• These include DNA damage repair, DNA replication, transcriptional regulation, and cell cycle checkpoint activation. (wikipedia.org)
  • Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. (elifesciences.org)
  • Although inherently unstable, growth factor signaling leads to increased MYC levels and its association with MAX forming a transcriptional heterodimer complex that binds to conserved E-box elements (consensus CACGTG) in the promoters of target genes leading to gene activation [ 1 ]. (oncotarget.com)
  • The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA. (lookformedical.com)
  • Eukaryotic cells can rapidly adjust their transcriptional profile in response to molecular needs. (biomedcentral.com)
  • H3.3 knockout followed by RNA-seq reveals large-scale transcriptional alterations in functionally important genes. (biomedcentral.com)
  • Our results provide an evolutionary perspective on H3.3's conserved role in maintaining the transcriptional landscape of cells and on the emergence of specialized chromatin assembly pathways. (biomedcentral.com)
  • Here we define the transcriptional response of B. anthracis Sterne (34F2) to iron depleted conditions. (omictools.com)
  • TOPBP1 primarily regulates the DNA damage repair response through its ability to activate the damage response kinase, ataxia-telangiectasia mutated and RAD3-related (ATR). (wikipedia.org)
  • It also directly binds to BubR1, a kinetochore-associated kinase implicated in the mitotic checkpoint, the major cell cycle control pathway in which unattached kinetochores prevent anaphase onset. (rupress.org)
  • Thus, CENP-E is required for enhancing recruitment of its binding partner BubR1 to each unattached kinetochore and for stimulating BubR1 kinase activity, implicating it as an essential amplifier of a basal mitotic checkpoint signal. (rupress.org)
  • other specificity is tiny gene activity and distribution browser through the kinase of the R-RasGAP complex ileal to suitable or through the functionality of RhoA. (evakoch.com)
  • Through these BRCT specific interactions TOPBP1 mediates DNA damage repair, DNA replication, transcription, and mitosis. (wikipedia.org)
  • Therefore, the conversion of the DSB ends from double-stranded to single-stranded DNA, which is necessary to initiate DSB repair by homologous recombination, is responsible for loss of transcription around a DSB in S. cerevisiae . (elifesciences.org)
  • The proteins involved in homologous recombination have to work around other processes that go on inside the nucleus, such as the transcription of DNA in genes into RNA molecules. (elifesciences.org)
  • Previous research has reported that forming a double-strand break in the DNA reduces the levels of transcription for the genes that surround the break, but it was not clear how this occurred. (elifesciences.org)
  • In mammalian cells, inhibiting the transcription of genes around a double-strand DNA break depends on a signaling pathway that is activated whenever DNA damage is detected. (elifesciences.org)
  • Instead, the experiments indicate that it is the resection of the DNA around a double-strand break to form single-stranded tails that inhibits transcription in budding yeast. (elifesciences.org)
  • One of the next challenges will be to see if the resection process makes any contribution to changes in the transcription of genes that surround a double-strand break in mammals as well. (elifesciences.org)
  • A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the cyclophilins within pre-mRNA splicing and cellular signalling, and within transcription and cell cycle regulation for the parvulins. (biomedcentral.com)
  • Recent breakthroughs have uncovered more and more DNA replication licensing machinery proteins (ORC, Cdc6, Cdt1, geminin, etc.) functioning in other cell cycle events, including centrosome replication, mitotic events, transcription and so on. (intechopen.com)
  • ERCC2 is the plant around the proliferation in gap with the Phenylacetate IFT of ERCC3, encoding an many transcription( Coin et al. (evakoch.com)
  • e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens. (lookformedical.com)
  • These regulators include canonical genes that control lipid metabolism as well as genes involved in ubiquitination, transcription, and mitochondrial function. (stanford.edu)
  • ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over the promoters, gene bodies, and transcription termination sites of highly transcribed genes. (biomedcentral.com)
  • Once activated by DSBs, ATM/Tel1 and ATR/Mec1 promote DSB repair, delay cell cycle progression or trigger the elimination of genetically unstable cells by inducing cell death. (elifesciences.org)
  • The proto-oncogene c- MYC (referred to as MYC ) represents a master regulator via integration of external mitogenic signaling with the activation of genes required for cell cycle progression [ 1 ]. (oncotarget.com)
  • During cell growth and proliferation, ubiquitin plays an outsized role in promoting progression through the cell cycle. (intechopen.com)
  • Progression through the cell cycle is driven by the oscillating activity of Cyclin Dependent Kinases (CDKs). (intechopen.com)
  • Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. (lookformedical.com)
  • TIPI-gTOW is also useful for analyzing genetic interactions of essential genes whose deletion mutants cannot be obtained. (biomedcentral.com)
  • Following instances of DNA damage that lead to double stranded breaks (DSBs) and subsequent repair mediated resection, there will be long sequences of single stranded DNA (ssDNA) exposed. (wikipedia.org)
  • These single-stranded DNA 'tails' are then free to interact with an intact copy of the same DNA sequence from elsewhere in the cell's nucleus, which is used as a guide when repairing the damage. (elifesciences.org)
  • And, G-quadruplex formation on single stranded DNA is one of the ways that the telomeric DNA is protected from oxidative stress and from triggering the DNA-damage response (DDR), which causes cellular senescence. (anti-agingfirewalls.com)
  • The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. (lookformedical.com)
  • The G 2 gap phase further separates S-phase from mitosis, allowing for continued cell growth and maturation before cell division. (rupress.org)
  • The pre-replication complex (pre-RC) assembly or the DNA replication licensing is the first step in DNA replication initiation, characterized by the sequential recruitment of ORCs, Cdc6, Cdt1 and MCMs to the DNA replication origins to form the pre-RC at the end of mitosis ( Bell and Dutta 2002 ). (intechopen.com)
  • DksA-DnaJ redox interactions provide a theoretical explanation for why spindle checkpoint activity with direct comparisons between meiosis and mitosis in cells containing the gene of interest were used to generate cDNA using 100 U M-MLV reverse transcriptase (Promega). (kameshwarmahadev.com)
  • The MYC proto-oncogene serves as a rheostat coupling mitogenic signaling with the activation of genes regulating growth, metabolism and mitochondrial biogenesis. (oncotarget.com)
  • Genes encoding proteins involved in cell growth, metabolism, ribosome biogenesis, protein synthesis and mitochondrial function have all be defined as potential MYC targets. (oncotarget.com)
  • Homologous recombination' is one of the main mechanisms used by cells to repair DNA double-strand breaks. (elifesciences.org)
  • some of lost genes are homologous to those of host cells. (bvsalud.org)
  • In this chapter, we mainly discuss the coordination regulations between DNA replication initiation and other cell cycle events that ensure genomic integrity. (intechopen.com)
  • The precise regulations of pre-RC protein levels and assembly are effective ways to prevent reassembly of de novo MCM2-7 onto the replicated origins to re-license and re-replicate the genomic DNA in the subsequent phases of the same cell cycle ( Figure 1) . (intechopen.com)
  • Problems that arise during DNA replication can drive genomic alterations that are instrumental in the development of cancers and many human genetic disorders. (elifesciences.org)
  • The term "oncotarget" encompasses all molecules, pathways, cellular functions, cell types, and even tissues that can be viewed as targets relevant to cancer as well as other diseases. (oncotarget.com)
  • Meiosis is a specialized cellular program required to create haploid gametes from diploid parent cells. (biorxiv.org)
  • Although a number of approaches have been used to predict gene functions and interactions, tools that analyze the essential coordination of functional components in cellular processes still need to be developed. (biomedcentral.com)
  • In this work, we present a new approach to study the cooperation of functional modules (sets of functionally related genes) in a specific cellular process. (biomedcentral.com)
  • A cooperative module pair is defined as two modules that significantly cooperate with certain functional genes in a cellular process. (biomedcentral.com)
  • This method identifies cooperative module pairs that significantly influence a cellular process and the correlated genes and interactions that are essential to that process. (biomedcentral.com)
  • These results provide a global view of the cell cycle and the method can be used to discover the dynamic coordination properties of functional components in other cellular processes. (biomedcentral.com)
  • Identifying the essential components in a specific biological process and detecting the associations among these components in response to various conditions are important for understanding cellular functions. (biomedcentral.com)
  • In addition to supplying cellular energy, mitochondria are involved in other tasks, such as signaling , cellular differentiation , and cell death , as well as maintaining control of the cell cycle and cell growth . (wikipedia.org)
  • [20] This finding has led to general acceptance of the endosymbiotic hypothesis - that free-living prokaryotic ancestors of modern mitochondria permanently fused with eukaryotic cells in the distant past, evolving such that modern animals, plants, fungi, and other eukaryotes are able to respire to generate cellular energy . (wikipedia.org)
  • If the target protein expression reaches the upper limit, i.e., essential cellular functions come to a halt when the level of protein exceeds a certain limit, the gene/plasmid copy number must decrease to below the upper limit. (biomedcentral.com)
  • It also plays a critical role in DNA replication initiation and regulation of the cell cycle. (wikipedia.org)
  • We now know those structures are very relevant to many critical biological processes like gene regulation, expression of telomerase and telomere maintenance, understanding of growth/oncogenes like C-myc, understanding of organismic development, comprehension of certain enigmatic diseases like ALS and possible new cancer treatments. (anti-agingfirewalls.com)
  • These unusual DNA structures play critical roles in regulation of very basic biological functions and are integral part of the complex regulatory systems of living beings. (anti-agingfirewalls.com)
  • In addition HIV-1 Vpr protein alters the cell-cycle regulation by hijacking centrosome functions. (biomedcentral.com)
  • Genome-wide transcript analysis showed that B. anthracis undergoes considerable changes in gene expression during growth in iron-depleted media, including the regulation of known and candidate virulence factors. (omictools.com)
  • TOPBP1/9-1-1 recruitment is conducted independent of ATRIP/ATR which serves as a regulatory mechanism that prevents both premature and non-specific activation of the DNA damage response pathway. (wikipedia.org)
  • Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. (omictools.com)
  • The identification of both replication factor C and DNA helicases as critical for sister chromatid pairing has brought new insights into this fundamental process. (rupress.org)
  • This so-called recombination-dependent replication (RDR) helps ensure that DNA is fully replicated prior to sister chromatid segregation, thereby avoiding mitotic catastrophes. (elifesciences.org)
  • In human TOPBP1 the BRCT0, BRCT1, and BRCT2 domains uniquely exist in triple domain form, which is in contrast to the yeast Dpb11 canonical double domain. (wikipedia.org)
  • We find that this type of non-canonical fork convergence in fission yeast is prone to trigger deletions between repetitive DNA sequences via a mechanism we call Inter-Fork Strand Annealing (IFSA) that depends on the recombination proteins Rad52, Exo1 and Mus81, and is countered by the FANCM-related DNA helicase Fml1. (elifesciences.org)
  • In most eukaryotes, two classes of histones have been described: (1) replicative or canonical histones, expressed only during the S phase of the cell cycle, which are assembled onto chromatin in a DNA replication-dependent (RD) manner, and (2) variant histones, which differ in their primary amino acid sequences, are expressed throughout the cell cycle, and can be deposited in a replication-independent (RI) fashion [ 2 ]. (biomedcentral.com)
  • [1] pl. mitochondria ) is an organelle found in the cells of most eukaryotes , such as animals , plants and fungi . (wikipedia.org)
  • The commonly used gene-deletion experiments reduce the expression of a target protein to 0. (biomedcentral.com)
  • Deletion of either gene (GBAA0552 or GBAA1340) resulted in attenuation in a murine model of infection. (omictools.com)
  • These results are consistent with previous studies and demonstrate that our methodology is effective for studying cooperative mechanisms in the cell cycle. (biomedcentral.com)
  • In past decades, theories were divided for your understanding in two main aspects: they considered aging as a process scheduled under the control of genes and other mechanisms due to unscheduled (stochastic) [7-9]. (medcraveonline.com)
  • also, the 5' download volatility trading of the cytoplasm is involved actually by cationic end-product by the RNase proximity water cell, which has a direct RNA( RNA H1 in pathways) and at least 10 Fructose-6-phosphate nucleus( activated in Jarrous 2002, Xiao et al. (evakoch.com)
  • and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell. (lookformedical.com)
  • Proteins found in the nucleus of a cell. (lookformedical.com)
  • Although most of a eukaryotic cell's DNA is contained in the cell nucleus , the mitochondrion has its own genome ("mitogenome") that is substantially similar to bacterial genomes. (wikipedia.org)
  • They localize in close proximity to the nucleus for the duration of interphase and play major roles in numerous cell functions. (biomedcentral.com)
  • Centrosomes are animal-specific non-membranous organelles that localize in close proximity to the cell nucleus for the duration of interphase. (biomedcentral.com)
  • The cell cycle is the process of accurate self-reproduction and proliferation of a cell. (intechopen.com)
  • Misregulation of the cell cycle may result in malignant cell proliferation, tumorigenesis or cell death. (intechopen.com)
  • Notably, the G1/S boundary represents a major barrier to cell proliferation and is universally dysfunctional in cancer cells, allowing for the unbridled proliferation observed in malignancy. (intechopen.com)
  • Numerous E3 ubiquitin ligases, which facilitate the ubiquitination of specific substrates, have been shown to control G1/S. In this chapter, we will discuss components in the ubiquitin proteasome system that are implicated in G1/S control, how these enzymes are interconnected, gaps in our current knowledge, and the potential role of these pathways in the cancer cycle and disease proliferation. (intechopen.com)
  • PCNA expression correlates with the proliferation activity of several malignant and non-malignant cell types. (lookformedical.com)
  • G-quadruplexes are secondary semi-stable folded structures found in our DNA and RNA which tend to assemble around guanine-rich sequences in the presence of cation molecules like potassium. (anti-agingfirewalls.com)
  • This traditional approach has now changed as well as considering the role of evolution in aging, divide the theories into two broad categories: biological, where it continues case aging as an evolutionary event genetically controlled, and chemical as a somatic process resulting from the cumulative chemical damage to bio molecules [10,11]. (medcraveonline.com)
  • The TOPBP1 gene encodes a scaffold protein which facilitates interactions between different proteins at specific times and locations. (wikipedia.org)
  • It accomplishes these interactions with other protein partners through its breast cancer associated gene 1 C-terminus (BRCT) domains. (wikipedia.org)
  • In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
  • In this work, we propose a new approach to identifying condition-related cooperative interactions, and importantly, we establish a cell cycle-specific cooperation module network. (biomedcentral.com)
  • Distinct functions of macrophage-derived and cancer cell-derived cathepsin Z combine to promote tumor malignancy via interactions with the extracellular matrix. (uni-freiburg.de)
  • It studied well assembled as a 9+0 download climate change forests and redd lessons for institutional design 2012 that is solved damage interactions for macromolecular turnover into small class reactions. (evakoch.com)
  • We first tested the feasibility of this method using ADE2 as a marker and then analyzed some cell cycle regulators to reveal genetic interactions. (biomedcentral.com)
  • Using this strain, we studied genetic interactions between cell cycle regulators and CDC20 , and the result was highly consistent with the previously identified interactions. (biomedcentral.com)
  • After the XPC p16-INK4A and the UV-DDB hemolytic digestion substituted DNA, a separate localization adaptor TFIIH controls identified to the subunit recycling ubiquitin( many) dephosphorylation( Volker et al. (evakoch.com)
  • High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds. (waseda.jp)
  • In this study, we developed a reliable high-throughput (HT) platform for yeast morphological profiling using drug-hypersensitive strains to minimize compound use, HT microscopy to speed up data generation and analysis, and a generalized linear model to predict targets with high reliability. (waseda.jp)
  • Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. (omictools.com)
  • Model organisms such as yeast, fruit flies, and worms have advanced the study of genomics, eukaryotic biology, and evolution. (cshlpress.org)
  • Changes in TOPBP1 gene expression are associated with pulmonary hypertension, breast cancer, glioblastoma, non-small cell lung cancer, and sarcomas. (wikipedia.org)
  • A large number of E-box containing genes have been identified underlying the important role of MYC as a master regulator of gene expression [ 2 ]. (oncotarget.com)
  • Here, we leverage a set of genome-edited human PLIN2 reporter cell lines in a series of CRISPR-Cas9 loss-of-function screens, identifying genetic modifiers that influence PLIN2 expression and post-translational stability under different metabolic conditions and in different cell types. (stanford.edu)
  • In gTOW, we thus increase the expression of a protein to a limit by increasing the copy number and then determine the upper limit by measuring the corresponding copy number of the gene. (biomedcentral.com)
  • To reduce the expression of a gene/protein, we need to reduce the production rate of the transcript, increase the degradation rate of the transcript, decrease the production rate of the protein, or increase the degradation rate of the protein. (biomedcentral.com)
  • The RI histone variants have an uneven distribution across the genome, carry specific posttranslational modifications (PTMs), and can affect gene expression by altering the chromatin state [ 3 ]. (biomedcentral.com)
  • Single-cell imaging of ATP-reduced yeast mutants revealed that ATP levels in these mutants underwent stochastic and transient depletion, which promoted the cytotoxic aggregation of endogenous proteins and pathogenic proteins, such as huntingtin and α-synuclein. (waseda.jp)
  • Nup2 is a nonessential nucleoporin that functions in nuclear transport, boundary activity, and telomere silencing in mitotically dividing cells. (biorxiv.org)
  • FANCD2 modulates the mitochondrial stress response to prevent common fragile site instability. (u-paris.fr)
  • To mediate these aspects of DNA repair, TOPBP1 was found to associate with Rad9, which forms a complex with Rad1 and Hus1, hereby termed the 9-1-1 DNA repair clamp. (wikipedia.org)
  • This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. (bvsalud.org)
  • We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. (omictools.com)
  • Tseng BS, Tan L, Kapoor TM, Funabiki H. Spc105 recruits PP1 to bind Spc105KNL1 and silence the spindle checkpoint is less persistent in meiosis I has a more robust to confounding (Fig 3B), allowing larger p values approximate the SDE estimator and result in bending. (kameshwarmahadev.com)
  • The Long-Term Public Health Implications for the analysis of differentially expressed genes in Drosophila. (kameshwarmahadev.com)
  • Alternatively, dasatinib may possibly not be capable of mitigating non apoptotic pathways of motor neuron degeneration caused by mutant SOD1, because non apoptotic programmed cell death has also been implicated in motor neuron harm in G93A mice. (smadpathway.com)
  • Most of the identified module pairs cover cooperative pathways and components essential to the cell cycle. (biomedcentral.com)
  • Initial, we tested for statistical enrichment of genes with individual Gene Ontology functional annotations, using ONTOLOGIZER version two.0, with the Phrase for Term calculation method and Bonferroni corrected P 0. (smadpathway.com)
  • The fundamental repeating unit of chromatin is the nucleosome which is composed of two copies each of the four core histones H2A, H2B, H3, and H4 around which about 147 bp of DNA is wrapped [ 1 ]. (biomedcentral.com)
  • loop kappa p21 D cell 4( ABCD4) is shown to reduce the CD127 performance of cobalamin( Cbl membrane parking B12) into the mitochondrion, interacting it ED for the composition of Cbl lives. (evakoch.com)
  • Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used throughout the cell as a source of chemical energy . (wikipedia.org)
  • Cold Spring Harbor, NY -- Cold Spring Harbor Laboratory Press (CSHLP) announced the release of The Digital Cell: Cell Biology as a Data Science, available on its website in hardcover format. (cshlpress.com)
  • This mechanism requires enzymes to eat away at the end of one of the DNA strands on each side of the double-strand break. (elifesciences.org)
  • Centrosome duplication is tightly regulated and limited at once per cell cycle through a mechanism that prevents re-duplication. (biomedcentral.com)
  • Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. (researchgate.net)
  • In addition to basic science investigations in such areas as tumor cell invasion, oncogenes, immunotherapy and genetic inheritance, our scientists and physicians participate in national cancer trials. (upstate.edu)
  • Breaks that form across both strands in a DNA double helix are considered the most dangerous type of DNA damage, and can cause a cell to die or become cancerous if they are not repaired accurately. (elifesciences.org)
  • This process is called 'resection' and it exposes single strands of DNA. (elifesciences.org)
  • PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. (lookformedical.com)
  • These two levels serve degraded by a phosphorylation including at least 6 membranes in a such tail that both leaves the 2' disorder ubiquitination and adducts the 3' heart to the 5' cell. (evakoch.com)
  • DNA damage repair is initiated and maintained by two kinases, ataxia-telangiectasia mutated (ATM) and ATR, with ATR proving to be more important for maintaining the genome. (wikipedia.org)
  • 13 Genome Plasticity and B Cell, University of Paris-Sud, Centre National de la Recherche Scientifique, Cancer Institute Gustave Roussy, Villejuif, France. (jci.org)
  • In particular, ubiquitin-mediated degradation is critically important at transition points where it provides directionality and irreversibility to the cell cycle, which is essential for maintaining genome integrity. (intechopen.com)
  • In participating UK research institutions, investigators can publish open access in Genome Research, Genes & Development, RNA, and Learning & Memory without article publication charges and all staff can read the entire renowned Cold Spring Harbor journal collection. (cshlpress.com)
  • The cell cycle is a finely orchestrated event dependent on the sequential activation of genes regulating cell growth and metabolism. (oncotarget.com)
  • Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy. (u-paris.fr)
  • functional ATP by a full cell signal reticulum 1. (evakoch.com)