Cancer and Gene Regulation

Cancer and Gene Regulation tài liệu, giáo án, bài giảng , luận văn, luận án, đồ án, bài tập lớn về tất cả các lĩnh vực k...

Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker’s yeast Karen van Eunen 1 , Jildau Bouwman 1, *, Alexander Lindenbergh 1 , Hans V. Westerhoff 1,2 and Barbara M. Bakker 1,3 1 Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands 2 Manchester Centre for Integrative Systems Biology, University of Manchester, UK 3 Department of Pediatrics, University of Groningen, The Netherlands Introduction Living organisms have the option to regulate their molecular activities by altering expression of the cor- responding genes. For example, in the yeast Saccharo- myces cerevisiae changes in glycolytic flux have frequently been found to be accompanied by changes in enzyme capacities [1–3] or amounts [4]. However, a change in flux through a certain enzyme can also be regulated through the interaction of that enzyme with altering concentrations of its substrate(s), product(s) and ⁄ or modifier(s) (metabolic properties). To quantify the extent to which the change in flux through an individual enzyme is regulated by a change in enzyme Keywords fermentative capacity; glycolysis; regulation analysis; Saccharomyces cerevisiae; systems biology Correspondence B. M. Bakker, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands Fax: +31 50 361 1746 Tel: +31 50 361 1542 E-mail: b.m.bakker@med.umcg.nl *Present address Physiological Genomics, TNO Quality of Life, Zeist, The Netherlands (Received 11 February 2009, revised 6 July 2009, accepted 23 July 2009) doi:10.1111/j.1742-4658.2009.07235.x Time-dependent regulation analysis is a new methodology that allows us to unravel, both quantitatively and dynamically, how and when functional changes in the cell are brought about by the interplay of gene expression and metabolism. In this first experimental implementation, we dissect the initial and late response of baker’s yeast upon a switch from glucose-lim- ited growth to nitrogen starvation. During nitrogen starvation, unspecific bulk degradation of cytosolic proteins and small organelles (autophagy) occurs. If this is the primary cause of loss of glycolytic capacity, one would expect the cells to regulate their glycolytic capacity through decreasing simultaneously and proportionally the capacities of the enzymes in the first hour of nitrogen starvation. This should lead to regulation of the flux which is initially dominated by changes in the enzyme capacity. However, metabolic regulation is also known to act fast. To analyse the interplay between autophagy and metabolism, we examined the first 4 h of nitrogen starvation in detail using time-dependent regulation analysis. Some enzymes were initially regulated more by a breakdown of enzyme capacity and only later through metabolic regulation. However, other enzymes were regulated metabolically in the first hours and then shifted towards regula- tion via enzyme capacity. We conclude that even initial regulation is subtle and governed by different molecular levels. Abbreviations ADH, alcohol dehydrogenase; ALD, aldolase; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; GPM, phosphoglycerate mutase; HXK, hexokinase; PDC, pyruvate decarboxylase; PFK, phosphofructokinase; PGI, phosphoglucose isomerase; PGK, 3-phosphoglycerate kinase; PYK, pyruvate kinase. FEBS Journal 276 (2009) 5521–5536 ª 2009 The Authors Journal compilation ª 2009 FEBS 5521 capacity ( V max ) and by changes in the interactions of the enzyme with the rest of metabolism, Cancer and Gene Regulation Cancer and Gene Regulation Bởi: OpenStaxCollege Cancer is not a single disease but includes many different diseases In cancer cells, mutations modify cell-cycle control and cells don’t stop growing as they normally would Mutations can also alter the growth rate or the progression of the cell through the cell cycle One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein For cells to move through each phase of the cell cycle, the cell must pass through checkpoints This ensures that the cell has properly completed the step and has not encountered any mutation that will alter its function Many proteins, including cyclin B, control these checkpoints The phosphorylation of cyclin B, a post-translational event, alters its function As a result, cells can progress through the cell cycle unimpeded, even if mutations exist in the cell and its growth should be terminated This post-translational change of cyclin B prevents it from controlling the cell cycle and contributes to the development of cancer Cancer: Disease of Altered Gene Expression Cancer can be described as a disease of altered gene expression There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell A gene that is not normally expressed in that cell can be switched on and expressed at high levels This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation) Changes in epigenetic regulation, transcription, RNA stability, protein translation, and post-translational control can be detected in cancer While these changes don’t occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals Therefore, changes in histone acetylation (epigenetic modification that leads to gene silencing), activation of transcription factors by phosphorylation, increased RNA stability, increased translational control, and protein modification can all be detected at some point in various cancer cells Scientists are working to understand the common changes that give 1/6 Cancer and Gene Regulation rise to certain types of cancer or how a modification might be exploited to destroy a tumor cell Tumor Suppressor Genes, Oncogenes, and Cancer In normal cells, some genes function to prevent excess, inappropriate cell growth These are tumor suppressor genes, which are active in normal cells to prevent uncontrolled cell growth There are many tumor suppressor genes in cells The most studied tumor suppressor gene is p53, which is mutated in over 50 percent of all cancer types The p53 protein itself functions as a transcription factor It can bind to sites in the promoters of genes to initiate transcription Therefore, the mutation of p53 in cancer will dramatically alter the transcriptional activity of its target genes Link to Learning Watch this animation to learn more about the use of p53 in fighting cancer Proto-oncogenes are positive cell-cycle regulators When mutated, proto-oncogenes can become oncogenes and cause cancer Overexpression of the oncogene can lead to uncontrolled cell growth This is because oncogenes can alter transcriptional activity, stability, or protein translation of another gene that directly or indirectly controls cell growth An example of an oncogene involved in cancer is a protein called myc Myc is a transcription factor that is aberrantly activated in Burkett’s Lymphoma, a cancer of the lymph system Overexpression of myc transforms normal B cells into cancerous cells that continue to grow uncontrollably High B-cell numbers can result in tumors that can interfere with normal bodily function Patients with Burkett’s lymphoma can develop tumors on their jaw or in their mouth that interfere with the ability to eat Cancer and Epigenetic Alterations Silencing genes through epigenetic mechanisms is also very common in cancer cells There are characteristic modifications to histone proteins and DNA that are associated with silenced genes In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found 2/6 Cancer and Gene Regulation in cancer When these modifications occur, the gene present in that chromosomal region is silenced Increasingly, scientists understand how epigenetic changes are altered in cancer Because these changes are temporary and can be reversed—for example, by preventing the action of the ...Complex transcriptional and translational regulation of iPLA 2 c resulting in multiple gene products containing dual competing sites for mitochondrial or peroxisomal localization David J. Mancuso 1,2 , Christopher M. Jenkins 1,2 , Harold F. Sims 1,2 , Joshua M. Cohen 1,2 , Jingyue Yang 1,2 and Richard W. Gross 1,2,3,4 1 Division of Bioorganic Chemistry and Molecular Pharmacology, and Departments of 2 Medicine, 3 Chemistry and 4 Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO, USA Membrane-associated calcium-independent phospholipase A 2 c (iP LA 2 c) contains four potential in-frame methionine start s ites (Mancuso, D.J. Je nkins, C .M. & Gross, R.W. (2000) J. Biol. Chem. 275, 9937–9945), but the mechanisms regulating the types, amount and subcellular localization of iPLA 2 c in cells are i ncompletely understood. We now: (a) demonstrate the dramatic transcriptional repression of mRNA synthesis encoding iPLA 2 c by a nucleotide sequence nested in the coding sequence itself; (b) localize the site of transcriptional repression to the most 5¢ sequence encoding the iPLA 2 c holoprotein; (c) identify the presence of nuclear protein c onstituents w hich bind to the repressor region by gel shift analysis; (d) demonstrate the translational regulation of distinct iPLA 2 c isoforms; (e) identify multiple novel exons, promoters, and alternative splice variants o f human iPLA 2 c; (f) document the presence of dual-competing subcellular localization s ignals in discrete isoforms of iPLA 2 c;and (g) demonstrate t he functional integrity of an N-terminal mitochondrial localization signal by fluorescen ce imagi ng and the presence of iPLA 2 c in the mitochondrial compart- ment of rat myocardium. The intricacy of the r egulatory mechanisms of iPLA 2 c biosynthesis in rat myocardium is underscored by the identification of seven distinct protein products that utilize multiple mechanisms (transcription, translation and proteolysis) to produce discrete iPLA 2 c polypeptides containing either single or dual subcellular localization s ignals. T his unanticipated complex i nterplay between peroxisomes and mitochondria mediated by com- petition for uptake of the nascent iPLA 2 c polypeptide identifies a new level of phospholipase-mediated m etabolic regulation. Because uncoupling protein function is regulated by free fatty acids in mitochondria, these results suggest that iPLA 2 c processing contributes to integrating respiration a nd thermogenesis in mitochondria. Keywords: phospholipase; mitochondria; p eroxisomes; tran- scription; translation. Phospholipases A 2 (PLA 2 s) play critical roles in cellular growth, lipid homeostasis and lipid second messenger generation by catalyzing the esterolytic cleavage of the sn-2 fatty acid o f glycerophospholipids [1–5]. The resultant fatty acids and lysolipids are potent lipid mediators of signal transduction and a lter the biophysical properties o f the membrane bilayer, collectively contributing t o the critic al roles that phospholipases play in cellular adaptation, proliferation and signaling. PLA 2 s constitute a d iverse family of enzymes, which include the intracellular phos- pholipase families, cytosolic PLA 2 s(cPLA 2 ) and calcium- independent PLA 2 s(iPLA 2 ) as well as the secretory PLA 2 s (sPLA 2 ). More than a decade ago, we identified multiple types of kinetically distinguishable iPLA 2 activities in the cytosolic, microsomal and mitochondrial fractions from multiple species REVIEW ARTICLE Nuclear actin and actin-binding proteins in the regulation of transcription and gene expression Bin Zheng 1 , Mei Han 1 , Michel Bernier 2 and Jin-kun Wen 1 1 Department of Biochemistry and Molecular Biology, Hebei Medical University, Shijiazhuang, China 2 Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA Actin is a major component of the cytoskeleton and plays a critical role in all eukaryotic cells. The actin cytoskeleton functions in diverse cellular processes, including cell motility, contractility, mitosis and cytoki- nesis, intracellular transport, endocytosis and secretion [1,2]. In addition to these mechanical functions, actin has also been implicated in the regulation of gene tran- scription, through either cytoplasmic changes in cyto- skeletal actin dynamics [3] or the assembly of transcriptional regulatory complexes [4]. Cytoskeletal actin dynamics, i.e. actin polymerization by which monomeric actin (globular actin or G-actin) is assem- bled into long actin polymers (filamentous actin or F-actin) and actin deploymerization by which F-actin is severed into G-actin, is key for these diverse func- tions. The dynamic nature of the actin cytoskeleton is determined spatiotemporally by the actions of numerous actin-binding proteins (ABPs). The activity of different classes of ABP controls actin nucle- ation, bundling, filament capping, fragmentation and Keywords actin dynamics; actin-binding protein; chromatin remodeling; gene regulation; muscle-specific gene; nuclear actin; nuclear receptor; ribonucleoprotein; RNA polymerases; transcription complex Correspondence J k. Wen, Department of Biochemistry and Molecular Biology, Hebei Medical University, No. 361, Zhongshan East Road, Shijiazhuang 050017, China Fax: +86 311 866 96180 Tel: +86 311 862 65563 E-mail: wjk@hebmu.edu.cn (Received 12 January 2009, revised 20 February 2009, accepted 26 February 2009) doi:10.1111/j.1742-4658.2009.06986.x Nuclear actin is involoved in the transcription of all three RNA polymerases, in chromatin remodeling and in the formation of heterogeneous nuclear ribonucleoprotein complexes, as well as in recruitment of the histone modi- fier to the active gene. In addition, actin-binding proteins (ABPs) control actin nucleation, bundling, filament capping, fragmentation and monomer availability in the cytoplasm. In recent years, more and more attention has focused on the role of actin and ABPs in the modulation of the subcellular localization of transcriptional regulators. This review focuses on recent developments in the study of transcription and transcriptional regulation by nuclear actin, and the regulation of muscle-specific gene expression, nuclear receptor and transcription complexes by ABPs. Among the ABPs, striated muscle activator of Rho signaling and actin-binding LIM protein regulate actin dynamics and serum response factor-dependent muscle-specific gene expression. Functionally and structurally unrelated cytoplasmic ABPs interact cooperatively with nuclear receptor and regulate its transactiva- tion. Furthermore, ABPs also participate in the formation of transcription complexes. Abbreviations ABLIM, actin-binding LIM protein; ABP, Characterization of the Drosophila Methoprene -tolerant gene product Juvenile hormone binding and ligand-dependent gene regulation Ken Miura, Masahito Oda, Sumiko Makita and Yasuo Chinzei Department of Medical Zoology, School of Medicine, Mie University, Tsu City, Japan Insect development and reproduction are regulated by two classes of lipid-soluble hormones, the ecdysteroids and juvenile hormones (JHs). The ecdysteroids activate target genes through a heterodimeric receptor complex composing the ecdysone receptor and ultraspiracle (USP) proteins, both of which are members of the nuc- lear steroid ⁄ thyroid ⁄ retinoid receptor superfamily [1]. During insect development, ecdysteroids induce molting while JH determines the nature of each molt by modu- lating the ecdysteroid-induced gene expression cascade [2–4]. In addition, in adult insects, JH has a wide variety of actions related to reproduction, including oogenesis, migratory behaviour and diapause [2,5,6]. The mode of molecular action of JH, however, is still obscure [7]. JHs are a family of esterified sesquiterpe- noids, whose lipid-soluble nature has suggested action directly on the genome through nuclear receptors such as ecdysteroids and the vertebrate steroid ⁄ thyroid ⁄ reti- noid hormones [5,8] although actions of JH through the cell membrane are also documented [9,10]. Many attempts have been made to identify nuclear JH receptors. Jones and Sharp [11] showed that JH III binds to the Drosophila USP protein, which is a homo- logue of the vertebrate retinoid X receptor, promoting Keywords juvenile hormone; juvenile hormone receptor; Methoprene-tolerant; Drosophila; transcription factor Correspondence K. Miura, Department of Medical Zoology, School of Medicine, Mie University, Edobashi 2-174, Tsu514-8507, Japan Fax: +81 59 231 5215 Tel: +81 59 231 5013 E-mail: k-miura@doc.medic.mie-u.ac.jp (Received 27 October 2004, revised 20 December 2004, accepted 4 January 2005) doi:10.1111/j.1742-4658.2005.04552.x Juvenile hormones (JHs) of insects are sesquiterpenoids that regulate a great diversity of processes in development and reproduction. As yet the molecular modes of action of JH are poorly understood. The Methoprene- tolerant (Met) gene of Drosophila melanogaster has been found to be responsible for resistance to a JH analogue (JHA) insecticide, methoprene. Previous studies on Met have implicated its involvement in JH signaling, although direct evidence is lacking. We have now examined the product of Met (MET) in terms of its binding to JH and ligand-dependent gene regu- lation. In vitro synthesized MET directly bound to JH III with high affinity (K d ¼ 5.3 ± 1.5 nm, mean ± SD), consistent with the physiological JH concentration. In transient transfection assays using Drosophila S2 cells the yeast GAL4-DNA binding domain fused to MET exerted JH- or JHA- dependent activation of a reporter gene. Activation of the reporter gene was highly JH- or JHA-specific with the order of effectiveness: JH III  JH II > JH I > methoprene; compounds which are only structur- ally related to JH or JHA did not induce any activation. Localization of MET in the S2 cells was nuclear irrespective of the presence or absence of JH. These results suggest that MET may function as a JH-dependent tran- scription factor. Abbreviations Ahr, aryl hydrocarbon receptor; Arnt, Ahr nuclear translocator; bHLH, basic helix-loop-helix; DBD, DNA binding domain; DCC, dextran-coated charcoal; EGFP, enhanced green Genome Biology 2005, 6:R87 comment reviews reports deposited research refereed research interactions information Open Access 2005Granek and ClarkeVolume 6, Issue 10, Article R87 Method Explicit equilibrium modeling of transcription-factor binding and gene regulation Joshua A Granek *† and Neil D Clarke *‡ Addresses: * Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, North Wolfe Street, Baltimore, MD 21205, USA. † National Evolutionary Synthesis Center, Broad Street, Durham, NC 27705, USA. ‡ Genome Institute of Singapore, Biopolis Street, Singapore 138672, Republic of Singapore. Correspondence: Neil D Clarke. E-mail: nclarke@jhmi.edu © 2005 Granek and Clarke; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Explicit equilibrium modeling of transcription-factor binding and gene regulation<p>A computational model, GOMER, is presented that predicts transcription-factor binding and incorporates effects of cooperativity and competition.</p> Abstract We have developed a computational model that predicts the probability of transcription factor binding to any site in the genome. GOMER (generalizable occupancy model of expression regulation) calculates binding probabilities on the basis of position weight matrices, and incorporates the effects of cooperativity and competition by explicit calculation of coupled binding equilibria. GOMER can be used to test hypotheses regarding gene regulation that build upon this physically principled prediction of protein-DNA binding. Background Transcription is regulated by the binding of proteins to spe- cific DNA sequences. Until recently, binding and regulation could only be studied at the level of individual genes, but they can now be studied as a complex system due to the availability of genome-wide data on expression and transcription factor binding. Computational models are needed, however, to eval- uate co-regulated genes and the sequence motifs associated with them. A general strategy for testing the relevance of a DNA binding motif to gene regulation is to quantify the association of the motif with co-regulated genes. This can be done by comparing the regulatory sequences of co-regulated genes with the regu- latory sequences of all other genes [1-4]. One simple test is to score for the occurrence of a consensus site within a pre- scribed distance 5' to the start of transcription. If the fraction of regulated genes with a consensus site is significantly larger than the fraction of unregulated genes, as it often is, then the test has some predictive power [1,5-7]. As with all statistical tests, there is a model implicit in this test: in this case, the implicit model is that gene regulation is mediated by a single consensus binding site. There are problems with such a simple model. First, the use of consensus binding sites, even if degenerate, underesti- mates the importance of motifs that resemble the consensus but do not match it [8]. At the same time, degenerate consen- sus sites fail to distinguish among motifs that match the con- sensus even if the motifs that match differ in affinity. Second, regulated genes often contain more than one binding site for a given factor, so scoring based on a single site (or any other threshold number of sites) is arbitrary. Third, the binding of a factor is typically affected by cooperative and competitive interactions with other proteins, so binding sites for those other proteins may need to be considered. Fourth, gene expression can be affected by the location, orientation and spacing of bound transcription factors. Therefore, to be real- istic, a model for gene regulation should use to full advantage an accurate representation of .. .Cancer and Gene Regulation rise to certain types of cancer or how a modification might be exploited to destroy a tumor cell Tumor Suppressor Genes, Oncogenes, and Cancer In normal... like cancer Review Questions Cancer causing genes are called transformation genes tumor suppressor genes oncogenes mutated genes C Targeted therapies are used in patients with a set gene. .. ability to eat Cancer and Epigenetic Alterations Silencing genes through epigenetic mechanisms is also very common in cancer cells There are characteristic modifications to histone proteins and DNA