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Curr Biol. Author manuscript; available in PMC Sep 14, 2011.
Published in final edited form as:
Curr Biol. Sep 14, 2010; 20(17): R764–R771.
doi:  10.1016/j.cub.2010.06.037
PMCID: PMC3033598
NIHMSID: NIHMS231577

Transcriptional repression: conserved and evolved features

Abstract

Regulation of gene expression by transcriptional repression represents an ancient and conserved mechanism that manifests itself in diverse forms. Here we summarize conserved pathways for transcriptional repression prevalent throughout all forms of life, as well as indirect mechanisms that appear to have originated in eukaryotes, consistent with their unique chromatin environment. The direct interactions between transcriptional repressors and core machinery in bacteria and archaea are sufficient to generate a sophisticated suite of mechanisms that provide flexible control. These direct interactions contrast with the activity of corepressors, which provide an additional regulatory control in eukaryotes. Their modulation of chromatin structure represents an indirect pathway to downregulate transcription, and their diversity and modulation provides additional complexity suited to the requirements of elaborate eukaryotic repression patterns. New findings indicate that corepressors are not necessarily restricted to generating a single stereotypic output, but can rather exhibit diverse functional responses depending on the context in which they are recruited, providing a hitherto unsuspected additional source of diversity in transcriptional control. Mechanisms within eukaryotes appear to be highly conserved, with novel aspects chiefly represented by addition of lineage- specific corepressor scaffolds that provide additional opportunities for recruiting the same core machinery.

Introduction

Transcriptional repression embodies the original mechanism discovered for gene regulation, dating to the pioneering work of Jacob and Monod. Subsequent discoveries filled out a picture showing that bacterial genes are regulated by sophisticated layers of activation and repression, as well as complex posttranscriptional mechanisms. From basic biophysical considerations, simple bacterial cis regulatory transcriptional elements should be capable of generating complex outputs seen with eukaryotic genes [1]. Nature is not so parsimonious, however; the evolution of more sophisticated gene expression programs in eukaryotes has been accompanied by the appearance of more complex machinery and mechanisms of transcriptional control, including repression. A multitude of cellular processes control transcriptional activity of genes, and include negative regulatory pathways that limit production and activity of activator proteins. Dedicated DNA-binding transcription repressors that actively block transcription play equally crucial roles, however. Focusing on this latter aspect, here we survey current understanding of their repression mechanisms, and suggest how evolving complexity is matched by adoption of multitiered repressor/corepressor systems that themselves are subject to considerable elaboration and modification.

Transcriptional repression in bacteria: complex responses from streamlined systems

Bacterial RNA polymerase action has been characterized by binding of the enzyme to the promoter to form a closed complex, melting of the DNA to form the open complex, promoter escape after formation of the first few phosphodiester bonds, and elongation and termination [2, 3]. All of these steps are possible points for control (Figure 1). With the exception of antitermination mechanisms that involve proteins complexed to the nascent transcript, bacterial repression pathways invariably involve the direct action of DNA binding repressor proteins on the transcription machinery to block the activity of RNA polymerase at various steps, including interfering with recruitment initiation or elongation. A common mechanism involves an either/or occupancy of promoter regions by inhibitors and the polymerase. The well-studied LacI repressor utilizes a primary binding site close to the transcription initiation site to block RNA polymerase access to the promoter; this mechanism is greatly enhanced by loop formation involving distal auxiliary sites [4]. Interestingly, placing binding sites just 3′ of the initiation site can switch the mode of repression to blockage of promoter escape, suggesting a flexibility in possible effects mediated by these simple components [5]. Other bacterial repressors, including phage lambda cI repressor and the LexA repressor also target promoter proximal sites to block RNA polymerase binding [6, 7]. In cases where the repressor binding site does not overlap with the promoter, repressor binding can nucleate the binding of additional repressor molecules to occlude RNA polymerase, as seen with DnaA binding to E. coli dnaA gene [8]. Binding of this protein within the gene can also induce premature termination [9].

Figure 1
Distinct repression mechanisms used by prokaryotic and eukaryotic repressors

A second common mechanism involves simultaneous occupancy of RNA polymerase and repressor, with inhibitory consequences. The phage [var phi]29 protein p4 binds to sites 5′ of the viral A2b promoter and interacts with the α subunit of the RNA polymerase to prevent promoter escape, although abortive initiation can occur [10]. The MerR repressor acts at an earlier step; this repressor and the polymerase bind simultaneously to the merT promoter, resulting in a complex that is blocked in the transition from closed to open complex in the absence of mercury [11, 12]. Upon binding of the metal, allosteric alterations in MerR change DNA bending to permit open complex formation [13]. Similar allosteric controls of RNA polymerase closed to open complex formation have been reported for the E.coli GalR repressor and the plasmid-borne KorB repressor. The latter protein occupies promoter proximal sites to exert a moderate level of repression, but strongly synergizes with two other plasmid encoded repressors, KorA and TrbA, that can functionally interact with KorB at a distance, suggesting that distally-acting multiprotein complexes can also be utilized to repress bacterial genes [14].

Reviewing these examples, a major theme regarding transcriptional regulation in bacteria is the direct physical interactions of repressors (and activators) with the basal transcription machinery, programmed by the structure of cis regulatory regions. More complex responses are effected by utilization of additional auxiliary sites, as with the LacI repressor, but there are relatively few instances where two distinct DNA binding proteins are jointly employed to effect repression (or activation), and in no cases do the repressors need to mediate their control of polymerase through intermediate protein complexes. This direct interaction contrasts strongly with the situation in eukaryotes, as we discuss below.

Archaeal transcription – complex core machinery, simple repression mechanisms

Recent studies of the third domain of life, the archaea, indicate that the transcriptional machinery of these organisms shares similarities with both bacteria and eukaryotes. The archaeal RNA polymerase of M. jannaschi has twelve subunits homologous to those of eukaryotic RNA polymerase II; a core complex containing just the homologs to bacterial ββ′α is sufficient for in vitro initiation [15]. The holoenzyme is positioned by basal factors TFB and TBP that bind to the basal promoter, similar to the case in eukaryotes [16].

Some Euryarchaea contain H3 and H4-like histones that serve to compact DNA, but these histones lack the tail regions frequently modified for gene regulatory purposes in eukaryotes, and they bind less tightly to DNA than eukaryotic histones [17]. Other archaeal genomes lack these eukaryotic-like histone genes, but appear to have basic DNA-binding proteins that serve a similar purpose [18, 19]. It is not clear if archaeal histones are as inherently inhibitory to transcription as those present in eukaryotes, and whether all type of histone analogs in archea have similar repressive potential.

Archaeal genomes contain numerous homologs to bacterial transcription factors, and insight into transcriptional repression in archaea was first obtained through characterization of one of these, the metal-dependent regulator Mdr1 of A. fulgidus. Similar to repression mechanisms observed in bacteria, the Mdr1 protein regulates transcription of its own gene by blocking recruitment of the RNA polymerase to the promoter [20, 21]. Another transcriptional repressor, the Phr protein of P. furiosus acts through promoter-proximal binding sites to similarly prevent RNA polymerase from accessing the promoter [22]. The basal factors bound at the transcription start site can also be targeted; Lrs14, an archaeal homolog of the bacterial leucine responsive regulatory protein family, inhibits the promoter binding of archaeal general transcription factors TBP and TFB, thus interfering with early steps of transcription initiation [23, 24]. In vitro experiments have revealed that NpR, a regulator of nitrogen metabolism in M. maripaludis can also inhibit binding of TFB and TBP.

Thus, even though archaeal core transcription machinery bears strong resemblance to that of eukaryotes, transcriptional repression appears to follow the simple scenario seen in bacteria, whereby DNA binding proteins directly target basal machinery at the promoter. These mechanistic studies have relied largely on in vitro assays in the absence of archaeal nucleosome-like proteins, where possible effects of covalent modification of nucleosome-like proteins is neglected [25]. A more complete picture is likely to emerge as biochemical studies progress. One potentially unifying notion is that the small bacterial-sized genomes found in archaea may demand no more highly sophisticated repression mechanisms than those present in bacteria. However, it is striking that the bacterial-sized S. cerevisiae genome does feature a full panoply of chromatin-mediated repression mechanisms. It is possible that other features of the eukaryotic lifestyle dictate elaboration of more complex mechanisms for transcriptional control.

Repression features layers of regulation in eukaryotes

To consider how eukaryotic repression mechanisms compare with those bacterial and archaeal, we should note key general features of eukaryotic transcription control. The distinctly different set of proteins and mechanisms involved in eukaryotic repression correlates with enhanced structural and functional demands in eukaryotes (Figure 1). Especially in multicellular eukaryotes, achieving correct temporal- and tissue-specific gene expression poses enormous functional challenges. In addition, the large size of many eukaryotic genomes dilutes regulatory sequences in a sea of noncoding elements, making establishment of the correct interactions between regulatory proteins and target genes problematic. Presumably as an adaptation to these demands, the chromatin structure of eukaryotes is profoundly different from that of bacteria and archaea. Eukaryotic histone proteins, assembled on DNA as nucleosomes, pose a formidable intrinsic barrier to access of transcription machinery, reducing background transcriptional noise that fortuitous interactions may generate [26]. Eukaryotic histones, with flexible ‘tail’ regions, also provide a platform for elaboration of various modification marks of regulatory significance. An additional newly appreciated feature of eukaryotic transcriptional regulation is the presence of RNA polymerase at many promoters even when the genes are in a quiescent state, suggesting that promoter escape may be the rate limiting step [27, 28]. In bacteria, such stalled complexes reflect either a deficient closed-to-open complex transition, a function of the DNA template that is compensated for by activators, or the active intervention by repressors that prevent an otherwise favorable reaction. In eukaryotes, it is not clear whether stalled polymerases are influenced by DNA binding repressors, or if such stalling is solely a consequence of basal promoter sequences and chromatin composition [29].

Eukaryotic transcriptional systems may have developed a number of specific features to provide additional complexity necessary for gene regulatory demands in these organisms. First, increased complexity in a transcriptional system may be generated by increasing the number of transcription factors, a trend also noted in bacteria, where those species with complex developmental life cycles tend to possess a large number of RNA polymerase binding sigma factors. Genomic studies have indeed revealed lineage-specific expansions of specific eukaryotic transcription families, suggesting that there are advantages in allocating functions among more actors [30]. When viewed at a global level, however, the percentage of genes annotated as DNA binding transcription factors is similar in eukaryotes and bacteria, ranging from 7% in E. coli to 12% in S. coelicolor, compared with 5.9% in A. thaliana and 10% in humans [31, 32]. Some eukaryotes, such as C. elegans, have a smaller percentage of genes devoted to DNA binding transcription factors (5%) than do many bacteria [33]. Alternative splicing and posttranslational modifications can of course increase the number of isoforms present in a cell, but this is not the sole source of complexity.

A second layer of complexity is the nature of eukaryotic cis regulatory elements; many bacterial elements consists of only a few binding sites, whereas eukaryotic promoters and enhancers commonly have dozens of motifs responsible for assembling core and regulatory machinery. Such combinatorial interactions provide an effective way to differentiate real from spurious cis elements in large genomes, facilitate cooperative mechanisms to overcome the barrier of histones, and offer more complex switch responses for fine-scale control. Yet with respect to transcriptional repressors, these proteins are generally capable of mediating effective transcriptional responses from rather simple cis elements; often from one or a few binding sites for transcription factors. Hwa's predictions that cis element structures need not be elaborate to generate proper readouts appear to be accurate in this context [34].

A third major area of difference between bacterial and eukaryotic systems is the elaboration of core transcriptional machinery, which is defined as the set of proteins required for assembly and initiation at a basal promoter. In addition to the twelve polypeptides associated with the RNA polymerase II responsible for transcription of protein coding genes, at least 60-80 other polypeptides are considered critical for the essential activity of the transcriptional initiation [35]. Clearly, this complexity should offer additional levels of regulation. In fact, recent discoveries of tissue-specific forms of this basal transcriptional machinery suggest that developmental gene regulation does involve alterations to this core set of factors [36]. It is less clear that with a larger complex of proteins assembling at promoters, a proportionally greater number of control points or available protein surfaces are directly contacted by different transcription factors. Many activator effects funnel through a limited number of targets in the basal machinery, and as we note below, repressors generally appear to predominantly interact with the chromatin.

The nature of transcription factor – transcription machinery/template interaction is where bacterial and eukaryotic regulation shows the greatest divergence. Transcriptional activators appear to function through two general levels, namely, recruiting coactivator complexes that can modify chromatin, and interacting with core transcriptional machinery [37]. In the latter category, some transcriptional activators directly target components of the basal machinery, such as TAF proteins of the TFIID complex, to recruit or allosterically affect these proteins, while other transcriptional factors interact with core machinery by means of coactivator complexes. DNA-binding eukaryotic transcriptional repressors, on the other hand, have only in rare instances been documented to directly contact and modify the activity of core machinery [38]. Some in vitro systems have documented competitive interactions between repressors and the basal transcriptional machinery, but the in vivo relevance of such studies remains uncertain [39]. Physical competition may provide a mechanism, as DNA binding repressors have also been shown to compete for overlapping activator binding sites, but the generality of this model is uncertain, for most repressor binding sites do not directly overlap activator sites [40]. Most DNA-binding transcriptional repressors appear to rely instead on indirect interactions, mediated by corepressors.

Corepressors – definition, function and conservation

The term corepressor refers to either a single protein or a scaffolding protein mediating the assembly of a multi-subunit complex that is recruited to a gene by transcription factors. Repressors possess discreet peptide motifs often contained within transcriptional repression domains that permit interaction with specific corepressors. It has been assumed that the transcription factor-corepressor complex is modular, because direct tethering of corepressors to DNA via a heterologous DNA-binding domain elicits transcriptional repression [41-43]. This assay neglects important context effects, however, as we discuss below. Corepressor complexes can exhibit a range of activities; they frequently contain histone deacetylase (HDAC) activity essential for stripping activation marks from histone tails. Corepressor complexes can contain other enzymatic activities as well, including histone methyl transferase or demethylase activities that can reset chromatin marks (Figure 1). Another conserved group of cofactors are SWI/SNF nucleosome remodeling complexes that generally serve an activating role, but in some cases are recruited by transcription factors to induce gene repression and thus can be considered a special type of corepressor. The Mi2/NuRD corepressor complex combines nucleosome remodeling activity with histone deacetylase activity, and does appear to play a dedicated repressive role [44-46]. In addition to nucleosome modification, corepressors have been shown to directly interfere with coactivators such as the CBP/p300 histone acetyltransferase or the mediator complex [47, 48]. These latter examples appear to be exceptions involving nonhistone targets, but in general, histone modifiying enzymes are capable of modifying transcription factors with the same posttranscriptional modifications as seen on histone tails. Nonetheless, our current understanding is that corepressors predominantly target chromatin structures. With hundreds of transcription factors in the cell, but only a dozen or so corepressor complexes, it may appear that implementing transcriptional repression through these cofactors produces a bottleneck of limited, generic activities. However, corepressors are not simply interchangeable levers to lower the nucleosome barrier, but sensitive control points that provide additional regulatory modulations through structural diversification, by sensing of signaling cascades, and context-dependent responses. These elaborations tune cell/tissue specific gene responses that are key for development.

A brief introduction to some widely studied corepressors sets the scene for a discussion of their diversity and regulation. One of the best studied corepressor complexes is the multisubunit Sin3 complex, a conserved corepressor found in yeast, plants, and animals. The Sin3 protein associates with histone deacetylases HDAC1 and HDAC2, as well as five additional polypeptides in higher eukaryotes [49]. Deacetylation appears to be the key repression mechanism mediated by Sin3 when it is recruited by transcription factors such as nuclear hormone receptors, p53, and Elk1. The Sin3 complex can be directly recruited by transcription factors or alternatively indirectly targeted through interaction with other corepressor complexes. For example, NCoR and SMRT, which are themselves recruited by nuclear hormone receptor type transcription factors, bind Sin3 complexes. [50, 51]. Besides deacetylation, this complex can also be associated with other enzymatic activities, including SWI/SNF chromatin remodelers, protein glycosylases, histone methylases and DNA methylases. Another widely studied factor is the Groucho corepressor, a prototypical member of a family of WD40-repeat containing proteins found in yeast, plants as well as metazoans [52, 53]. These corepressors form complexes with histone deacetylases, and some of the repression activity is dependent on this activity. Recruited by Hairy and HES transcription factors in metazoans, Groucho corepressors are important actors in the Notch signaling pathway, and play conserved roles in neurogenesis [52].

In contrast to the ubiquitous Sin3 and Groucho family proteins, a number of corepressors have been found that are restricted to metazoans. These proteins appear to function as adaptors to existing deeply conserved machinery. For instance, HDAC activity is an integral part of the CoREST (corepressor for repressor element 1 silencing transcription factor) complex that is recruited by the REST transcription factor to regulate neuronal gene expression. Besides recruiting HDAC 1 and 2, the CoREST complex also contains histone demethylase activity through the LSD 1 protein, thus expanding its chromatin remodeling capacity [54, 55]. Another extensively studied corepressor complex is the C terminal binding protein (CtBP) corepressor. Biochemical characterization of the CtBP complex has identified an array of enzymes with chromatin modifying action including histone deacetylase, histone methyltransferase and histone demethylase activity [56]. This complex modulates important cellular process, including differentiation, tumorigeneis and apoptosis [57]. CtBP is conserved from worms to flies to mammals but is represented by multiple genes in mammals, providing an additional source of diversification. As we shall see, gene duplication is one layer of corepressor elaboration.

Corepressor diversification

Although a relatively limited set of corepressors account for repression in the cell, greater diversity originates from the many forms of individual complexes, including the presence of paralogous genes. In mammals, the Groucho family consists of four Transducin-like Enhancer of Split genes with similar molecular structure. The proteins do not share functional redundancy; TLE1 is involved in hematogenesis, myogenesis, neural system development, and apoptosis, TLE2 regulates osteogenesis, TLE3 regulates placental development, while TLE4 maintains B cell lineage [53]. The SMRT and NCoR corepressors are highly similar proteins that form similar complexes with Sin3 but interact with distinct transcription factors. Subtle structural differences in the contact surfaces involved in binding nuclear hormone receptors cause NCoR to interact preferentially with the thyroid receptor (TR) and the SMRT complex to bind the retinoic acid receptor (RAR) [58, 59]. Similarly, CtBP proteins are encoded by two genes in mammals. Although these proteins are expressed in overlapping patterns and can perform similarly in cell based assays, they do show differences in genetic activity and control of subcellular localization [57]. Thus, the two isoforms differ when tested at the organismal level; CtBP2 is an essential gene for mouse development, while CtBP1 is not [60]. In this and other cases, the diversification of corepressor subfamilies may in some cases represent a way to merely generate tissue-specific expression patterns, but the latter two examples cited here suggest that diversification of protein function is also occurring. As with transcription factors themselves, further complexity arises in corepressors by generation of distinct isoforms through differential mRNA splicing. In some cases, these isoforms have been demonstrated to have distinct activities. A splice variant of NcoR that lacks the classical transcription factor interaction surface binds preferentially to orphan receptors Rev-Erb and Coup-TFII rather than TR [61]. The developmentally regulated unique splice forms of Drosophila Sin3 are similarly suggested to play different roles in development [62]. Particular splice forms may have gene-specific effects by preferential targeting but they may also exert global influences. ChIP-seq approaches should be used to determine if particular splice forms are used on most targets or if gene-specific effects are common.

Corepressors link signal pathways with transcription activity

Signaling pathways link environmental and physiological stimuli to transcription activity through posttranslational modifications (e.g. phosphorylation, acetylation, hydroxylation, and sumoylation) of transcription factors. Corepressor complexes are similarly targets of signaling pathways and may provide unique channels of communication with the cellular environment. Posttranslational modifications of corepressors can either change their subcellular localization or regulate the binding to transcription factors. In addition, some corepressors can bind to small molecule compounds in the environment, which can modulate repression potencies (Figure 2).

Figure 2
Modulation of corepressor activity through posttranslational modification and small molecules

A number of posttranslational modifications affect subcellular localization of corepressors. Mammalian CtBP1 is SUMOylated, a modification that is essential for its accumulation in the nucleus and repression of E-cadherin promoter [63]. Acetylation of CtBP2 by p300 can play a similar role; this modification is required for nuclear retention and repression activity [64]. The SMRT corepressor is phosphorylated by kinases of the MAPK pathway, leading to subcellular redistribution [65].

Posttranslational modifications of corepressors also affect the recruitment of corepressor complexes by transcription factors. Phosphorylation is one of the most prevalent post-translational modifications that modulate corepressor activities. During G1-S phase transition, the Rb corepressor is phosphorylated at multiple residues by the combinatorial effects of several CDKs, which leads to the disruption of the Rb/E2F complex [66]. Groucho activity is also modulated by phosphorylation, in response to signaling pathways. MAPK pathway phosphorylation attenuates Groucho's binding to the Eyeless transcription factor, while in contrast phosphorylation of the Groucho homolog TLE1 by casein kinase II enhances its association with the Hairy homolog Hes1 and with chromatin [67-69]. This mechanism is suggested to allow Groucho to play an integrating role between the EGFR and Notch signaling pathway [70]. A distinct modification, polyADP ribosylation by PARP1, is suggested to mediate the dismissal of the TLE1 corepressor complex from HES1-regulated promoter during neural stem cell differentiation [71].

In addition to these covalent modifications, binding of ligands has been suggested to provide a way for corepressors respond to the changes in the cellular environment. CtBP shares remarkable sequence similarity with dehydrogenases and contains a Rossman fold for binding to NAD+/NADH [72]. Binding of the cofactor is essential for CtBP's interaction with cellular and viral transcriptional repressors, and it was reported that NADH has a much higher affinity than NAD+ for CtBP [73]. CtBP might serve as a redox sensor to regulate transcription according to changes in nuclear NAD+/NADH ratios. These modifications provide a sampling of some of the ways that corepressor activity can be modulated by posttranslational effects that link corepressor function to cellular physiology.

Context-dependent activity of corepressors

Assuming a cofactor is in the correct subcellular location and is an active state, rather than simply switching a gene off, corepressors can be deployed in a context-dependent manner to mediate distinct types of repression. Recent studies of the Groucho corepressor provide a titillating insight into yet another level of functional complexity affecting repression systems. Molecular analysis of transcriptional repression in the Drosophila blastoderm embryo identified two fundamentally distinct classes of repressor proteins: those that function to locally interfere with or “quench” neighboring activators, so-called short-range repressors, and long-range repressors that can silence distally bound transcription factors [74]. Groucho has been widely recognized as a long-range co-repressor due to its function with the long-range repressors Hairy and Dorsal [75]. Later biochemical and molecular studies on the Groucho repression mechanism, including its spreading on large tracts of target genes, provided further support for its role as a long-range corepressor that oligomerizes and generates a large deactylated segment of chromatin [76, 77]. However, recent evidence indicates that Groucho is also an essential corepressor for the Slp1 and Knirps short-range repressors in the Drosophila embryo [78, 79]. The same component of the cellular corepression machinery can thus evince distinct functions—to what may we attribute this flexibility? Several molecular features of the protein and its complexes provide clues.

Because of differences in interaction surfaces, Groucho may adopt alternative configurations when recruited by different transcription factors, so that oligomerization and spreading is only possible when associated with a long-range repressor (Figure 3A). This hypothesis would suggest that chimeric repressor proteins carrying suitable interaction surfaces would adopt short- or long-range activities, regardless of the rest of the protein's structure. Alternatively, as noted above Groucho is phosphorylated in response to signaling pathways. Differently modified forms of the protein may exhibit different abilities to oligomerize, affecting short- or long-range activity. Or, as with other corepressor proteins, Groucho may assemble into distinct complexes with different abilities to mediate spreading, and these complexes may be separately recruited by short- or long-range repressors (Figure 3B).

Figure 3
Possible mechanisms underlying Groucho-mediated context-dependent repression

In some cases, transcription factors interact with multiple corepressors to elicit context-dependent effects. Different corepressor complexes are recruited to generate developmental stage-specific, or gene- or enhancer- specific effects. The Drosophila Runt repressor requires different corepressors for repression of engrailed at different developmental stages: initially repression is dependent on Tramtrack, and later Groucho, CtBP and Rpd3 are required for the maintenance of repression after blastoderm stage [80]. The Drosophila repressor Brinker protein displays gene specific effects, relying on either CtBP or Groucho complex to repress different target genes [81]. Even distinct enhancers from the same gene can show cofactor specific effects. The even skipped stripe 3/7 enhancer is repressed by Knirps even in the absence of CtBP, while this same repressor requires CtBP to inactivate the stripe 4/6 enhancer during the same period of development. Knirps relies on Groucho for repression of the stripe 3/7 enhancer [79, 82]. Such combinatorial usage of corepressor complex is not restricted to transcription factors in Drosophila but is also observed higher eukaryotes. For example, the Xenopus Tcf3 (XtCF3) interacts with both the Groucho and CtBP corepressors to regulate target gene expression [83].

Repression of Pol I and Pol III transcription

Our discussion has focused in eukaryotes on transcription repression of RNA polymerase II, which is involved in control of protein-coding genes, but the polymerases dedicated to transcription of ribosomal RNA and small RNAs are also subjected to transcription repression [84]. In contrast to the heavy reliance on chromatin modification for repression of Pol II transcription, repression of Pol I and Pol III often appears to involve direct targeting of the core transcriptional machinery. On mammalian rDNA genes, the p53 tumor suppressor binds to the SL1 core promoter complex to inhibit the Pol I recruitment. To interfere with tRNA gene transcription, p53 interacts with TBP subunits of TFIIIB to block assembly of Pol III machinery [85, 86]. The RB corepressor has a slightly different route to block rDNA transcription; it binds to the promoter-proximal UBF factor, and deacetylates UBF to block its interaction with SL1 [87, 88]. RB uses similar mechanism to repress Pol III. RB either interacts with SNAPc, blocking its interaction with TFIIIB, or binds to TFIIIB blocking its interaction with TFIIIC and Pol III [89, 90]. These examples highlight direct protein contacts between corepressors and the core Pol I and Pol III machinery, which is reminiscent of bacterial mechanisms. In light of the very compact nature of the relevant cis-regulatory regions, it is not surprising that contacting a single factor is sufficient to effect repression. Protein coding genes transcribed by Pol II have a more dispersed cis-regulatory structure that may demand alternative means of repression via chromatin modification. Despite these differences, chromatin modifications by corepressors can also regulate Pol I expression. rRNA gene repeats appear to be embedded in a unique chromatin environment that is also susceptible to regulation of chromatin modifying enzymes. The Sir2 histone deacetylase directly modulates chromatin structure and gene expression in yeast rDNA, and the JHDM1B histone demethylase associates with rRNA genes and demethylates H3K4, which leads to the dissociation of UBF from its target [91, 92].

Conclusions

An examination of mechanisms used by DNA-binding transcriptional repressors indicates that a relatively limited set of direct interactions is sufficient to regulate the activity of bacterial and archaeal promoters, which feature compact cis regulatory elements. Eukaryotic genes, whether because of their more complex cis regulatory structure, chromatin packaging, or regulatory demands tend to require the action of corepressors, proteins that directly or indirectly mediate histone modifications. These corepressors appear to work through a limited suite of chromatin modifying agents, but through their diversity and modifications permit fine-tuning of transcriptional output to the ever-changing cellular milieu. Future studies should elucidate the specific contexts in which different repression complexes are assembled on a genome wide level.

Acknowledgments

We thank Lee Kroos and William Henry for their comments on this manuscript. This work is supported by NIH grant GM 56976 to D.N.A.

Footnotes

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