Isolation and functional characterization of TIF-IB, a factor that confers promoter specificity to mouse RNA polymerase I

DNA sequence encoded repression of rRNA gene transcription in chromatin

Eukaryotic genomes are packaged into nucleosomes that occlude DNA from interacting with most DNA-binding proteins. Nucleosome positioning and chromatin organization is critical for gene regulation. We have investigated the mechanism by which nucleosomes are positioned at the promoters of active and silent rRNA genes (rDNA). The reconstitution of nucleosomes on rDNA results in sequence-dependent nucleosome positioning at the rDNA promoter that mimics the chromatin structure of silent rRNA genes in vivo, suggesting that active mechanisms are required to reorganize chromatin structure upon gene activation. Nucleosomes are excluded from positions observed at active rRNA genes, resulting in transcriptional repression on chromatin. We suggest that the repressed state is the default chromatin organization of the rDNA and gene activation requires ATP-dependent chromatin remodelling activities that move the promoter-bound nucleosome about 22-bp upstream. We suggest that nucleosome remodelling precedes promoter-dependent transcriptional activation as specific inhibition of ATP-dependent chromatin remodelling suppresses the initiation of RNA Polymerase I transcription in vitro. Once initiated, RNA Polymerase I is capable of elongating through reconstituted chromatin without apparent displacement of the nucleosomes. The results reveal the functional cooperation of DNA sequence and chromatin remodelling complexes in nucleosome positioning and in establishing the epigenetic active or silent state of rRNA genes.

The PTB interacting protein raver1 regulates alpha-tropomyosin alternative splicing

Regulated switching of the mutually exclusive exons 2 and 3 of alpha-tropomyosin (TM) involves repression of exon 3 in smooth muscle cells. Polypyrimidine tract-binding protein (PTB) is necessary but not sufficient for regulation of TM splicing. Raver1 was identified in two-hybrid screens by its interactions with the cytoskeletal proteins actinin and vinculin, and was also found to interact with PTB. Consistent with these interactions raver1 can be localized in either the nucleus or cytoplasm. Here we show that raver1 is able to promote the smooth muscle-specific alternative splicing of TM by enhancing PTB-mediated repression of exon 3. This activity of raver1 is dependent upon characterized PTB-binding regulatory elements and upon a region of raver1 necessary for interaction with PTB. Heterologous recruitment of raver1, or just its C-terminus, induced very high levels of exon 3 skipping, bypassing the usual need for PTB binding sites downstream of exon 3. This suggests a novel mechanism for PTB-mediated splicing repression involving recruitment of raver1 as a potent splicing co-repressor.

A novel RNA polymerase I transcription initiation factor, TIF-IE, commits rRNA genes by interaction with TIF-IB, not by DNA binding

In the small, free-living amoeba Acanthamoeba castellanii, rRNA transcription requires, in addition to RNA polymerase I, a single DNA-binding factor, transcription initiation factor IB (TIF-IB). TIF-IB is a multimeric protein that contains TATA-binding protein (TBP) and four TBP-associated factors that are specific for polymerase I transcription. TIF-IB is required for accurate and promoter-specific initiation of rRNA transcription, recruiting and positioning the polymerase on the start site by protein-protein interaction. In A. castellanii, partially purified TIF-IB can form a persistent complex with the ribosomal DNA (rDNA) promoter while homogeneous TIF-IB cannot. An additional factor, TIF-IE, is required along with homogeneous TIF-IB for the formation of a stable complex on the rDNA core promoter. We show that TIF-IE by itself, however, does not bind to the rDNA promoter and thus differs in its mechanism from the upstream binding factor and upstream activating factor, which carry out similar complex-stabilizing functions in vertebrates and yeast, respectively. In addition to its presence in impure TIF-IB, TIF-IE is found in highly purified fractions of polymerase I, with which it associates. Renaturation of polypeptides excised from sodium dodecyl sulfate-polyacrylamide gels showed that a 141-kDa polypeptide possesses all the known activities of TIF-IE.

Interactions between HMG boxes

Many proteins consist of subdomains that can fold and function independently. We investigate here the interaction between the two high mobility group (HMG) box subdomains of the nuclear protein rHMG1. An HMG box is a conserved amino acid sequence of approximately 80 amino acids rich in basic, aromatic and proline side chains that is active in binding DNA in a sequence or structure-specific manner. In the case of HMG1, each box can bind structural DNA substrates including four-way junctions (4WJs) and branched or kinked DNA duplexes. Since proteins containing up to six HMG boxes are known, the question arises whether linking subdomains together influences the folding or function of individual boxes. In an effort to understand interactions between individual DNA-binding domains in HMG1, we created new fusion proteins: one is an inversion of the order of the AB di-domain in HMG1 (BA); in the second, we added a third A domain C-terminal to the AB di-domain (ABA). Pairs of boxes, AB or BA, behave similarly and are functionally active. By contrast, the ABA triple subdomain construct is partially unfolded and is less active than individual boxes or di-domains. Thus, long-range inter-domain effects can influence the activity of HMG boxes.

Species-specific interaction of transcription factor p70 with the rDNA core promoter

p70 is a transcription factor that is involved in the initiation of transcription by RNA polymerase I and has been shown to cooperate with the selectivity factor SL1 for binding to the core promoter region of mammalian ribosomal RNA gene (rDNA). To examine a role of the p70-SL1 interaction in promoter recognition, mouse and human proteins were partially purified and analyzed by UV-cross linking. Mouse rDNA core promoter was recognized by any combination of p70 and SL1 prepared from either species. In contrast, human p70 no longer bound to the human core promoter when mouse SL1 was used. Thus, a species-specific interaction between p70 and SL1 may be involved in the promoter selection for rDNA transcription.

The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3

RNA polymerase I (Pol I) is dedicated to transcription of the large ribosomal DNA (rDNA). The mechanism of Pol I recruitment onto rDNA promoters is poorly understood. Here we present evidence that subunit A43 of Pol I interacts with transcription factor Rrn3: conditional mutations in A43 were found to disrupt the transcriptionally competent Pol I-Rrn3 complex, the two proteins formed a stable complex when co-expressed in Escherichia coli, overexpression of Rrn3 suppressed the mutant phenotype, and A43 and Rrn3 mutants showed synthetic lethality. Consistently, immunoelectron microscopy data showed that A43 and Rrn3 co-localize within the Pol I-Rrn3 complex. Rrn3 has several protein partners: a two-hybrid screen identified the C-terminus of subunit Rrn6 of the core factor as a Rrn3 contact, an interaction supported in vitro by affinity chromatography. Our results suggest that Rrn3 plays a central role in Pol I recruitment to rDNA promoters by bridging the enzyme to the core factor. The existence of mammalian orthologues of A43 and Rrn3 suggests evolutionary conservation of the molecular mechanisms underlying rDNA transcription in eukaryotes.

Regulation of RNA polymerase I transcription in yeast and vertebrates

This article focuses on what is currently known about the regulation of transcription by RNA polymerase I (pol I) in eukaryotic organisms at opposite ends of the evolutionary spectrum--a yeast, Saccharomyces cerevisiae, and vertebrates, including mice, frogs, and man. Contemporary studies that have defined the DNA sequence elements are described, as well as the majority of the basal transcription factors essential for pol I transcription. Situations in which pol I transcription is known to be regulated are reviewed and possible regulatory mechanisms are critically discussed. Some aspects of basal pol I transcription machinery appear to have been conserved from fungi to vertebrates, but other aspects have evolved, perhaps to meet the needs of a metazoan organism. Different parts of the pol I transcription machinery are regulatory targets depending on different physiological stimuli. This suggests that multiple signaling pathways may also be involved. The involvement of ribosomal genes and their transcripts in events such as mitosis, cancer, and aging is discussed.

Regulation of mammalian ribosomal gene transcription by RNA polymerase I

All cells, from prokaryotes to vertebrates, synthesize vast amounts of ribosomal RNA to produce the several million new ribosomes per generation that are required to maintain the protein synthetic capacity of the daughter cells. Ribosomal gene (rDNA) transcription is governed by RNA polymerase I (Pol I) assisted by a dedicated set of transcription factors that mediate the specificity of transcription and are the targets of the pleiotrophic pathways the cell uses to adapt rRNA synthesis to cell growth. In the past few years we have begun to understand the specific functions of individual factors involved in rDNA transcription and to elucidate on a molecular level how transcriptional regulation is achieved. This article reviews our present knowledge of the molecular mechanism of rDNA transcriptional regulation.

Dimerization and HMG box domains 1-3 present in Xenopus UBF are sufficient for its role in transcriptional enhancement

Transcription of Xenopus ribosomal genes by RNA polymerase I is directed by a stable transcription complex that forms on the gene promoter. This complex is comprised of the HMG box factor UBF and the TBP-containing complex Rib1. Repeated sequence elements found upstream of the ribosomal gene promoter act as RNA polymerase I-specific trans-criptional enhancers. These enhancers function by increasing the probability of a stable transcription complex forming on the adjacent promoter. UBF is required for enhancer function. This role in enhancement is distinct from that at the promoter and does not involve translocation of UBF from enhancer repeats to the promoter. Here we utilize an in vitro system to demonstrate that a combination of the dimerization domain of UBF and HMG boxes 1-3 are sufficient to specify its role in enhancement. We also demonstrate that the acidic C-terminus of UBF is primarilyresponsible for its observed interaction with Rib1. Thus, we have uncoupled the Rib1 interaction and enhancer functions of UBF and can conclude that direct interaction with Rib1 is not a prerequisite for the enhancer function of UBF.

TTF-I determines the chromatin architecture of the active rDNA promoter

Transcription of ribosomal genes assembled into chromatin requires binding of the transcription termination factor TTF-I to the promoter-proximal terminator T0. To analyze the mechanism of TTF-I-mediated transcriptional activation, we have used mutant templates with altered sequence, polarity and distance of T0 with respect to the transcription start site. Transcription activation by TTF-I is chromatin specific and requires the precise positioning of the terminator relative to the promoter. Whereas termination by TTF-I depends on the correct orientation of a terminator, TTF-I-mediated transcriptional activation is orientation independent. TTF-I can bind to nucleosomal DNA in the absence of enzymatic activities that destabilize nucleosome structure. Chromatin-bound TTF-I synergizes with ATP-dependent cofactors present in extracts of Drosophila embryos and mouse cells to position a nucleosome over the rDNA promoter and the transcription start site. Nucleosome positioning correlates tightly with the activation of rDNA transcription. We suggest that transcriptional activation by TTF-I is a stepwise process involving the creation of a defined promoter architecture and that the positioning of a nucleosome is compatible with, if not a prerequisite for, transcription initiation from rDNA chromatin.

Mammalian RNA polymerase I exists as a holoenzyme with associated basal transcription factors

Transcription initiation of ribosomal RNA genes requires RNA polymerase I (Pol I) and auxiliary factors which either bind directly to the rDNA promoter, e.g. TIF-IB/SL1 and UBF, or are assembled into productive transcription initiation complexes via interaction with Pol I, e.g. TIF-IA, and TIF-IC. Here we show that all components required for specific rDNA transcription initiation are capable of physical interaction with Pol I in the absence of DNA and can be co-immunoprecipitated with antibodies against defined subunits of murine Pol I. Sucrose gradient centrifugation and fractionation on gel filtration columns reveals that approximately 10% of cellular Pol I elutes as a defined complex with an apparent molecular mass of > 2000 kDa. The large Pol I complex contains saturating levels of TIF-IA, TIF-IB and UBF, but limiting amounts of TIF-IC. In support of the existence of a functional complex between Pol I and basal factors, the large complex is transcriptionally active after complementation with TIF-IC. The results suggest that, analogous to class II gene transcription, a pre-assembled complex, the "Pol I holoenzyme", exists that appears to be the initiation-competent form of Pol I.

The Xenopus RNA polymerase I transcription factor, UBF, has a role in transcriptional enhancement distinct from that at the promoter

Repeated sequence elements found upstream of the ribosomal gene promoter in Xenopus function as RNA polymerase I-specific transcriptional enhancers. Here we describe an in vitro system in which these enhancers function in many respects as in vivo. The principal requirement for enhancer function in vitro is the presence of a high concentration of upstream binding factor (UBF). This system is utilized to demonstrate that enhancers function by increasing the probability of a stable transcription complex forming on the adjacent promoter. Species differences in UBF are utilized to demonstrate that enhancers do not act by recruiting UBF to the promoter, rather UBF performs its own distinct role at the enhancers. UBF function in enhancement differs from that at the promoter, as it is flexible with respect to both the species of UBF and the enhancer element employed. Additionally, we identify a potential role for the mammalian UBF splice variant, UBF2, in enhancer function. We demonstrate that the TATA box binding protein (TBP)-containing component of Xenopus RNA polymerase I transcription, Rib1, can interact with an enhancer-UBF complex. This suggests a model in which enhancers act by recruiting Rib1 to the promoter.

The DNA supercoiling architecture induced by the transcription factor xUBF requires three of its five HMG-boxes

The formation of a near complete loop of DNA is a striking property of the architectural HMG-box factor xUBF. Here we show that DNA looping only requires a dimer of Nbox13, a C-terminal truncation mutant of xUBF containing just HMG-boxes 1-3. This segment of xUBF corresponds to that minimally required for activation of polymerase I transcription and is sufficient to generate the major characteristics of the footprint given by intact xUBF. Stepwise reduction in the number of HMG-boxes to less than three significantly diminishes DNA bending and provides an estimate of bend angle for each HMG-box. Together the data indicate that a 350 +/- 16 degree loop in 142 +/- 30 bp of DNA can be induced by binding of the six HMG-boxes in an Nbox13 dimer and that DNA looping is probably achieved by six in-phase bends. The positioning of each HMG-box on the DNA does not predominantly involve DNA sequence recognition and is thus an intrinsic property of xUBF.

Overexpression of the transcription factor UBF1 is sufficient to increase ribosomal DNA transcription in neonatal cardiomyocytes: implications for cardiac hypertrophy

The accelerated protein accumulation characteristic of cardiomyocyte hypertrophy results from increased cellular protein synthetic capacity (elevated ribosome content). The rate limiting step in ribosome accumulation is transcription of the rRNA genes. During neonatal cardiomyocyte hypertrophy induced by norepinephrine or spontaneous contraction, changes in the expression of a ribosomal DNA transcription factor, UBF, correlated with increased rates of ribosome biogenesis. We hypothesized that elevated expression of UBF was part of the mechanism by which these hypertrophic stimuli effected increases in the rate of transcription from the rDNA promoter. In this study, we have examined directly the effect of overexpressing UBF on rDNA transcription in neonatal cardiomyocytes in culture. In control experiments, a novel reporter construct for rDNA transcription (pSMECAT) showed similar increases in activity in response to hypertrophic stimuli (10(-4) M phenylephrine, 10(-7) M endothelin, and spontaneous contraction) as did the endogenous rRNA genes. When contraction-arrested cardiomyocytes were cotransfected with pSMECAT and increasing amounts of a UBF1 expression vector; a dose-dependent (3-5 fold) increase in rDNA transcription was observed. Western blot analysis confirmed that the overexpressed, FLAG-tagged UBF accumulated in the cardiomyocyte nuclei. The observation that overexpression of UBF1 is sufficient to increase rDNA transcription in neonatal cardiomyocytes provides evidence in support of the hypothesis that the regulation of UBF is a key component of the increased ribosome biogenesis and protein accumulation associated with cardiomyocyte hypertrophy.

HMG box 4 is the principal determinant of species specificity in the RNA polymerase I transcription factor UBF

Transcription of ribosomal genes requires, in addition to RNA polymerase I, the trans-acting factors UBF and Rib1 in Xenopus or SL1 in humans. RNA polymerase I transcription is remarkably species specific. Between closely related species SL1 is the sole determinant of this specificity. Between more distantly related species, however, UBF is also a component of this species specificity. Xenopus UBF cannot function in human RNA polymerase I transcription and human UBF cannot function in Xenopus RNA polymerase I transcription. Xenopus and human UBFs are remarkably similar at the amino acid sequence level, both containing multiple HMG box DNA binding motifs. The only major difference between xUBF and hUBF is the lack of a HMG box 4 equivalent in xUBF. Utilizing a series of hybrid UBF molecules we have identified HMG box 4 as the principal determinant of species specificity. Addition of human HMG box 4 to xUBF converts it to a form that functions in human RNA polymerase I transcription. Deletion of HMG box 4 from hUBF converts it to a form that functions in Xenopus RNA polymerase I transcription. Furthermore, mutations within Xenopus UBF demonstrate that UBF requires a precise arrangement and number of HMG boxes to function in RNA polymerase I transcription.

Characterization of the components of reconstituted Saccharomyces cerevisiae RNA polymerase I transcription complexes

We have reconstituted specific RNA polymerase I transcription from three partially purified chromatographic fractions (termed A, B, and C). Here, we present the chromatographic scheme and the initial biochemical characterization of these fractions. The A fraction contained the RNA polymerase I transcription factor(s), which was necessary and sufficient to form stable preinitiation complexes at the promoter. Of the three fractions, only fraction A contained a significant amount of the TATA binding factor. The B fraction contributed RNA polymerase I, and it contained an essential RNA polymerase I transcription factor that was specifically inactivated in response to a significant decrease in growth rate. The function of the C fraction remains unclear. This reconstituted transcription system provides a starting point for the biochemical dissection of the yeast RNA polymerase I transcription complex, thus allowing in vitro experiments designed to elucidate the molecular mechanisms controlling rRNA synthesis.

The affinity technology in downstream processing

The quality criteria imposed on several biochemicals are stringent, thus, high-separation purification technology is important to downstream processing. Affinity-based purification technologies are regarded as the finest available, and each one differs in its purifying ability, economy, processing speed and capacity. The most widely used affinity technology is classical affinity chromatography, however, other chromatography-based approaches have also been developed, for example, perfusion affinity chromatography, hyperdiffusion affinity chromatography, high-performance affinity chromatography, centrifugal affinity chromatography, affinity repulsion chromatography, heterobifunctional ligand affinity chromatography and the various chromatographic applications of 'affinity tails'. On the other hand, non-chromatographic affinity technologies aim at high throughput and seek to circumvent problems associated with diffusion limitations experienced with most chromatographic packings. Continuous affinity recycle extraction, aqueous two-phase affinity partitioning, membrane affinity filtration, affinity cross-flow ultrafiltration, reversible soluble affinity polymer separation and affinity precipitation are all non-chromatographic technologies. Several types of affinity ligands are used to different extents; antibodies and their fragments, receptors and their binding substances, avidin/biotin systems, textile and biomimetic dyes, (oligo)peptides, antisense peptides, chelated metal cations, lectins and phenylboronates, protein A and G, calmodulin, DNA, sequence-specific DNA, (oligo)nucleotides and heparin. Likewise, there are several support types developed and used; natural, synthetic, inorganic and composite materials.

Factor C*, the specific initiation component of the mouse RNA polymerase I holoenzyme, is inactivated early in the transcription process

Factor C* is the component of the RNA polymerase I holoenzyme (factor C) that allows specific transcriptional initiation on a factor D (SL1)- and UBF-activated rRNA gene promoter. The in vitro transcriptional capacity of a preincubated rDNA promoter complex becomes exhausted very rapidly upon initiation of transcription. This is due to the rapid depletion of C* activity. In contrast, C* activity is not unstable in the absence of transcription, even in the presence of nucleoside triphosphates (NTPs). By using 3'dNTPs to specifically halt elongation, C* is seen to remain active through transcription complex assembly, initiation, and the first approximately 37 nucleotides of elongation, but it is inactivated before synthesis proceeds beyond approximately 40 nucleotides. When elongation is halted before this critical distance, the C* remains active and on that template complex, greatly extending the kinetics of transcription and generating manyfold more transcripts than would have been synthesized if elongation had proceeded past the critical distance where C* is inactivated. In complementary in vivo analysis under conditions where C* activity is not replenished, C* activity becomes depleted from cells, but this also occurs only when there is ongoing rDNA transcription. Thus, both in vitro and in vivo, the specific initiation-conferring component of the RNA polymerase I holoenzyme is used stoichiometrically in the transcription process.

Factor C*, the specific initiation component of the mouse RNA polymerase I holoenzyme, is inactivated early in the transcription process

Factor C* is the component of the RNA polymerase I holoenzyme (factor C) that allows specific transcriptional initiation on a factor D (SL1)- and UBF-activated rRNA gene promoter. The in vitro transcriptional capacity of a preincubated rDNA promoter complex becomes exhausted very rapidly upon initiation of transcription. This is due to the rapid depletion of C* activity. In contrast, C* activity is not unstable in the absence of transcription, even in the presence of nucleoside triphosphates (NTPs). By using 3'dNTPs to specifically halt elongation, C* is seen to remain active through transcription complex assembly, initiation, and the first approximately 37 nucleotides of elongation, but it is inactivated before synthesis proceeds beyond approximately 40 nucleotides. When elongation is halted before this critical distance, the C* remains active and on that template complex, greatly extending the kinetics of transcription and generating manyfold more transcripts than would have been synthesized if elongation had proceeded past the critical distance where C* is inactivated. In complementary in vivo analysis under conditions where C* activity is not replenished, C* activity becomes depleted from cells, but this also occurs only when there is ongoing rDNA transcription. Thus, both in vitro and in vivo, the specific initiation-conferring component of the RNA polymerase I holoenzyme is used stoichiometrically in the transcription process.

A TBP-containing multiprotein complex (TIF-IB) mediates transcription specificity of murine RNA polymerase I

TIF-IB is a transcription factor which interacts with the mouse ribosomal gene promoter and nucleates the formation of an initiation complex containing RNA polymerase I (Pol I). We have purified this factor to near homogeneity and demonstrate that TIF-IB is a large complex (< 200 kDa) which contains several polypeptides. One of the subunits present in this protein complex is the TATA-binding protein (TBP) as revealed by copurification of TIF-IB activity and TBP over different chromatographic steps including immunoaffinity purification. In addition to TBP, three tightly associated proteins (TAFs-I) with apparent molecular weights of 95, 68, and 48 kDa are contained in this multimeric complex. This subunit composition is similar--but not identical--to the analogous human factor SL1. Depletion of TBP from TIF-IB-containing fractions by immunoprecipitation eliminates TIF-IB activity. Neither TBP alone nor fractions containing other TBP complexes are capable of substituting for TIF-IB activity. Therefore, TIF-IB is a unique complex with Pol I-specific TAFs distinct from other TBP-containing complexes. The identification of TBP as an integral part of the murine rDNA promoter-specific transcription initiation factor extends the previously noted similarity of transcriptional initiation by the three nuclear RNA polymerases and underscores the importance of TAFs in determining promoter specificity.

The nucleolar transcription activator UBF relieves Ku antigen-mediated repression of mouse ribosomal gene transcription

Previously we have shown that the RNA polymerase I (Pol I)-specific transcription factor UBF stimulates transcription by both facilitating transcription complex formation and by relieving repression exerted by a negative-acting factor which competes for binding of the murine factor TIF-IB to the ribosomal gene promoter (1). We have purified and functionally characterized this repressor protein from Ehrlich ascites cells. The final preparation contained two polypeptides with molecular masses of 75 and 90 kDa, respectively. Both polypeptides interact with the rDNA promoter as revealed by UV-crosslinking experiments. The specificity of binding to the ribosomal gene promoter was demonstrated in an electrophoretic mobility shift assay and by DNase footprinting. The biochemical properties of this negative-acting factor closely resemble those of the Ku antigen, a human nuclear DNA-binding heterodimer which is the target of autoantibodies in several autoimmune diseases. Anti-Ku antibodies precipitate the repressor activity and overcome transcription inhibition. The data demonstrate that regulation of Pol I gene transcription may involve an antirepression mechanism as already documented for Pol II genes and suggest that Ku protein may be causally involved in repressor-mediated down regulation of rRNA synthesis.

Preliminary characterisation and partial purification of ribosomal gene promoter-binding proteins from Trypanosoma brucei

DNA fragments including the promoter region of the major ribosomal RNA gene of Trypanosoma brucei (r-promoter) were identified and subcloned using a synthetic oligonucleotide probe corresponding to the putative core promoter. These fragments were used in mobility shift assays with proteins extracted from T. brucei nuclei, and demonstrated the presence in 0.15 M NaCl extracts of protein(s) with specific binding affinities for the r-promoter region. Binding was stable in the presence of a 100-fold excess of competitor DNA, and occurred at the relatively low salt concentrations (< 50 mM NaCl) characteristic of many enzyme activity optima in this organism. A control DNA fragment not including the r-promoter region was not retarded in the mobility shift assays, and the r-promoter-binding activity had a molecular weight of about 140,000. Nuclear extracts from T. brucei contained large amounts of DNase activity, and the promoter-binding proteins were partially purified from the crude extract using ammonium sulphate precipitation, sephacryl S-200 and Heparin-sepharose chromatography.

Presence of an inhibitor of RNA polymerase I mediated transcription in extracts from growth arrested mouse cells

Extracts obtained from mouse cells growth arrested at stationary phase or under serum starvation exhibit no specific rDNA transcription activity. Experiments with mixed transcriptionally active and inactive whole cell extracts (WCE) obtained from rapidly dividing or growth arrested cells, respectively, demonstrate that rRNA synthesis in vitro can be suppressed by a polymerase I transcription inhibitory activity (PIN), present in inactive extracts. This inhibition effect is not related to increased nuclease activity and affects neither the non-specific Pol I transcription, nor a polymerase II promoter. A comparison of WCE isolated under different growth conditions indicates that PIN changes according to the physiological state of the cell. It reaches a maximal level soon after serum depletion and disappears rapidly when cells are allowed to recover in serum-rich medium. PIN can be clearly demonstrated in WCE but not in nuclear or cytoplasmic extracts and can be also obtained by an additional high salt extraction of nuclei. Furthermore, gel retardation and transcription-in-pellet assays demonstrate that rDNA promoter binding and preinitiation complex stability are similar in active and inactive WCE. This indicates that some later stage(s) of rDNA transcription, rather than the preinitiation complex formation, are attenuated by inactive extracts. Analysis of partially fractionated extracts suggests that PIN is not associated with but can be separated from polymerase I.

Dual role of the nucleolar transcription factor UBF: trans-activator and antirepressor

In a reconstituted system consisting of partially purified RNA polymerase I (pol I) and the initiation factors TIF-IA, TIF-IB, and TIF-IC, the nucleolar factor UBF (upstream binding factor) stimulates transcription from the rRNA-encoding DNA (rDNA) promoter at least 50-fold. This activation is not observed at high template concentrations or in the presence of highly purified pol I. Template commitment experiments suggest that UBF activates transcription by relieving inhibition exerted by a negative-acting factor(s) in the polymerase fraction that competes for TIF-IB binding to the rDNA promoter and prevents the formation of preinitiation complexes. Using purified histone H1 bound to DNA as a model for the repressed state of the rDNA promoter, we show that UBF counteracts H1-mediated repression of pol I transcription. The implications of these findings are discussed with respect to the protein-protein and protein-DNA interactions at the rDNA promoter and the possible involvement of UBF in control of ribosomal gene transcription.

Complex formation of nuclear proteins with the RNA polymerase I promoter and repeated elements in the external transcribed spacer of Cucumis sativus ribosomal DNA

Complex repetitive structures are located downstream of the transcription initiation site in the intergenic spacer (IGS) of the rRNA genes in Cucumis sativus (cucumber). In order to show that these repetitive elements of the 5'external transcribed spacer (ETS) are probably involved in transcriptional regulation as protein binding sites DNA-protein binding assays were carried out. The same proteins that recognize two binding sites in the promoter region analysed (upstream binding element between -164 and -105, and core promoter between -41 and +16) show binding affinity to the complex structures of the 5'external transcribed spacer. These proteins also seem to interact with the single strands of the respective DNA regions suggesting an effect on transcriptional regulation while the DNA is transcribed and, therefore, is single-stranded. Three proteins were isolated by affinity column chromatography; these proteins turned out to be much smaller (16, 22, and 24 kDa, respectively) than promoter and enhancer binding proteins in animal systems. Additionally, a 70-kDa protein could be characterized cooperating with a small segment of the repeated elements but not with the promoter.

Variants of the Xenopus laevis ribosomal transcription factor xUBF are developmentally regulated by differential splicing

XUBF is a Xenopus ribosomal transcription factor of the HMG-box family which contains five tandemly disposed homologies to the HMG1 & 2 DNA binding domains. XUBF has been isolated as a protein doublet and two cDNAs encoding the two molecular weight variants have been characterised. The major two forms of xUBF identified differ by the presence or absence of a 22 amino acid segment lying between HMG-boxes 3 and 4. Here we show that the mRNAs for these two forms of xUBF are regulated during development and differentiation over a range of nearly 20 fold. By isolating two of the xUBF genes, it was possible to show that both encoded the variable 22 amino acid segment in exon 12. Oocyte splicing assays and the sequencing of PCR-generated cDNA fragments, demonstrated that the transcripts from one of these genes were differentially spliced in a developmentally regulated manner. Transcripts from the second gene were found to be predominantly or exclusively spliced to produce the lower molecular weight form of xUBF. Expression of a high molecular weight form from yet a third gene was also detected. Although the intron-exon structures of the Xenopus and mouse UBF genes were found to be essentially identical, the differential splicing of exon 8 found in mammals, was not detected in Xenopus.

Identification of cis-regulatory sequences in ascidian ribosomal DNA using a rapid filter-binding assay

Using 32P-labelled random primed ribosomal DNA (rDNA) from the ascidian, Herdmania momus, multiple and large-scale filter-binding assays were performed to identify cis-regulatory sequences interacting with H. momus oocyte germinal vesicle protein. A vacublot apparatus was used to isolate DNA-protein complexes, providing a means of filtering multiple binding reactions simultaneously and for isolating sufficient amounts of bound DNA for further investigations. DNA bound to the filter was used to identify unknown cis-elements in the rDNA by Southern-blot analysis. The trapped rDNA hybridized specifically to the intergenic spacer, a region which contains cis-regulatory sequences that interact with rDNA transcription factors in several other species. Gel shift analysis of intergenic spacer fragments and native Southwestern blots confirmed that cis-elements were localized in the rDNA intergenic spacer. In principle, this method allows for the rapid identification of cis-regulatory sequences within any large, cloned DNA fragment which interact with nuclear extract.

Identification of a sequence-specific protein binding the 5'-transcribed spacer of rat ribosomal genes

A novel 85-kD protein factor which interacts specifically with the 5'-transcribed spacer of rat ribosomal genes was identified using the gel mobility shift, DNase I protection and UV-crosslinking techniques. The binding site of the factor is located inside the 36 bp Alul-HindIII fragment of transcribed spacer, most probably in the region +94 to +115 with respect to the transcription initiation site. Factors giving very similar gel mobility shift patterns were also found in mouse and human cell extracts. Sequences resembling the binding site of this factor were revealed in corresponding regions of mouse and human ribosomal genes. The biological function of FTS remains to be elucidated.

Isolation of multiple protein factors involved in ribosomal DNA transcription

Studies were made of the molecular mechanisms which regulate ribosomal gene transcription in response to changes in the growth rate of cells. Extracts prepared from exponentially growing Ehrlich ascites cells faithfully and efficiently transcribe cloned mouse rDNA, whereas extracts from growth-arrested cells are virtually inactive. In an attempt to identify and characterize functionally the proteins that mediate the accuracy and the control of transcription initiation, a fractionation procedure was developed which allows the purification of RNA polymerase I and four accessory factors that are required for transcription initiation at the ribosomal gene promoter. Starting from about 300 ml of cell extract, each of the individual factors and the polymerase was purified on at least four different chromatographic columns, including ion-exchange chromatography on DEAE-Sepharose, heparin-Ultrogel, Mono Q and Mono S, gel filtration and specific affinity chromatography. The resulting protein fractions are functionally active, as shown by reconstitution of specific rDNA transcription in the presence of purified polymerase and the additional factors.

xUBF contains a novel dimerization domain essential for RNA polymerase I transcription

Xenopus laevis upstream binding factor (xUBF) is an RNA polymerase I transcription factor that is required for formation of the stable initiation complex. The 701-amino-acid protein contains three regions of homology to the chromosomal protein HMG1 (the HMG boxes), which act in comparative independence to cause DNA binding. DNA binding is augmented by a 102-residue amino-terminal domain that causes xUBF to form dimers. The dimerization domain is bipartite in structure, consisting of two regions with the potential to form amphipathic helices, separated by a gap of at least 22 amino acids. The carboxyl half of xUBF is relatively dispensable for transcription (including an 87-residue acidic tail). However, either altering the number of HMG boxes or interfering with dimerization eliminates transcription. The gap region of the dimerization domain is dispensable for dimerization but is absolutely required for transcription. This suggests that the gap region has a critical function in transcription distinct from any effect on dimerization or DNA binding.

The yeast RNA polymerase I promoter: ribosomal DNA sequences involved in transcription initiation and complex formation in vitro

Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie between -38 and -26. The 3'-deletion extending to -2 and -5 still allowed some transcription, suggesting that the positioning of Pol I is directed by upstream sequences. The results of in vitro analysis of linker scanning mutants (LSMs) combined with the deletion analysis showed that the promoter consists of three domains: two essential core domains (I: -28 to +8 and II: -76 to -51) and a transcription modulating upstream domain (III: -146 to -91). These results are in general agreement with those obtained in vivo (1). Using a template competition assay we also analyzed these mutant promoters for their ability to form a stable preinitiation complex. We found that the ability of 5'-deletion mutants to sequester an essential factor(s) correlates with their transcriptional activity. In contrast, several 3'-deletions and some LSMs in domain I and II decrease transcription activity greatly without significantly decreasing competition ability. The results indicate that the stimulatory function of domain III is achieved through its interaction with an essential transcription factor(s), although the other domains also participate in this interaction, perhaps directly or through another protein factor.

Cloning and structural analysis of cDNA and the gene for mouse transcription factor UBF

The gene and protein structure of the mouse UBF (mUBF), a transcription factor for mouse ribosomal RNA gene, have been determined by cDNA and genomic clones. The unique mUBF gene consists of 21 exons spanning over 13 kb. Two mRNAs coding for mUBF1 and mUBF2 having 765 a.a. and 728 a.a., respectively, are produced by an alternative splicing of exon 8. It specifies 37 amino acids constituting a part of the regions homologous to high mobility group proteins (HMG box 2). A human UBF (hUBF) cDNA obtained by polymerase chain reaction also indicates the presence of two kinds of mRNAs, the shorter form lacking the same region as mUBF2. Comparison of the cDNAs from hUBF and mUBF revealed an unusual conservation of nucleotide sequence in the 3'-terminal non-coding region. We examined the relative amounts of expression of mUBF1 and mUBF2. The eight tissues studied contained both molecular species, although mUBF2 was the predominant form of UBF. The mRNA of mUBF1 was expressed one half of the mUBF2 in quiescent mouse fibroblasts but reached the same amount in growing state.

Trans-acting factors involved in species-specificity and control of mouse ribosomal gene transcription

Faithful and efficient transcription initiation at the mouse ribosomal gene promoter requires besides RNA polymerase I (pol I) four polypeptide trans-acting factors, termed TIF-IA, TIF-IB, TIF-IC, and mUBF. We have partially purified these proteins from cultured Ehrlich ascites cells and show that in the presence of TIF-IA and TIF-IB, pol I directs very low amounts of specific transcripts. Neither TIF-IC nor mUBF on their own significantly stimulate the efficiency of template utilization. However, both factors together strongly activate transcription. Interestingly, factor TIF-IB - the murine homologue of human SL1 - fails to program a human extract to transcribe the murine template, but requires its homologous RNA polymerase I. This finding implicates that not only some rDNA transcription factors but also pol I exhibits species-specific differences. The growth-related factor TIF-IA, on the other hand, stimulates both mouse and human rDNA transcription. This regulatory factor whose amount or activity fluctuates according to the proliferation rate of the cells, is functionally inactivated by antibodies against cdc2 protein kinase. This result together with the observation that transcription is stimulated by ATP-gamma S, an ATP analogue which is a substrate for protein kinases but not for protein phosphatases, strongly suggests that post-translational protein modification is involved in rDNA transcription regulation.

Initiation and regulation mechanisms of ribosomal RNA transcription in the eukaryote Acanthamoeba castellanii

Acanthamoeba rRNA transcription involves the binding of a transcription initiation factor (TIF) to the core promoter of rDNA to form the preinitiation complex. This complex is formed in the absence of RNA polymerase I, and persists for multiple rounds of initiation. Polymerase I next binds to form the initiation complex. This binding is DNA sequence-independent, and is directed by protein-protein contacts with TIF. DNA melting occurs in a separate step. In contrast to most prokaryotic transcription, melting occurs only following nucleotide addition and beta-gamma hydrolysis of ATP is not required as for polymerase II. Growth-dependent regulation of rRNA transcription is accomplished by modification of RNA polymerase I. The inactive form of polymerase (PolE) is unable to bind to the promoter and has altered heat stability. PolE is still active in elongation; thus, the modification affects the polymerase site involved in TIF contact. Modification of a polymerases I and III common subunit has been detected leading to the suggestion that transcription of stable RNAs of the ribosome might be co-regulated by this mechanism.

The RNA polymerase I transcription factor xUBF contains 5 tandemly repeated HMG homology boxes

The RNA polymerase I transcription factor UBF has been identified in human, mouse, rat and Xenopus and the primary structure of the human protein has been determined. Human UBF was shown to contain four tandem homologies to the folding domains of the HMG1 and 2 proteins and hence to belong to a previously unrecognised family of 'HMG-box' transcription factors. Here, cDNA clones encoding the Xenopus laevis UBF (xUBF) have been isolated and sequenced. Northern and Southern blots revealed that in tissue culture cells, xUBF is coded on a single major mRNA size species by a small number of genes. The deduced primary structure of xUBF is highly homologous with the human protein except for a central deletion which removes most of one HMG-box. This explains the major size difference between the X. laevis and human proteins and may well explain their different transcriptional specificities. It is shown that xUBF contains 5 tandemly repeated HMG-boxes and that by analogy the human protein contains 6.

Structure of the core promoter of human and mouse ribosomal RNA gene. Asymmetry of species-specific transcription

In vitro transcription of the ribosomal RNA gene (rDNA) shows a remarkable species specificity such that human and mouse rDNA cannot use heterologous extracts of each other. The region that is responsible for this specificity has been studied using human-mouse chimeric genes and characteristic structures of both core promoters are presented. When the mouse sequence is substituted by the corresponding human sequence from upstream, the promoter activity in the mouse extract begins to decline at nucleotide -32 or -30, decreasing gradually and is lost completely at -19. A similar gradual decrease was noted for the 3' side substitution, which started at nucleotide -14 and was completed when up to the nucleotide -22 mouse position was replaced by the corresponding sequence from human. Thus, in the mouse rDNA core promoter, the sequence that is involved in species specificity resides only in a stretch encompassing the non-conserved region between the distal conserved sequence (DCS) and the proximal conserved sequence (PCS), plus two altered nucleotides in the PCS. When human rDNA is transcribed with human cell extract, the mouse sequence cannot substitute for the human sequence within the region from nucleotide -43 to +17 without affecting promoter activity significantly. This asymmetry of species specificity is due to the presence of nucleotides -43, +1 and +17, which are sensitive to change in only the human core promoter. The difference in the 5' border is ascribed to the species specificity of a transcription factor TFID, which recognizes this region. But the large difference of the 3' border is apparently due to another factor, possibly RNA polymerase I itself, because this region is not recognized by TFID in either human or mouse. Mammalian rDNA core promoter appears to consist of a tandem mosaic in which three evolutionarily conserved sequences alternate with non-conserved sequences having certain functionally important nucleotides. Not only non-conserved sequences and non-conserved nucleotides in conserved sequences, but also the spacings between the three conserved regions, play a crucial role in species specificity.

News from the nucleolus: rRNA gene expression

Although the typical, actively growing eukaryotic cell contains over 10,000 different transcripts, half of its RNA synthetic capacity is devoted to the production of a single kind of RNA. This is the pre-ribosomal RNA, which is synthesized in a special compartment of the nucleus, the nucleolus, and is the exclusive product of transcription by RNA polymerase I. In vivo and in vitro approaches have revealed the major features of rRNA gene transcription and of the subsequent processing of the primary transcript.

rRNA synthesis in the nucleolus

The past year has seen advances in our understanding of three broad areas that concern ribosomal RNA production. It is becoming apparent that for a large number of eukaryotes, sequence elements that regulate ribosomal RNA transcription are arranged in a similar pattern. This conservation of arrangement implies conservation of regulatory mechanisms. Better understanding of the ribosomal gene transcription factors has emerged, and one factor has been purified and cloned. In vitro systems for processing ribosomal RNA are beginning to be developed, allowing the first direct proof that a small nuclear ribonucleoprotein (U3) is involved in ribosomal RNA processing.

A 140-base-pair repetitive sequence element in the mouse rRNA gene spacer enhances transcription by RNA polymerase I in a cell-free system

We show that the repetitive 140-base-pair (bp) elements present in the spacer of mouse rRNA genes function as enhancers for RNA polymerase I. Attachment of these elements to the rDNA promoter stimulates rRNA synthesis both in vivo and in vitro. The cis-activating effect of the spacer repeats is orientation-independent and increases with increasing numbers of the 140-bp elements. Competition experiments demonstrate that the spacer repeats bind one or more of the transcription factors interaction with the rDNA promoter. Both the 140-bp elements and the core promoter act cooperatively and thus are functionally linked. The 60/81-bp enhancer repeats from Xenopus laevis rDNA compete for a murine transcription factor(s) and stimulate transcription often fused to the mouse rDNA promoter. The results indicate that despite the marked species specificity of rDNA transcription initiation, common factors may interact with both the rDNA promoter and the enhancer.