Regulation of gene expression 553121 224636375 2008-07-09T19:28:34Z 128.231.88.7 /* Structural */ In the next to last line of this section, it's histone "de"acetylation that leads to gene silencing, as at http://en.wikipedia.org/wiki/HDAC_inhibitors {{MolBioGeneExp}} {{Expand|date=February 2008}} ''Gene modulation redirects here. For information on therapeutic regulation of gene expression, see [[therapeutic gene modulation]].'' :''For vocabulary, see [[Glossary of gene expression terms]]'' '''Regulation of gene expression''' (or '''gene regulation''') refers to the cellular control of the amount and timing of changes to the appearance of the functional [[Gene product|product of a gene]]. Although a functional gene product may be an [[RNA]] or a [[protein]], the majority of known mechanisms regulate protein coding genes. Any step of the [[gene expression|gene's expression]] may be modulated, from DNA-RNA [[transcription (genetics)|transcription]] to the [[post-translational modification]] of a protein. Gene regulation is essential for [[viruses]], [[prokaryote]]s and [[eukaryote]]s as it increases the versatility and adaptability of an [[organism]] by allowing the cell to express protein when needed. The first example of gene regulation system was the [[lac operon]], discovered by [[Jacques Monod]], in which protein involved in lactose metabolism are expressed by [[E.coli]] only in the presence of lactose and absence of glucose. Furthermore, gene regulation allows the presence in a multicellular organism of different cells types arranged in a complex pattern, hence different transcriptomes despite them having all the same genome and the generation of patterns by [[cellular differentiation]] and [[morphogenesis]]. ==Regulated stages of gene expression== Any step of gene expression may be modulated, from the DNA-RNA [[transcription (genetics)|transcription]] step to [[post-translational modification]] of a protein. The following is a list of stages where gene expression is regulated: *[[Epigenome|chromatin domains]] *[[Transcription (genetics)|Transcription]] *[[Post-transcriptional modification]] * RNA transport *[[translation (genetics)|Translation]] *[[mRNA#Degradation|mRNA]] degradation *[[Post-translational modification]]s ==Modification of DNA== {{Main article|Epigenetic regulation}} In eukaryotes, the accessibility of large regions of DNA can depend on its chromatin structure which can be altered as a result of histone modifications which are directed by DNA methylation, ncRNA or DNA binding protein. ===Chemical=== [[DNA methylation|Methylation of DNA]] is a common method of gene silencing. DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called "[[CpG island]]s" when densely clustered). Analysis of the pattern of methylation in a given region of DNA (which can be a promoter) can be achieved through a method called bisulfite mapping. Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences are analyzed by DNA sequencing or by methods developed to quantify SNPs, such as [[Pyrosequencing]] ([[Biotage]]) or [[MassArray]] ([[Sequenom]]), measuring the relative amounts of C/T at the CG dinucleotide. Abnormal methylation patterns are thought to be involved in carcinogenesis. ===Structural=== Transcription of DNA is dictated by its structure. In general, the density of its packing is indicative of the frequency of transcription. Octameric protein complexes called [[histone]]s are responsible for the amount of [[supercoiling]] of DNA, and these complexes can be temporarily modified by processes such as [[phosphorylation]] or more permanently modified by processes such as [[methylation]]. Such modifications are considered to be responsible for more or less permanent changes in gene expression levels. [[Histone acetylation]] is also an important process in transcription. [[Histone acetyltransferase]] enzymes (HATs) such as [[CREB-binding protein]] also dissociate the DNA from the histone complex, allowing transcription to proceed. Often, DNA methylation and histone deacetylation work together in [[gene silencing]]. The combination of the two seems to be a signal for DNA to be packed more densely, lowering gene expression. ==Regulation of transcription== {{main|transcriptional regulation}} Regulation of transcription controls when transcription occurs and how much RNA is created. Transcription of a gene by [[RNA polymerase]] can be regulated by at least five mechanisms: *'''[[Specificity factor]]s''' alter the specificity of RNA polymerase for a given [[promoter]] or set of promoters, making it more or less likely to bind to them (i.e. [[sigma factor]]s used in [[prokaryotic transcription]]). *'''[[Repressor]]s''' bind to non-coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene. *'''[[General transcription factor]]s''' These transcription factors position RNA polymerase at the start of a protein-coding sequence and then release the polymerase to transcribe the mRNA. *'''[[Activator (genetics)|Activator]]s''' enhance the interaction between RNA polymerase and a particular [[promoter]], encouraging the expression of the gene. Activators do this by increasing the attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly by changing the structure of the DNA. *'''[[Enhancer]]s''' are sites on the DNA helix that are bound to by activators in order to loop the DNA bringing a specific promoter to the initiation complex. ==Posttranscriptional Regulation== {{main|Post-transcriptional regulation}} After the DNA is transcribed and mRNA is formed there must be some sort of regulation on how much the mRNA is translated into Proteins. Cells do this by modulating the Capping, Splicing, addition of a Poly(A) Tail, the sequence-specific nuclear export rates and in several contexts sequestration of the RNA transcript. These processes occur in eukaryotes but not in prokaryotes. This modulation is a result of a protein or transcript which in turn is regulated and may have an affinity for certain sequences. *'''Capping''' changes the five prime end of the mRNA to a three prime end by 5'-5' linkage, which protects the mRNA from 5' exonuclease, which degrades foreign RNA. The cap also helps in ribosomal binding. *'''Splicing''' removes the introns, noncoding regions that are transcribed into RNA, in order to make the mRNA able to create proteins. Cells do this by spliceosome's binding on either side of an intron, looping the intron into a circle and then cleaving it off. The two ends of the exons are then joined together. *'''Addition of poly(A) tail''' otherwise known as poly-adenylation. Junk RNA is added to the 3' end, and acts as a buffer to the 3' exonuclease in order to increase the [[half life]] of mRNA. In both prokaryotes and eukaryotes a large number of RNA binding protein exist, with often are directed to their target sequence by the secondary structure of the transcript, which may change depending on certain conditions, such as temperature or presence of a ligand (aptamer), some transcripts act as [[ribozyme]]s and self-regulate their expression. ==Examples of gene regulation== *[[Enzyme induction and inhibition|Enzyme induction]] is a process in which a molecule (e.g. a drug) induces (i.e. initiates or enhances) the expression of an enzyme. *The induction of [[heat shock protein]]s in the fruit fly ''[[Drosophila melanogaster]]''. * The [[Lac operon]] is an interesting example of how gene expression can be regulated. * Viruses despite having only a few genes, possess mechanisms to regulate their gene expression, typically into a early and late phase, using collinear systems regulated by anti-terminators ([[lambda phage]]) or splicing modulators ([[HIV]]) ==Circuitry== {{main|Gene regulatory network}} ===Up-regulation and down-regulation=== '''Up-regulation''' is a process which occurs within a cell triggered by a signal (originating internal or external to the cell) which results in increased expression of one or more genes and as a result the protein(s) encoded by those genes. Conversely '''down-regulation''' is a process resulting in decreased gene and corresponding protein expression. * [[Up-regulation]] occurs for example when a cell is deficient in some kind of receptor. In this case, more receptor protein is synthesized and transported to the membrane of the cell and thus the sensitivity of the cell is brought back to normal reestablishing [[homeostasis]]. * [[Down-regulation]] occurs for example when a cell is overly stimulated by a [[neurotransmitter]], [[hormone]], or drug for a prolonged period of time and the expression of the receptor protein is decreased in order to protect the cell (see also [[tachyphylaxis]]). ===Inducible vs. repressible systems=== Gene Regulation can be summarized as how they respond: *Inducible systems - An inducible system is off unless there is the presence of some molecule (called an inducer) that allows for gene expression. The molecule is said to "induce expression". The manner in which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells. *Repressible systems - A repressible system is on except in the presence of some molecule (called a corepressor) that suppresses gene expression. The molecule is said to "repress expression". The manner in which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells. ===Developmental biology=== {{main|morphogen}} A large number of studied regulatory systems come from developmental biology. Examples include: *The collinearity of the [[Hox gene]] cluster with their nested antero-posterior patterning *It has been speculated that pattern generation of the hand (digits - interdigits) The gradient of [[Sonic hedgehog]] (secreted inducing factor) from the zone of polarizing activity in the limb which creates a gradient of active Gli3 which activates Gremlin which inhibits BMPs also secreted in the limb resulting in the formation of an alternating pattern of activity as a result of this [[reaction-diffusion system]]. *Somatogenesis is the creation of segmatation (somites) form a uniform tissue (PSM) sequentially from anterior to posterior, this is a achieved in amniotes possibly by means of two opposing gradients, Retinoic acid in the anterior (wavefront) and an oscillating gradient in the posterior (clock) composed of FGF + Notch and Wnt in antiphase<ref>Dequéant ML, Pourquié O. Segmental patterning of the vertebrate embryonic axis. Nat Rev Genet. 2008 May;9(5):370-82. PMID: 18414404 </ref>. *Sex determination in the soma of a Drosophila requires the sensing of the ratio of autosomal genes to sex chromosome encoded genes, which results in the production of sexless splicing factor in females resulting in the female isoform of doublesex.<ref>Gilbert SF (2003). Developmental biology, 7th ed., Sunderland, Mass: Sinauer Associates, 65–6. ISBN 0-87893-258-5.</ref> ===Theoretical circuits=== *Repressor/Inducer: a activation of a sensor results in the change of expression of a gene *negative feedback: the gene product downregulates its own production directly or indirectly, which can result in **keeping transcript levels constant/proportional to a factor **inhibition of run-away reactions when coupled with a positive feedback loop **creating an oscillator by taking advantage in the time delay of transcription and translation, given that the mRNA and protein half-life is shorter *positive feedback: the gene product upregulates its own production directly or indirectly, which can result in **signal amplification **bistable switches when two genes inhibit each other and have both positive feedback **pattern generation ==Methods== {{for|DNA and RNA methods|nucleic acid methods}} {{for|protein methods|protein methods}} Generally, most experiments investigating differential expression used whole cell extracts of RNA, called steady-state levels, to determined which genes changed and by how much they did, these are however not informative of where the regulation has occurred and may actually mask conflicting regulatory processess (''see [[post-transcriptional regulation]]''), it is the most commonly analysed ([[QPCR]] and [[DNA microarray]]). When studying gene expression there are several methods to look at the various stages. In eukaryotes these include: * The chromatin conformation of the region can be determined by [[ChIP-chip]] analysis by pulling down [[RNA Polymerase II]], [[Histone 3]] modifications, [[Trithorax-group protein]],[[Polycomb-group protein]] or any other DNA binding element to which a good antibody is available. * Due to post-transcriptional regulation, transcription rates and total RNA levels differ significantly, to measure the transcription rates [[nuclear run-on]] assays can be done and newer high-throughput methods are being developed, using [[thiol]] labelling instead of [[radioactivity in biology|radioactivity]]. <ref name="pmid15907206">{{cite journal | author = Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, Do L, Gorospe M, Becker KG | title = Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability | journal = BMC Genomics | volume = 6 | issue = 1 | pages = 75 | year = 2005 | pmid = 15907206 | doi = 10.1186/1471-2164-6-75 }}</ref> * Only 5% of the RNA polymerised in the nucleus actually exists <ref name="pmid10657981">{{cite journal | author = Jackson DA, Pombo A, Iborra F | title = The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells | journal = FASEB J. | volume = 14 | issue = 2 | pages = 242–54 | year = 2000 | pmid = 10657981 | doi = | issn = | url = http://www.fasebj.org/cgi/content/abstract/14/2/242 }}</ref>and not only introns, abortive products and non-sense transcripts are degradated therefore the differences in nuclear and cytoplasmic levels can be see by separating the two fractions by gentle lysis .<ref name="pmid16962184">{{cite journal | author = Schwanekamp JA, Sartor MA, Karyala S, Halbleib D, Medvedovic M, Tomlinson CR | title = Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin | journal = Biochim. Biophys. Acta | volume = 1759 | issue = 8-9 | pages = 388–402 | year = 2006 | pmid = 16962184 | doi = 10.1016/j.bbaexp.2006.07.005 }}</ref> * Alternative splicing can be analysed with a splicing array or with a tiling array (''see [[DNA microarray]]''). * All [[in vivo]] RNA is complexed as [[RNP]]s. The quantity of transcripts bound to specific protein can be also analysed by [[RIP-Chip]], for example [[DCP2]] will give an indication of sequestered protein, [[ribosome]] bound gives and indication of transcripts active in transcription (although it should be noted that a more dated method, called [[polysome]] fractionation, is still popular in some labs) * Protein levels can be analysed by [[Mass spectrometry]], which can only be compare to [[QPCR]] data as [[DNA microarray|microarray]] data is relative and not absolute. * RNA and protein degradation rates are measured by means of transcription inhibitors ([[actinomycin D]] or [[α-amanitin]]) or translation inhibitors ([[Cycloheximide]]) respectively. ==References== {{reflist}} ==See also== * [[Enhancer (genetics)]] * [[Artificial transcription factor]]s (small molecules which mimic transcription factor protein) ==External links== * {{MeshName|Regulation+of+Gene+Expression|3=Regulation of Gene Expression}} * [[Genevestigator]] - an online resource to study how genes are regulated by different internal or external factors (e.g. anatomy part, developmental stage, stimuli, drugs, diseases, or genetic modifications). {{Molecular Biology}} [[Category:Gene expression]] [[Category:DNA]] [[Category:RNA]] [[Category:Posttranslational modification]] [[de:Genregulation]] [[es:Regulación genética]] [[it:Regolazione genica]] [[he:בקרת גנים]] [[pt:Regulação genética]]