Breaking through to the other side: silencers and barriers

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2[Formula: see text], dot1[Formula: see text]) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.

TFIIIC bound DNA elements in nuclear organization and insulation

tRNA genes (tDNAs) have been known to have barrier insulator function in budding yeast, Saccharomyces cerevisiae, for over a decade. tDNAs also play a role in genome organization by clustering at sites in the nucleus and both of these functions are dependent on the transcription factor TFIIIC. More recently TFIIIC bound sites devoid of pol III, termed Extra-TFIIIC sites (ETC) have been identified in budding yeast and these sites also function as insulators and affect genome organization. Subsequent studies in Schizosaccharomyces pombe showed that TFIIIC bound sites were insulators and also functioned as Chromosome Organization Clamps (COC); tethering the sites to the nuclear periphery. Very recently studies have moved to mammalian systems where pol III genes and their associated factors have been investigated in both mouse and human cells. Short interspersed nuclear elements (SINEs) that bind TFIIIC, function as insulator elements and tDNAs can also function as both enhancer - blocking and barrier insulators in these organisms. It was also recently shown that tDNAs cluster with other tDNAs and with ETCs but not with pol II transcribed genes. Intriguingly, TFIIIC is often found near pol II transcription start sites and it remains unclear what the consequences of TFIIIC based genomic organization are and what influence pol III factors have on pol II transcribed genes and vice versa. In this review we provide a comprehensive overview of the known data on pol III factors in insulation and genome organization and identify the many open questions that require further investigation. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Transcription independent insulation at TFIIIC-dependent insulators

Chromatin insulators separate active from repressed chromatin domains. In yeast the RNA pol III transcription machinery bound to tRNA genes function with histone acetylases and chromatin remodelers to restrict the spread of heterochromatin. Our results collectively demonstrate that binding of TFIIIC is necessary for insulation but binding of TFIIIB along with TFIIIC likely improves the probability of complex formation at an insulator. Insulation by this transcription factor occurs in the absence of RNA polymerase III or polymerase II but requires specific histone acetylases and chromatin remodelers. This analysis identifies a minimal set of factors required for insulation.

Repeat organization and epigenetic regulation of the DH-Cmu domain of the immunoglobulin heavy-chain gene locus

The first steps of murine immunoglobulin heavy-chain (IgH) gene recombination take place within a chromosomal domain that contains diversity (D(H)) and joining (J(H)) gene segments, but not variable (V(H)) gene segments. Here we show that the chromatin state of this domain is markedly heterogeneous. Specifically, only 5'- and 3'-most D(H) gene segments carry active chromatin modifications, whereas intervening D(H)s are associated with heterochromatic marks that are maintained by ongoing histone deacetylation. The intervening D(H)s form part of a tandemly repeated sequence that expresses tissue-specific, antisense oriented transcripts. We propose that the intervening D(H) genes are actively suppressed by repeat-induced epigenetic silencing, which is reflected in their infrequent representation in DJ(H) junctions compared to the flanking D(H) genes.

Heterochromatin-mediated control of virulence gene expression

In recent years, the sequencing and annotation of complete genomes, together with the development of genetic and proteomic techniques to study previously intractable eukaryotic microbes, has revealed interesting new themes in the control of virulence gene expression. Families of variantly expressed genes are found adjacent to telomeres in the genomes of both pathogenic and non-pathogenic organisms. This subtelomeric DNA is normally heterochromatic and higher-order chromatin structure has now come to be recognized as an important factor controlling both the evolution and expression dynamics of these multigene families. In eukaryotic cells, higher-order chromatin structure plays a central role in many DNA processes including the control of chromosome integrity and recombination, DNA partitioning during cell division, and transcriptional control. DNA can be packaged in two distinct forms: euchromatin is relatively accessible to DNA binding proteins and generally contains active genes, while heterochromatin is densely packaged, relatively inaccessible and usually transcriptionally silent. These features of chromatin are epigenetically inherited from cell cycle to cell cycle. This review will focus on the epigenetic mechanisms used to control expression of virulence genes in medically important microbial pathogens. Examples of such control have now been reported in several evolutionarily distant species, revealing what may be a common strategy used to regulate many very different families of genes.

Epigenetic aberrations and cancer

The correlation between epigenetic aberrations and disease underscores the importance of epigenetic mechanisms. Here, we review recent findings regarding chromatin modifications and their relevance to cancer.

Dual roles for Mcm10 in DNA replication initiation and silencing at the mating-type loci

Recent studies linking DNA replication proteins to transcriptional silencing suggest that some of the same mechanisms that facilitate the initiation of replication at origins might be involved in establishing repressed chromatin at silencer elements. Our ongoing studies of several mutants of the replication initiation factor Mcm10 of budding yeast revealed an associated defect in the production of mating type pheromones. This observation prompted us to look more directly at the effect of MCM10 mutations on the expression of a reporter gene in the mating type locus and to assay for physical interactions between Mcm10 and known silencing factors. Our findings, that Mcm10 mutants disrupt mating loci silencing and that Mcm10 interacts with Sir2 and Sir3, suggest that Mcm10 also plays an essential, and separable role in transcriptional silencing.

Chromosome organization and chromatin modification: influence on genome function and evolution

Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.

Genomic and epigenomic approaches to the study of X chromosome inactivation

X chromosome inactivation represents a compelling example of chromosome-wide, long-range epigenetic gene-silencing in mammals. The cis- and trans-acting factors that establish and maintain the patterns and levels of gene expression from the active and inactive X chromosomes remain incompletely understood; however, the availability of the complete genomic sequence of the human X chromosome, together with complementary approaches that explore the computational biology, epigenetic modifications and gene expression-profiling along the chromosome, suggests that the features of the X chromosome that are responsible for its unique forms of gene regulation are increasingly amenable to experimental analysis.

Histone H1 of Saccharomyces cerevisiae inhibits transcriptional silencing

Eukaryotic genomes contain euchromatic regions, which are transcriptionally active, and heterochromatic regions, which are repressed. These domains are separated by "barrier elements": DNA sequences that protect euchromatic regions from encroachment by neighboring heterochromatin. To identify proteins that play a role in the function of barrier elements we have carried out a screen in S. cerevisiae. We recovered the gene HHO1, which encodes the yeast ortholog of histone H1, as a high-copy modifier of barrier activity. Histone H1 is a linker histone that binds the outside of nucleosomes and modifies chromatin dynamics. Here we show that Hho1p reinforces the action of several types of barrier elements, and also inhibits silencing on its own.

Assembly of silent chromatin during thymocyte development

Epigenetic events that contribute to the assembly and maintenance of silent chromatin structures have been defined through genetic, molecular, and cytological studies in a variety of eukaryotic model organisms. However, the precise cascade of events responsible for converting a developmentally regulated gene from an active euchromatic state to a heritably silent heterochromatic state remains to be elucidated. To establish a molecular framework for studying this cascade, we examined the temporal order of events associated with silencing of the murine terminal transferase (Dntt) gene during thymocyte maturation. This article describes our findings in the context of current knowledge of gene silencing mechanisms.

Proteomic and genomic characterization of chromatin complexes at a boundary

We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin. These assemblies contain characteristic stretches of DNA that flank particular regions of silent chromatin, as well as five distinctively modified histones and a set of protein complexes. The complexes consist of at least 15 chromatin-associated proteins, including DNA pol ɛ, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase. We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states.

BLG-e1 - a novel regulatory element in the distal region of the beta-lactoglobulin gene promoter

beta-Lactoglobulin (BLG) is a major ruminant milk protein. A regulatory element, termed BLG-e1, was defined in the distal region of the ovine BLG gene promoter. This 299-bp element lacks the established cis-regulatory sequences that affect milk-protein gene expression. Nevertheless, it alters the binding of downstream BLG sequences to histone H4 and the sensitivity of the histone-DNA complexes to trichostatin A treatment. In mammary cells cultured under favorable lactogenic conditions, BLG-e1 acts as a potent, position-independent silencer of BLG/luciferase expression, and similarly affects the promoter activity of the mouse whey acidic protein gene. Intragenic sequences upstream of BLG exon 2 reverse the silencing effect of BLG-e1 in vitro and in transgenic mice.

Hyperacetylated chromatin domains: lessons from heterochromatin

A small but growing number of loci that exhibit covalent histone modifications, such as hyperacetylation, over broad regions of 10 kb or more have been characterized. These hyperacetylated domains occur exclusively at loci containing highly expressed, tissue-specific genes, and the available evidence suggests that they are involved in the activation of these genes. Although to date little is known concerning the formation or function of these domains, rather more is known concerning repressive, heterochromatic domains, and the example provided by heterochromatin may be instructive in considering mechanisms of active domain formation.

Molecular Mechanisms of Epigenetics

The main epigenetic mechanisms in regulation of gene expression are discussed. The definition of epigenetics and its specific mechanisms including DNA methylation and gene imprinting, modifications of nucleosomal histones associated with silencing or activation of gene transcription, RNA interference, chromosomal silencing, and the role of mobile elements are discussed.

Clusters of biotin-responsive genes in human peripheral blood mononuclear cells

Effects of biotin in cell signaling are mediated by transcription factors such as nuclear factor-kappa B (NF-kappa B) and Sp1/Sp3 as well as by posttranslational modifications of DNA-binding proteins. These signaling pathways play roles in the transcriptional regulation of numerous genes. Here we tested the hypothesis that biotin-dependent genes are not randomly distributed in the human genome but are arranged in clusters. Peripheral blood mononuclear cells were isolated from healthy adults before and after supplementation with 8.8 micromol/day biotin for 21 days. Cells were cultured ex vivo with concanavalin A for 3 hours to stimulate gene expression. Abundances of mRNA encoding approximately 14,000 genes were quantified by both DNA microarray and reverse transcriptase-polymerase chain reaction. The expression of 139 genes increased by at least 40% in response to biotin supplementation, whereas the expression of 131 genes decreased by at least 40% in response to biotin supplementation. The following clusters of biotin-responsive genes were identified: 1) 16% of biotin-responsive gene products localized to the cell nucleus; at least 28% of biotin-responsive genes play roles in signal transduction (these findings are consistent with a role for biotin in cell signaling); and 2) of the biotin-responsive genes, 54% clustered on chromosomes 1, 2, 3, 11, 12, and 19, whereas no biotin-responsive genes were found on chromosomes 10, 16, 18, 21, and heterosomes. This suggests that position effects play a role in biotin-dependent gene expression. Collectively, these findings suggest that the human genome contains clusters of biotin-dependent genes.

Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location

Heterochromatin proteins are thought to play key roles in chromatin structure and gene regulation, yet very few genes have been identified that are regulated by these proteins. We performed large-scale mapping and analysis of in vivo target loci of the proteins HP1, HP1c, and Su(var)3-9 in Drosophila Kc cells, which are of embryonic origin. For each protein, we identified approximately 100-200 target genes among >6000 probed loci. We found that HP1 and Su(var)3-9 bind together to transposable elements and genes that are predominantly pericentric. In addition, Su(var)3-9 binds without HP1 to a distinct set of nonpericentric genes. On chromosome 4, HP1 binds to many genes, mostly independent of Su(var)3-9. The binding pattern of HP1c is largely different from those of HP1 and Su(var)3-9. Target genes of HP1 and Su(var)3-9 show lower expression levels in Kc cells than do nontarget genes, but not if they are located in pericentric regions. Strikingly, in pericentric regions, target genes of Su(var)3-9 and HP1 are predominantly embryo-specific genes, whereas on the chromosome arms Su(var)3-9 is preferentially associated with a set of male-specific genes. These results demonstrate that, depending on chromosomal location, the HP1 and Su(var)3-9 proteins form different complexes that associate with specific sets of developmentally coexpressed genes.

Gene Organization: Selection, Selfishness, and Serendipity

The apparati behind the replication, transcription, and translation of prokaryotic and eukaryotic genes are quite different. Yet in both classes of organisms, genes may be organized in their respective chromosomes in similar ways by virtue of similarly acting selective forces. In addition, some gene organizations reflect biology unique to each class of organisms. Levels of organization are more complex than those of the simple operon. Multiple transcription units may be organized into larger units, local control regions may act over large chromosomal regions in eukaryotic chromosomes, and cis-acting genes may control the expression of downstream genes in all classes of organisms. All these mechanisms lead to genomes being far more organized, in both prokaryotes and eukaryotes, than hitherto imagined.

Repair of UV lesions in silenced chromatin provides in vivo evidence for a compact chromatin structure

Genes positioned close to telomeres in yeast are silenced by a heterochromatin-like structure containing Sir proteins. To investigate whether silencing also affects DNA repair, we studied removal of UV lesions by photolyase and nucleotide excision repair (NER) in strains containing the URA3 gene inserted 2 kilobases from a telomere. URA3 was transcriptionally active in sir3delta mutants, partially silenced in SIR3 cells, or completely silenced by overexpression of SIR3 or deletion of RPD3. The active URA3 showed efficient repair by both pathways. Fast repair of the promoter and 3' end by photolyase reflected a non-nucleosomal structure. Partial silencing had no remarkable effect on photolyase but reduced repair by NER, indicating differential accessibility for the two repair reactions. Complete silencing inhibits NER and photolyase in the coding region as well as in the promoter and the 3'-end. Conventional nuclease footprinting analyses revealed subtle changes in the promoter proximal nucleosome under partially silenced conditions but a pronounced reorganization of chromatin extending over the whole gene in silenced chromatin. Thus, both repair systems are sensitive to chromatin changes associated with silencing and provide direct evidence for a compact structure of heterochromatin.

Heterochromatin and epigenetic control of gene expression

Eukaryotic DNA is organized into structurally distinct domains that regulate gene expression and chromosome behavior. Epigenetically heritable domains of heterochromatin control the structure and expression of large chromosome domains and are required for proper chromosome segregation. Recent studies have identified many of the enzymes and structural proteins that work together to assemble heterochromatin. The assembly process appears to occur in a stepwise manner involving sequential rounds of histone modification by silencing complexes that spread along the chromatin fiber by self-oligomerization, as well as by association with specifically modified histone amino-terminal tails. Finally, an unexpected role for noncoding RNAs and RNA interference in the formation of epigenetic chromatin domains has been uncovered.

The establishment and maintenance of lymphocyte identity through gene silencing

Cell identity is determined by selective gene activation and by the maintenance of other regulated genes in a silent state. Although activation mechanisms have been dissected in considerable depth, great strides towards an understanding of the molecular control of gene silencing have been made only recently. Molecular hallmarks of silent chromatin and proteins involved in its assembly and maintenance have been identified through genetic, cytological and biochemical studies in a variety of organisms. Immunologists are now beginning to use this knowledge to elucidate mechanisms underlying cell fate decisions and key developmental steps. This review surveys the current knowledge of gene silencing, with an emphasis on studies in lymphocytes that are advancing our general understanding of silencing mechanisms during development.

Heterochromatin: proteins in flux lead to stable repression

Heterochromatin is a phenotypically stable entity, but recent studies on the binding of HP1 protein in heterochromatin indicate that the individual components within these domains are not stably bound but in constant flux. These results force us to reexamine previous models of heterochromatin.

The vertebrate protein CTCF functions as an insulator in Saccharomyces cerevisiae

Insulators are elements that shelter genes from the effects of silencers or enhancers. CTCF is the only vertebrate protein that has a recognized role in transcriptional insulation, but how it exerts its effect is unknown. In an attempt to better understand how CTCF functions, we have used an insulation assay in Saccharomyces cerevisiae. We show that CTCF acts as an insulator in yeast, where it can efficiently block the spreading of repressive telomeric chromatin. We identify two domains of the protein that are responsible for this activity: a short and very potent N-terminal domain, as well as the C-terminus of the protein.

Chromatin: a connection between loops and barriers?

A genetic screen for proteins that can block the spread of silenced heterochromatin has identified components of the nuclear pores with potential barrier activity. These results suggest that formation of loops of chromatin anchored to the pore could be one mechanism of barrier function.

Blockers and barriers to transcription: competing activities?

In the eukaryotic cell active and inactive genes reside adjacent to one another and are modulated by numerous regulatory elements. Insulator elements prevent the misregulation of adjacent genes by restricting the effects of the regulatory elements to specific domains. Enhancer blockers prevent enhancers from inadvertently activating neighboring genes, and recent results suggest that they might function by a conserved mechanism across species. These elements appear to disrupt enhancer-promoter "communications" by interacting with the regulatory elements and sequestering these elements into specific regions of the nucleus thus rendering them non-functional. Barrier elements insulate active genes from neighboring heterochromatin and recent results suggest that they function by specific localized recruitment of acetyltransferases that antagonize the spread of heterochromatin-associated deacetylases, thus preventing the propagation of heterochromatin.