, which is taken up at a greater rate by proliferating cells, and then uses a film to image the distribution of radiolabeled bromodeoxyuridine in cells. Evaluating DNA histograms through flow cytometry provides an estimate of the fractions of cells within each of the phases in the cell cycle. Cell nuclei are stained with a DNA binding stain and the amount of staining is measured from the histogram. The fractions of cells within the different cell cycle phases (G0/G1, S and G2/M compartments) can then be calculated from the histogram by computerized cell cycle

neg: DNA replication factor CDT1 Null-mutations for CDT1 are lethal in yeast; the spores undergo mitosis without DNA replication. The overexpression of CDT1 causes rereplication in H. sapiens, which activates the CHK1 pathway, preventing entry into mitosis. DNA replication factor CDT1 CDT1 (Chromatin licensing and DNA replication factor 1) is a protein that in humans is encoded by the "CDT1" gene. It is a licensing factor that functions to limit DNA from replicating more than once per cell cycle. The protein encoded by this gene is a key licensing factor in the assembly of pre-replication complexes (pre-RC), which occurs during the G1 phase of the

neg: Direct DNA damage Direct DNA damage Direct DNA damage can occur when DNA directly absorbs a UVB photon, or for numerous other reasons. UVB light causes thymine base pairs next to each other in genetic sequences to bond together into pyrimidine dimers, a disruption in the strand, which reproductive enzymes cannot copy. It causes sunburn and it triggers the production of melanin. Other names for the "direct DNA damage" are: Due to the excellent photochemical properties of DNA, this nature-made molecule is damaged by only a tiny fraction of the absorbed photons. DNA transforms more than 99.9% of the photons into harmless heat

neg: DNA damage (naturally occurring) for life is that cells make large investments in DNA repair processes. As pointed out by Hoeijmakers, repairing just one double-strand break could require more than 10,000 ATP molecules, as used in signaling the presence of the damage, the generation of repair foci, and the formation (in humans) of the RAD51 nucleofilament (an intermediate in homologous recombinational repair). (RAD51 is a homologue of bacterial RecA.) If the structural modification occurs during the G1 phase of DNA replication, the G1-S checkpoint arrests or postpones the furtherance of the cell cycle before the product enters the S phase. Differentiated somatic cells of

neg: Polyomaviridae small tumor antigen (ST) and large tumor antigen (LT) - are expressed first, from a single alternatively spliced messenger RNA strand. These proteins serve to manipulate the host's cell cycle - dysregulating the transition from G1 phase to S phase, when the host cell's genome is replicated - because host cell DNA replication machinery is needed for viral genome replication. The precise mechanism of this dysregulation depends on the virus; for example, SV40 LT can directly bind host cell p53, but murine polyomavirus LT does not. LT induces DNA replication from the viral genome's non-coding control region (NCCR), after which

neg: Cell synchronization This serves to halt DNA synthesis by depriving DNA polymerase of dNTPs at replication forks. Hydroxyurea is also used to treat certain types of cancer and blood disorders. Aphidocolin is a fungus-derived tetracyclic diterpenoid that acts as a selective inhibitor for DNA polymerase α. This enzyme is necessary for replicative DNA synthesis, but does not disrupt DNA repair synthesis or mitochondrial DNA replication. A single commonly-used chemical method exists for synchronization of cells in G1. It involves Lovastatin, a reversible competitive inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A reductase, an enzyme vital in the production of mevalonic acid. Mevalonic acid is a key

neg: Bert Vogelstein now one of the core technologies used in some next-generation, massively parallel sequencing instruments.More recently, they developed a digital-PCR based technique called SafeSeqS, in which every DNA template molecule is recognized by a unique molecular barcode. SafeSeqS dramatically enhances the ability to identify rare variants among DNA sequences, allowing such variants to be detected when they are present in only 1 in more than 10,000 total DNA molecules. In the mid 2000s, Vogelstein started collaborating with the group of Martin Nowak at Harvard University. Together with their groups, they developed mathematical models to explain the evolution of resistance against targeted

neg: DNA replication the template DNA and initiates synthesis of a short complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the fragments of DNA are joined together by DNA ligase. As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate. This process results in a build-up of twists in the DNA ahead. This build-up forms a torsional resistance that would eventually halt the progress of the replication fork. Topoisomerases are enzymes that temporarily break the strands of DNA, relieving the tension caused

neg: Transduction (genetics) thousands of generations. If the lysogen is induced (by UV light for example), the phage genome is excised from the bacterial chromosome and initiates the lytic cycle, which culminates in lysis of the cell and the release of phage particles. The lytic cycle leads to the production of new phage particles which are released by lysis of the host." The packaging of bacteriophage DNA has low fidelity and small pieces of bacterial DNA, together with the bacteriophage genome, may become packaged into the bacteriophage genome. At the same time, some phage genes are left behind in the bacterial chromosome. There

neg: Fluorescent in situ sequencing entire sample can be imaged in each cycle. The fluorescent tags are then cleaved and washed away, and the next cycle is initiated. Each rolony – corresponding to a single “parent” DNA or RNA molecule in the tissue – thus appears across a series of fluorescent images, as a localized “spot” with a sequence of colors corresponding to the nucleotide sequence of the parent molecule. The nucleotide sequence of each DNA or RNA molecule is thus read out in-situ via fluorescent microscopy. The development of FISSEQ began in the Church laboratory over a decade ago. The underlying principles are similar

neg: Cisplatin cell because the intracellular chloride concentration is only 3–20% of the approximately 100 mM chloride concentration in the extracellular fluid. The water molecule in "cis"-[PtCl(NH)(HO)] is itself easily displaced by the "N"-heterocyclic bases on DNA. Guanine preferentially binds. Subsequent to formation of [PtCl(guanine-DNA)(NH)], crosslinking can occur via displacement of the other chloride, typically by another guanine. Cisplatin crosslinks DNA in several different ways, interfering with cell division by mitosis. The damaged DNA elicits DNA repair mechanisms, which in turn activate apoptosis when repair proves impossible. In 2008, researchers were able to show that the apoptosis induced by cisplatin on human

neg: Cell cycle checkpoint gene family is a group of transcription factors that target many genes that are important for control of the cell cycle, including cyclins, CDKs, checkpoint regulators, and DNA repair proteins. Misregulation of the E2F family is often found in cancer cases, providing evidence that the E2F family is essential for the tight regulation of DNA replication and division. The three pocket proteins are Retinoblastoma (Rb), p107, and p130, which bind to the E2F transcription factors to prevent progression past the G1 checkpoint. The E2F gene family contains some proteins with activator mechanisms and some proteins with repressing mechanisms. P107 and

neg: Satraplatin while satraplatin's cyclohexamine makes it asymmetrical which contributes to some of the drug's special properties. A large problem with cisplatin and other platinum based anti-cancer drugs is that the body can develop resistance to them. A major way that this happens is through a mammalian nucleotide excision repair pathway which repairs damaged DNA. However, some studies show that satraplatin compared to other platinum anti-cancer drugs can be elusive and are not recognized by the DNA repair proteins due to the different adducts on the molecule (cyclohexamine). Since satraplatin is not recognized by the DNA repair proteins the DNA remains damaged,

neg: Cyclin A makes chromatin capable of replication. When the amount of cyclin A/CDK2 complex reaches a threshold level, it terminates the assembly of the pre-replication complex made by cyclin E/CDK2. As the amount of Cyclin A/CDK2 complex increases, the complex initiates DNA replication. Cyclin A has a second function in S phase. In addition to initiating DNA synthesis, Cyclin A ensures that DNA is replicated once per cell cycle by preventing the assembly of additional replication complexes. This is thought to occur through the phosphorylation of particular DNA replication machinery components, such as CDC6, by the cyclin A/CDK2 complex. Since the action

neg: E2F member: Homo sapiens E2F1 mRNA or E2F1 protein sequences from NCBI protein and nucleotide database. X-ray crystallographic analysis has shown that the E2F family of transcription factors has a fold similar to the winged-helix DNA-binding motif. E2F family members play a major role during the G1/S transition in mammalian and plant cell cycle (see KEGG cell cycle pathway). DNA microarray analysis reveals unique sets of target promoters among E2F family members suggesting that each protein has a unique role in the cell cycle. Among E2F transcriptional targets are cyclins, CDKs, checkpoints regulators, DNA repair and replication proteins. Nonetheless, there is

neg: Single-molecule magnetic sequencing drag force. Currently, it is possible to measure 10 hairpin open-close cycle per second. Additional complications include the existence of a secondary hairpin structure in the DNA of interest. In such a case the DNA loop to be ligated must be designed such that it its closing is favored over the closing of the endogenous loop in the DNA of interest. Single-molecule magnetic sequencing Magnetic sequencing is a single-molecule sequencing method in development. A DNA hairpin, containing the sequence of interest, is bound between a magnetic bead and a glass surface. A magnetic field is applied to stretch the hairpin

neg: DNA unwinding element is replicated only once and that this is occurring in the proper location at the proper time. Operates in response to extracellular signals that coordinate initiation of division, differently from tissue to tissue. External signals trigger replication in S phase via production of cyclins which activate cyclin-dependent kinases (CDK) to form complexes. DNA replication in eukaryotes initiates upon origin recognition complex (ORC) binding to the origin. This occurs at G cell phase serving to drive the cell cycle forward into S phase. This binding allows for further factor binding to create a pre-replicative complex (pre-RC). Pre-RC triggered to initiate when

neg: G1/S transition DNA separation in the M phase. After complete synthesis of its DNA, the cell enters the G2 phase where it continues to grow in preparation for mitosis. Following interphase, the cell transitions into mitosis, containing four sub stages: prophase, anaphase, metaphase, and telophase. In mitosis, DNA condenses into chromosomes, which are lined up and separated by the mitotic spindle. After duplicate DNA is separated on opposite ends of the cell, the cytoplasm of the cell is split in two during cytokinesis resulting in two daughter cells. As with most processes in the body, the cell cycle is highly regulated to

neg: Biochemical switches in the cell cycle that parameterization is very important for circuit function. If the dynamics of the input are comparable or faster than the response of the system, the response may appear hysteretic. Three cell cycle switches are described below that achieve abrupt and/or irreversible transitions by exploiting some of the mechanisms described above. The G1/S transition, more commonly known as the Start checkpoint in budding yeast (the restriction point in other organisms) regulates cell cycle commitment. At this checkpoint, cells either arrest before DNA replication (due to limiting nutrients or a pheromone signal), prolong G1 (size control), or begin replication and progress through

neg: CDK-activating kinase controls basal gene transcription. In addition to regulating transcription, CAK also enhances transcription by phosphorylating retinoic acid and estrogen receptors. Phosphorylation of these receptors leads to increased expression of target genes. In leukemic cells, where DNA is damaged, CAK’s ability to phosphorylate retinoic acid and estrogen receptors is decreased. Decreased CAK activity creates a feedback loop, which turns off TFIIH activity. CAK also plays a role in DNA damage response. The activity of CAK associated with TFIIH decreases when DNA is damaged by UV irradiation. Inhibition of CAK prevents cell cycle from progressing. This mechanism ensures the fidelity of chromosome

neg: FOXO1 active. A study detects that FOXO1 regulates the nuclear localization of p27KIP1 in porcine granulosa cells and impacts cell cycle progression. Furthermore, FOXO1-mediated cell cycle arrest is linked with cyclin D1 and cyclin D2 suppression in mammals. It was detected that human FOXO1 is linked with the cyclin D1 promoter using chromatin immunoprecipitation assays (ChIP assays). H215R is a human FOXO1 mutant, which cannot bind to the canonical FRE to induce expression of p27KIP1, repress cyclin D1 and cyclin D2 promoter activity and encourages cell cycle arrest at cyclin G1 (CCNG1). As a result of that, activation of FOXO1 prevents

neg: Colocalization in real-time single-molecule fluorescence microscopy to detect interactions between fluorescently labeled molecular species. In this case, one species (e.g. a DNA molecule) is typically immobilized on the imaging surface, and the other species (e.g. a DNA-binding protein) is supplied to the solution. The two species are labeled with dyes of spectrally resolved (>50 nm) colors, e.g. cyanine-3 and cyanine-5. Fluorescence excitation is typically carried out in total internal reflection mode which increases the signal-to-noise ratio for the molecules at the surface with respect to the molecules in bulk solution. The molecules are detected as spots appearing on the surface in

neg: Excinuclease Excinuclease Excision endonuclease, also known as excinuclease or UV-specific endonuclease, is a nuclease (enzyme) which excises a fragment of nucleotides during DNA repair. The excinuclease cuts out a fragment by hydrolyzing two phosphodiester bonds, one on either side of the lesion in the DNA. This process is part of "nucleotide excision repair", a mechanism that can fix specific types of damage to the DNA in the G1 phase of the eukaryotic cell cycle. Such damage may include thymine dimers created by UV rays as well as the bulky distortions in DNA caused by oxidized benzopyrenes from sources such as cigarette

neg: Biochemical switches in the cell cycle the rest of the cell cycle. The G1/S regulatory network or regulon in budding yeast includes the G1 cyclins Cln1, Cln2 and Cln3, Cdc28 (Cdk1), the transcription factors SBF and MBF, and the transcriptional inhibitor Whi5. Cln3 interacts with Cdk1 to initiate the sequence of events by phosphorylating a large number of targets, including SBF, MBF and Whi5. Phosphorylation of Whi5 causes it to translocate out of the nucleus, preventing it from inhibiting SBF and MBF. Active SBF/MBF drive the G1/S transition by turning on the B-type cyclins and initiating DNA replication, bud formation and spindle body duplication. Moreover, SBF/MBF

neg: Esther Lederberg agar plate, she saw plaques, which were known to be caused by bacteriophages. The source of the bacteriophage was the parental K12 strain. The UV treatment had "cured" the bacteriophage from the mutant, making it sensitive to infection by the same bacteriophage that the parent produced. The bacteriophage was named λ. Lambda phage genetic material consists of a double-stranded DNA molecule with 5' twelve-base-pair sticky ends (cos sites), which permit circularization of the DNA molecule. It shows a lytic cycle and a lysogenic cycle. Studies on the control of these alternative cycles have been very important for our understanding of