Regulation of Transcription

Regulation of Transcription Principles of transcription regulation Any step in the transcription cycle can be regulated The RNA polymerase holoenzyme can transcribe any gene that has an intact promoter. Yet at any given time, the relative rate at which a complete transcript is generated varies tremendously among different genes Cells of all types contain a remarkable array of proteins that control the relative amount of transcription from each promoter, increasing or decreasing the rate at which RNA transcripts of selected genes are produced Activator: sequence specific DNA-binding protein that leads to increased transcription Repressor: sequence-specific DNA binding protein that leads to decreased transcription The structures adopted can be influenced by the binding of proteins or small metabolites that exert control over transcription through their effect on RNA structure Proteins that bind to DNA target specific genes for regulation Specific regions in the chromosome called regulatory sequences are the sites in DNA to which regulatory proteins bind. Regulatory sequences are most commonly located upstream of the promoter and dan be immediately adjacent to the promoter (or even overlapping) or op to many kilo-bases away In bacteria, the DNA sequences recognized by transcriptional regulators are termed operator sites. This term was originally used exclusively for repressors but has come to refer to DNA sites to which any transcriptional regulator binds Bacterial operators to which repressors bind are located upstream of the transcription start site, typically close to or overlapping the promoter, whereas sites to which activators bind lie just upstream In this case, a loop forms in the intervening DNA, thus bringing the operator site and promoter region close enough to enable the DNA -bound regulatory protein to interact with the polymerase enzyme Complex regulatory sequences located far from the gene are common in higher eukaryotes In multicellular organisms, regulatory sequences can encompass binding sites for six or more individual proteins and may be located at great distances from the promoter region - sometimes several thousand base pairs or more away. These sequences, called enhancers, bind proteins that activate transcription Enhancers are able to regulate transcription at distant promoters because the DNA forms a loop that allows proteins bound to the enhancer region to contact proteins bound to the promoter region Eukaryotic DNA-binding proteins recruit protein complexes that regulate transcription In eukaryotic cells, DNA-binding proteins typically do not control transcription directly, but rather exert their function by recruiting additional protein complexes that either activate or repress transcription Co-activator: protein or complex of proteins recruited to DNA by sequence-specific DNA-binding proteins that activates transcription Co-repressor: protein or complex of proteins recruited to DNA by sequence-specific DNA binding proteins that represses transcription Proteas that regulate transcription in eukaryotes are typically modular in nature, with a DNA-binding domain that recognizes specific DNA sequences and a separate activation or repression domain that recruits a co-activator or co-repressor Additional distinct domains that serve additional functions, such as dimerization or binding to additional regulatory proteins, can also be found in some proteins that regulate eukaryotic transcription Chromatin modifications play a central role in the regulation of eukaryotic transcription An important mechanism by which genes are activated or repressed in eukaryotes is the binding to DNA of activator or repressor proteins that recruit enzymes that modify chromatin The activation of many eukaryotic genes is linked to recruitment of histone acetyltransferase enzymes, also known as HATs, which acetylate lysine residues within specific histone proteins The activity of regulatory proteins can be modified The transcription of some genes can be altered by small molecules that bind directly to regulatory proteins and act as allosteric effectors. Allosteric effectors trigger a conformational change in the proteins to which they bind, altering the proteins DNA binding properties or its interactions with other proteins Covalent modification of proteins that regulate transcription, such as phosphorylation or acetylation, can also be used to alter the DNA-binding properties of a protein or its effect on transcription Whether or not a transcriptional regulator is localized in the nucleus, and is thus available to bind DNA and regulate transcription, can be controlled by regulating nuclear import or export DNA-binding Domains in Proteins That Regulate Transcription Sequence-specific DNA-binding proteins can be classified broadly by different DNA-binding motifs A remarkable variety of domains that recognize specific DNA sequences are found among transcription regulators. Called DNA-binding motifs, these protein folds are tailored to accommodate the structural features characteristic of B-DNA The helix-turn-helix is a common DNA-binding motif found in all organisms The helix-turn-helix was the first DNA-binding motif to be identified. It consists of two alpha helices related by a fixed angle and connected by a tight bend (the "turn") The second, the C-terminal helix, is the recognition helix that fits in the major groove of the DNA and forms contacts with the base pairs that "read" the DNA sequence Many helix-turn-helix proteins are dimers that position the recognition helices of the two monomers 34 angstrom apart, which matches the spacing of successive major grooves in B-DNA The homeodomain, one of the most common types of DNA-binding domains in eukaryotes, is a monomeric helix-turn-helix protein whose recognition helix is somewhat longer than its bacterial counterparts The zine finger is the most common DNA-binding domain in the human genome Most prominent of these is the zine finger, a small domain of about 30 amino acids whose single alpha helix and two antiparallel beta strands are held together by a central zine ion Each zine finger inserts its alpha helix end-on into the major groove, where side chains form base contacts Variation in the number of zinc fingers per protein, as well as the amino acid sequence of each finger, facilitated the evolution of a large array of different proteins that recognize DNA sequences of differing length and sequence DNA binding triggers folding of basic region-leucine zipper proteins For instance, basic region-leucine zipper (bZIP) proteins consist of long, uninterrupted alpha helices of about 60 residues. These proteins associate via their C-terminal halves, forming a parallel coiled coil with leucine residues at the hydrophobic dimer interface A striking feature of these proteins is that the helical structure of the DNAbinding region is coupled to DNA binding; these residues are unstructured in the absence of DNA and only form the organized alphahelical DNA - binding motif in the presence of DNA DNA recognition can also be mediated by beta sheets or loops An the structures described so far recognize DNA through alpha-helical elements. As mentioned earlier, the major groove of B-DNA can also accommodate a pair of beta strands Mechanisms for Regulating Transcription Initiation in Bacteria Trp repressor blocks RNA polymerase binding This type of gene regulation is illustrated by the E. coli Trp repressor, a helix-turn-helix protein whose DNA - binding activity is controlled by the level of tryptophan in the cell The genes encoding the enzymes needed to synthesize the amino acid tryptophan are clustered together in the E. coli chromosome and are under the control of a single promoter and operator Operon: a set of genes with a common promoter and operator that are transcribed as a single polycistronic mRNA When cellular levels of the amino acid tryptophan are low, genes that encode enzymes required for the synthesis of tryptophan are expressed. When levels of tryptophan are sufficiently high, transcription from the trp open is repressed When sufficient amounts of tryptophan are present, one molecule of tryptophan binds to each monomer in the Trp depressor dimer and orients the helix-turn-helix motif of the repressor so that it is presented properly to the DNA major groove With the recognition helices no longer properly aligned to fit in successive major grooves of the DNA, the protein cannot bind to the operator or repress transcription and the genes in the trp open are transcribed The catabolite activator protein recruits RNA polymerase by contacting the C-terminal domain of the RNA polymerase alpha subunit Just as blocking the binding of RNA polymerase to the promoter represses transcription, enhancing the binding of polymerase to the promoter can activate transcription The CAP dimer binds to specific DNA sites overlapping or near target promoters and enhances the ability of the RNA polymerase holoenzyme to bind to its promoter and initiate transcription CAP can activate transcription in several ways, and promoters can be grouped according to the mechanism by which CAP stimulates transcription at that particular promoter At class I promoters, CAP binds DNA upstream of the promoter and recruits RNA polymerase by binding directly to the C-terminal domain (CTD) of the RNA polymerase alpha subunit CAP and LacI depressor regulate the lac operon The regulation of the lac operon is a classic example of how transcription of a set of genes can be modulated in response to two distinct signals: the relative availability of glucose and lactose Consequently, when both sugars are available, the bacterium will preferentially metabolize glucose over lactose, so the genes required for lactose utilization are only expressed at a low level Only when glucose levels are low and lactose levels are high will the genes required for lactose utilization be switched on The key to regulating the lac operon in response to two separate signals is the use of two different regulatory proteins: CAP, which indirectly responds to glucose levels, and the lac repressor (or LacI), which senses lactose levels CAP binds DNA and activates transcription only when it is bound to cAMP, which is found in abundance when glucose levels are low In the presence of lactose, the allolactose metabolite binds to the lac repressor, and causes the protein to dissociate from DNA and thus no longer repress transcription If glucose levels are low, CAP will bind upstream of the operon and activate transcription of the lac operon, since cAMP binding enables CAP to bind DNA MerR-family activators alter promoter structure If the spacing between the -35 and -10 sites is much larger than is optimal, RNA polymerase binding to the promoter is significantly weakened The MerR family, named for a protein that activates expression of genes required for mercury detoxification, forms a unique group of transcriptional regulators that can change the way the promoter elements are organized in space relative to each other The two additional base pairs not only place the - 35 and -10 promoter elements further apart, but also affect the relative orientation of the two promoter elements about the DNA axis MerR activates transcription by altering the relation between the - 10 and -35 regions to more closely resemble an ideal promoter. The binding site for the MerR protein overlaps the promoter region Activation by NtrC involves DNA looping and ATP hydrolysis Promoters that are transcribed by RNA polymerase holoenzyme containing the sigma 54 subunit must be activated by protein complexes that use ATP hydrolysis to drive promoter opening Genes regulated by NtrC generally contain two or more binding sites for NrtC well upstream of the promoter. NrtC can bind to these sites, but it does not activate transcription until a regulatory domain within the protein is phosphorylated First, oligomerization of NrtC promotes interaction of the NrtC protein with the RNA polymerase enzyme that is bound to the promoter, causing the intervening DNA to loop out Two-component signal transduction pathways are composed of histidine kinases and response regulators There are many examples in which the first response to an extracellular signal is the phosphorylation of a cytoplasmic protein. The phosphorylated protein, in turn, triggers additional biochemical events that eventually lead to a change in transcription Two-component systems have a sensor kinase, which detects the relative amounts of specific molecules in the cell's environment, and a response regulator, which is activated when it is phosphorylated by the sensor protein The sensor protein is a histidine kinase, typically membrane-bound, that becomes autophosphorylated on a histidine residue when it detects a certain signal. This phosphate is then transferred to an aspartame residue on the response regulator, which often contains a DNA - binding domain There are sensor kinases that are cytoplasmic, response regulators that have functions other than transcriptional regulation, and more complex networks that involve more than two proteins Competition Between cI and Cro and Control of the Fate of Bacteriophage Lambda Bacteriophage lambda can undergo lytic growth or lysogeny Phage lambda can undergo lytic growth, reproducing many virus particles within the cell and leading to eventual lysis (bursting of the host cell). Alternatively, the phage can undergo lysogeny, whereby the phage DNA integrates into the bacterial chromosome and becomes dormant The ability to be propagated as part of the host DNA allows the phage to multiply under conditions where there might not be enough other nearby cells to infect and grow lyrically The integrated phage is denoted a prophage, and a bacterial cell whose chromosome contains an integrated copy of the bacteriophage chromosome is called a lysogen Conditions that threaten the viability of the bacterial host cell, such as DNA damage, can trigger the prophase to excise itself from the chromosome, undergo lytic growth, and produce viral progeny that burst out of the damaged host cell The choice between lysis and lysogeny is controlled by the levels of the cI, cII, and Cro proteins The lysogenic state is favored in a nutrient-poor environment, when the host cell is growing slowly; by contrast, lysis is favored when the host is growing rapidly in a nutrient-rich environment If conditions are favorable to the host, it is likely that there are many other hosts around to infect, so lytic growth would generate more phage that could, in turn, infect many more hosts. If conditions are not favorable to the host, it is less likely that there will be other potential hosts in the vicinity, so lysogeny makes more sense for the survival of the phage Whether phage lambda grows lytically or as a lysogen is determined by the relative levels of three DNA binding proteins encoded by the phage: cI (also called the lambda repressor), cII, and Cro These three regulators, which are the first proteins to be synthesized after phage lambda infects an E. coli cell, bind to specific sites in the phage chromosome and control transcription from the four promoters: PR (rightward promoter), PL (leftward promoter), PRE (promoter for repressor establishment), and PRM (promoter for repressor maintenance) After a lambda phage injects its genetic material into a bacterial cell, the linear phage chromosome circularizes and the host cell RNA polymerase initiates basal transcription from PL to PR The first genes in the PR transcript encode the Cro and cII regulators, while the first gene in the PL transcript is the N protein. N prevents premature termination of the PR transcript and thereby allows transcription of both Cro and cII If sufficient cII protein accumulates, it binds DNA and stimulates transcription from the PRE promoter, producing an mRNA transcript encoding the cI regulator As the cI protein builds up in the cell, the protein binds to sites in the PL an PR promoter regions and represses transcription of the lytic genes encoded by the PL and PR transcripts By contrast, if cII does not accumulate in sufficient amounts and too little cI protein is synthesized, the Cro protein will bind the PRM promoter and repress transcription of the cI gene The DNA - binding affinities of cI and Cro are a key component in the choice between lysis and lysogeny A closer look at the PL and PR promoters reveals that a key component of the molecular switch controlled by cI and Cro is the relative affinities of these proteins for six DNA sites cI dinners further digomerize to form tetramers, which, in turn, can associate to form an octamer. These higher-order interactions are required for cooperative cI binding to DNA In contrast, the Cro protein consists of a single small domain (also with a helix-turn-helix) that also binds DNA as a dimer, but cannot form higher-order interactions with other cro dimers At both OL and OR, cI binds first to its highest-affinity sites, OL1 and OR1, and recruits a second cI dimer to the weaker OL2 and OR2 binding sites through cooperative interactions This autoregulation, whereby cI regulates its own synthesis through a balance of both positive and negative feedback, ensures that there is sufficient cI in the cell to maintain the lysogenic state, but not so much that prophage induction is prevented With each cell division, the daughter lens receive a copy of the circular chromosome containing the integrated prophage, along with enough cI protein to stimulate fresh cI synthesis, thus maintaining the lysogenic state The prophage is induced on cI cleavage However, under conditions that threaten survival of the host cell, and hence of the integrated phage DNA, the prophase can excise itself from the host chromosome and undergo lytic growth, thereby producing new phage and escaping the compromised host Damage of the host cell DNA - for example, by chemical agents or by ultraviolet light - triggers the bacterial SOS response, which leads to activation of the RecA protein Without the CTD, cI can no longer dimerize efficiently or form highly cooperative interactions between adjacent cI dimers Regulation of Transcription Termination in Bacteria The bacteriophage lambda N and Q proteins prevent stalling and termination by altering the properties of bacterial RNA polymerase The transcription of the phage lambda lytic genes begins at the divergent PL and PR promoters. Initially, the transcripts produced are short because RNA polymerase encounters sequences in the RNA, tL and tR, that lead to termination of transcription We previously described the role of Cro in binding DNA and preventing reestablishment of the lysogenic state; the other important lytic gene product is the N protein, which also begins to build up in the cell At sufficient concentrations, the N protein alleviates termination at the tL and tR sites. This allows RNA polymerase to transcribe genes needed early in the lytic cycle Within each nut (N utilization) site are two RNA sequences called box A and box B. Box B forms an RNA stem-loop to which N binds, while box A is a binding site for the E. coli protein NusB The binding of N protein, together with NusB and other cellular proteins, alters the properties of RNA polymerase such that it gains the ability to transcribe efficiently through the transcription termination size With termination suppressed, RNA polymerase can now continue to transcribe the downstream genes, which encode several proteins, including those needed for phage chromosome replication In contrast to the N protein, the Q protein prevents termination by binding directly to DNA. The binding site for the Q protein, called QBE, is located between the -35 and -10 regions of the PR’ promoter, which is transcribed by RNA polymerase holoenzyme containing the sigma 70 subunit In the absence of Q, RNA polymerase pauses just downstream of the - 10 region. When sufficient Q protein is present, it binds to the QBE side and directly contacts the sigma 70 subunit, causing elongation to resume Attenuation is a mechanism for controlling the effect of terminator sequences One form of regulation in bacteria takes advantage of the ability of certain mRNA sequences to form two alternative RNA secondary structures - one that leads to transcription termination and another to productive gene expression Consequently, under certain conditions, expression of the full-length transcript is promoted, whereas under other conditions, termination of transcription is favored The leader sequence, which encodes a small open reading frame that is rich in codons for the amino acid tryptophan contains four key blocks of ribonucleotides - regions 1, 2, 3, and 4 - which can form alternative pairing arrangements Regions 1 and 2 are complementary and can form a stem-loop structure, while regions 3 and 4 can also base-pair and form a rho-independent terminator. Regions 2 and 3 can form an alternative stem-loop structure, which then leaves regions, and 4 unpaired Once RNA polymerase transcribes the beginning of the reader sequence, the ribosome binds to the message and begins to translate the leader peptide, while RNA polymerase continues to transcribe the downstream sequences When levels of tryptophan are low, however, the ribosome stalls within the short open reading frame, while waiting for a tRNA to be charged with tryptophan. at high levels of tryptophan, however, there is enough charged tRNA to allow the ribosome to more rapidly to the end of the small open reading frame Direct binding of metabolites to RNA riboswitches can control transcription termination The formation of alternative RNA structures can be regulated even more directly, for example by the binding of small metabolites to specific regions of RNA transcripts denoted riboswitches Riboswitch: RNA element typically found in the 5' untranslated region (UTR) of transcripts that, on binding to small-molecule metabolites, change their conformation in a way that affects transcription or translation Riboswitches regulate transcription by controlling whether or not a terminator or anti-terminator stemloop forms in the mRNA, which determines whether transcription is completed appropriately All riboswitches contain two key regions: the aptamer, a sometimes complex RNA structure that binds to the metabolite being sensed, and an expression platform, which consists of segments of the RNA that control the output, such as transcription Expression of these genes depends upon whether a terminator or an anti-terminator forms in the 5' end of the mRNA transcript; the formation of a terminator or anti-terminator is determined, in turn, by the binding of adenine to the aptamer Regulation of Transcription Initiation and Elongation in Eukaryotes ELK1 activates transcription by recruiting the mediator complex Mediator is thought to stimulate transcription by promoting assembly of the transcription pre-initiation complex, recruiting RNA polymerase to the promoter, and stimulating phosphorylation of the RNA polymerase II CTD The mammalian ELK1 protein activates transcription in response to extracellular signals known as mitogens, which are molecules that cause a cell to enter mitosis However, mitogen binding to a cell surface receptor activates protein kinases in the cytoplasm, which subsequently phosphorylase the activation domain of ELK1 Instead, the response to an extracellular signal is communicated to the transcriptional regulator via an enzyme that phosphorylates ELK1, thereby altering its ability to recruit co-activator complexes Gal4 recounts RNA polymerase through a co-activator complex The regulation of transcription by the yeast Gal4 protein provides an example of a more complex interplay between several proteins that regulate transcription in response to the presence of a particular signal Gal4 regulates genes that encode proteins required for galactose metabolism. When galactose levels are elevated, Gal4 activates transcription of genes encoding enzymes that convert galactose into glucose-1phosphate The separation of the DNA - binding and activation functions of Gal4 into discrete domains has been exploited to produce chimeric proteins that are useful tools to molecular biologists Unlike the bacterial Trp repressor and CAP activator, Gal4 does not bind directly to the allosteric effector galactose. Instead, the ability of Gal4 to activate transcription is controlled by two proteins, Gal80 and Gal3 In the absence of galactose, Gal80 binds to the activation domain of Gal4 and prevents it from activating transcription. Under these conditions,Gal80 can be found both in the nucleus and in the cytoplasm, whereas Gal3 is found only in the cytoplasm One of these functions is to recruit Mediator, which, together with SAGA, promotes assembly of the transcription initiation complex by contacting the basal transcription factors, which, in turn, help to recruit RNA polymerase II Ume6 represses transcription by recruiting a co-repressor complex with histone deacetylase activity Ume6 ensures that cells respond appropriately to their nutritional environment, binding upstream of genes whose expression is modulated in response to changes in the levels of metabolites such as glucose, nitrogen, and inositol The deacetylase targets the N-terminal tails of adjacently bound histones, removing acetyl groups from the lysine residues. Deacetylation of residues of the tail of histone H4, in particular, allows more compact chromatin states to form, and consequently represses transcription At the same time, the nucleosome-remodeling enzyme helps to establish an altered chromatin structure that further contributes to repression of transcription Heat shock factor regulates transcription elongation by receiving promoter proximal pausing Yet, even after RNA polymerase has initiated transcription and broken free of the promoter, there are additional points at which the cell regulates whether the full-length transcript is made The hsp70 protein is a molecular chaperone that plays a variety of protective roles when cells are subject to abnormally high temperatures, a condition known as heat shock One of the functions of hsp70 is to prevent aggregation of partially synthesized or unfolded proteins, which can accumulate rapidly under conditions of heat shock To enable rapid activation, hsp70 and other heat shock genes have a paused RNA polymerase that is activated upon heat shock, thus leading to a rapid transcriptional response Under normal conditions, GAGA factor binds to the hsp70 promoter and recruits the ATP-dependent nucleosome-remodeling factor (NURF). NURF helps to maintain the promoter in a nucleosome-free open configuration that allows binding of the RNA polymerase II basal transcription machinery When subjected to head shock, in which the temperature is shifted to 37 degrees Celsius, the previously monomer Hsf protein forms timers that are able to bind to DNA sequences cared heat shock elements (HSEs) in the hsp70 promoter Combinatorial Regulation of Eukaryotic Transcription Yeast cell type is determined by different combinations of four transcriptional regulators The a and alpha cell types are haploid, meaning that they each have just a single complement of chromosomes. The a/alpha cell type is a diploid and forms when an a cell fuses with an alpha cell in a process that is known as mating Only haploid cells of the opposite mating type can mate with one another - that is, a and alpha cells can mate, but not two a cells or two alpha cells The diploid a/alpha cell that results from mating of an a cell and an alpha cell is incapable of mating but, under conditions of starvation, can undergo meiosis to form haploid sports In a cells, transcription of the a-specific genes, which encode proteins that confer the a phenotype, is activated by the Mcm1 protein The pattern of activation and repression is reversed in alpha cells; the alpha1 protein activates transcription of alpha-specific genes, while alpha 2 represses transcription of a-specific genes by recruiting a co-repressor complex called Tup1/Ssn6 The a1 and alpha 2 proteins combine to form a heterodimer that binds to a different set of DNA sites than either alpha 2 or a1 alone As in alpha cells, the alpha 2 protein also represses transcription of a-specific genes. With no expression of either a for alpha genes, the diploid cells are incapable of mating Regulation of the human interferon - beta enhancer integrates signals from several pathways The regulation of the human interferon-beta gene provides an example of how synergy between several regulatory proteins makes it possible to regulate transcription of a single gene in response to multiple signals The interferon protein encoded by the interferon-beta gene helps to defend cells from viral infection by inhibiting synthesis of the viral genome and stimulating the host immune response These proteins bind to precisely positioned sites within the enhancer to form a complex of DNA - bound transcriptional regulators called the enhancesome When HMG-I(Y) binds DNA in the first step in enhancesome assembly, it introduces bending of the DNA, which facilitates binding of the other transcriptional regulators All of the proteins bind to the DNA in a highly cooperative manner, with the binding of certain proteins early in complex formation facilitating the binding of further components of the enhacesome In general, the requirement for using a large number of proteins to activate a single gene ensures that the gene is activated only under a very precise set of conditions The Role of Signaling Cascades in the Regulation of Transcription Nuclear receptor proteins respond to effector molecules that diffuse through the membrane One of the simplest ways in which an extracellular signal can be transmitted to the nucleus is through steroid hormones, which are allosteric effectors of regulatory proteins These hormones are lipid-soluble and can therefore diffuse through membranes into the cell, where they bind directly to nuclear receptor proteins Nuclear receptor proteins contain a DNA - binding domain that recognizes specific DNA sequences and a ligand-binding domain, which binds the hormone or other small ligand Rather than affecting the binding of the receptor to DNA, as in the case of the bacterial Trp depressor, the ligand-induced conformational change instead affects the ability of the nuclear hormone receptor to recruit different co repressor and co-activator complexes to the DNA The ability to heterodimerize makes more complex regulatory networks possible, since two proteins that are capable of forming either homodimers or heterodimers can give rise to three different types of dimers In the case of other nuclear receptor proteins such as the glucocorticoid receptor, ligand binding also triggers translocation of the protein into the nucleus A cascade of events involving protein phosphorylation, proteolysis, and nuclear translocation regulates NF-kB activity Many signaling cascades involve multiple steps and may take advantage of a number of different mechanisms for transmitting a signal from one molecule to the next In unstimulated cells, the NF-kB heterodimers are held in the cytoplasm by an inhibitory protein called IkB, which binds to a specialized region of NF-kB that is responsible for targeting the nucleus Activated IKK (I-kB kinase) phosphorylates two serine residues in the regulatory domain of I-kB. The phosphorylated I-kB protein is now recognized by a type by a type of enzyme called an E3 ubiquitin ligase, which attaches a chain of ubiquitin proteins to I-kB Gene Silencing Gene silencing is brought about by changes in chromatin structure Gene silencing is brought about by an altercation in chromatin structure that can often be detected by assays that measure differences in nuclease accessibility and staining Another feature that distinguishes silencing from simple repression is that silenced regions can spread along a chromosome. Spreading can be blocked by boundary elements The budding yeast mating-type loci and telomeric regions are silenced by establishing a heterochromatic state Yeast a and alpha cells differ only in the genes encoded by the MAT locus - a cells contain the a1 regulatory gene at the MAT locus, and alpha cells have in its place the alpha regulatory genes alpha 1 and alpha 2 In to the actively transcribed sequence at the MAT locus, chromosome III contains an additional copy of the a and alpha gene sequences that are, however, not expressed