Transcription efficiency of human polymerase III genes in vitro does not depend on the RNP-forming autoantigen La.

Transcription of class III genes is conducted by multi-protein complexes consisting of polymerase III itself and several transcription factors. We established a reconstituted in vitro transcription system from which the autoantigen La was removed by immunodepletion. This system showed no RNP formation, but was still fully active in transcription. Supplementing such La-free transcription reactions with recombinant La restored the formation of La complexes with the newly synthesised RNA, but did not lead to enhanced transcription efficiency. Furthermore, we developed a technique for the generation and isolation of transcription complexes, assembled from purified transcription factors and isolated by glycerol centrifugation. These complexes were fully competent to re-initiate RNA synthesis but they were not associated with La and their transcription rate could not be stimulated by addition of recombinant La. Therefore, we conclude that La does not act as a human polymerase III transcription factor.

hTFIIIB-beta stably binds to pol II promoters and recruits RNA polymerase III in a hTFIIIC1 dependent way.

It has been shown that under specific conditions, transcription of protein coding genes can be efficiently initiated by RNA polymerase (pol) III in vitro. We examined the formation and composition of such pol III transcription complexes on the duck histone H5 and alphaA-globin promoters and found that the essential step for the formation of pol III transcription complexes on these pol II promoters was the stable binding of transcription factor (TF) IIIB-beta. For this process, the intact TFIIIB-beta complex, consisting of TBP and associated factors (TAFs) was needed and the prior association of pol III assembly factors was not necessary. We demonstrate for the first time that hTFIIIB-beta alone is able to bind to pol II promoter DNA. This resulted in a very stable complex which was resistant to high concentrations of heparin. Although immunodepletion revealed that TBP is essentially required for complex formation, other components of hTFIIIB-beta must also be involved, since TBP itself is unable to form heparin-resistant complexes and does not mediate pol III commitment per se. pol III is recruited to these pol II promoters in a strictly TFIIIC1 dependent way. After binding of TFIIIB-beta, the addition of TFIIIC1 and pol III were sufficient to yield productive pol III transcription complexes, which utilized the correct pol II initiation site. From these findings, we postulate that TFIIIC1 is involved in the recruitment of pol III and may thus form a bridge between TFIIIB-beta and the enzyme. This finding provides the first evidence for functional contacts between TFIIIC1 and pol III, which could be of general importance for the assembly of pol III transcription complexes.

The activity binding to the termination region of several pol III genes represents a separate entity and is distinct from a novel component enhancing U6 snRNA transcription.

Human TFIIIC1, a basal transcription factor essentially required for expression of all pol III genes, exerts its function without primarily binding to DNA. We report here the purification of a termination site binding activity (TBA) which was initially described to be contained in fractions designated as TFIIIC0. TBA specifically and strongly binds to the termination region of pol III genes with internal promoters and can be completely separated from TFIIIC1and a TFIIIC1related activity (TFIIIC1-like), proving that DNA-binding of TBA is independent of these latter activites. Although TBA is not essentially required for, it strongly stimulates pol III transcription from intragenic promoters. This stimulation strictly depends on the presence of TFIIIC1and is not observed in conjunction with TFIIIC1-like. We further present the identification of a novel activity, TFIIIU, which is also contained in crude fractions of TFIIIC0. TFIIIU can be separated from TBA by further purification and is essentially involved in transcription of the mammalian U6 gene. TFIIIU cannot be substituted for by any of the established U6 transcription factors and thus represents a novel U6 transcription factor.

A nucleosome positioned in the distal promoter region activates transcription of the human U6 gene.

To investigate the consequences of chromatin reconstitution for transcription of the human U6 gene, we assembled nucleosomes on both plasmids and linear DNA fragments containing the U6 gene. Initial experiments with DNA fragments revealed that U6 sequences located between the distal sequence element (DSE) and the proximal sequence element (PSE) lead to the positioning of a nucleosome partially encompassing these promoter elements. Furthermore, indirect end-labelling analyses of the reconstituted U6 wild-type plasmids showed strong micrococcal nuclease cuts near the DSE and PSE, indicating that a nucleosome is located between these elements. To investigate the influence that nucleosomes exert on U6 transcription, we used two different experimental approaches for chromatin reconstitution, both of which resulted in the observation that transcription of the U6 wild-type gene was enhanced after chromatin assembly. To ensure that the facilitated transcription of the nucleosomal templates is in fact due to a positioned nucleosome, we constructed mutants of the U6 gene in which the sequences between the DSE and PSE were progressively deleted. In contrast to what was observed with the wild-type genes, transcription of these deletion mutants was significantly inhibited when they were packaged into nucleosomes.

Functional interchangeability of TFIIIB components from yeast and human cells in vitro.

In eukaryotes, TFIIIB is required for proper initiation by RNA polymerase III. In the yeast Saccharomyces cerevisiae a single form of TFIIIB (gammaTFIIIB) is sufficient for transcription of all pol III genes, whereas in extracts derived from human cells two different hTFIIIB complexes exist which we have previously designated as hTFIIIB-alpha and hTFIIIB-beta. Human TFIIIB-alpha is a TBP-free entity and must be complemented by TBP for transcription of pol III genes driven by gene external promoters, whereas hTFIIIB-beta is a TBP-TAF complex which governs transcription from internal pol III promoters. We show that hTFIIIB-beta cannot be replaced by yeast TFIIIB for transcription of tRNA genes, but that the B" component of gammaTFIIIB can substitute for hTFIIIB-alpha activity in transcription of the human U6 gene. Moreover, hTFIIIB-alpha can be chromatographically divided into activities which are functionally related to gammaTFIIIE and recombinant yB"90, suggesting that hTFIIIB-alpha is a human homolog of yeast TFIIIB". In addition, we show that yeast TBP can only be exchanged against human TBP for in vitro transcription of the human and yeast U6 gene but virtually not for that of the yeast tRNA4Sup gene. This deficiency can be counteracted by a mutant of human TBP (R231K) which is able to replace yeast TBP for transcription of yeast tRNA genes in vitro.

Human transcription factors IIIC2 , IIIC1 and a novel component IIIC0 fulfil different aspects of DNA binding to various pol III genes.

Human transcription factor IIIC2 interacts with the TFIIIA-5S DNA complex and forms a ternary TFIIIA/IIIC2-5S DNA complex. Formation of this complex does not preclude simultaneous binding of TFIIIC2to the B-box sequence of a second template. This suggests that the domain(s) or subunit(s) required for indirect recognition of the 5S promoter by TFIIIC2 are different from those necessary for direct binding of TFIIIC2 to B-box-containing pol III promoters. Whereas TFIIIC2 is only required for transcription of the 'classical' pol III genes, TFIIIC1 is generally required for transcription of all pol III genes, including that of the U6 gene. The activity of TFIIIC1 strongly enhances specific binding of basal pol III factors TFIIIA, TFIIIC2 and the PSE binding protein (PBP) to their cognate promoter elements and it acts independently of the corresponding termination regions. Moreover, we characterize an activity, TFIIIC0, purified from phosphocellulose fraction C, which shows strong DNase I protection of the termination region of several pol III genes and which is functionally and chromatographically distinct from TFIIIC1 and TFIIIC2.

The human S3a ribosomal protein: sequence, location and cell-free transcription of the functional gene.

The intron-containing gene encoding human ribosomal protein S3a (hRPS3a) was isolated by utilizing a PCR-based strategy to detect a gene-specific intron which was subsequently used as a probe for cloning of the entire gene. The hRPS3a gene is composed of six exons and five introns spanning 5013 bp. As described for other hRP-encoding genes, the promoter lacks a canonical TATA sequence and a defined CAAT box. Primer extension experiments, as well as cell-free transcription, revealed that a cytosine functions as the major transcription start point in a polypyrimidine region, but a guanosine at position -1 was also able to initiate transcription. Hybridization analysis of chromosomal DNA from a panel of human-rodent somatic cell hybrids revealed that hRPS3a is encoded by a single locus in the human genome, present on chromosome 4.

Physical separation of two different forms of human TFIIIB active in the transcription of the U6 or the VAI gene in vitro.

Human transcription factor hTFIIIB is necessary to initiate transcription correctly from all RNA polymerase III (pol III) genes which are governed by structurally different promoters, and it is unclear whether hTFIIIB complexes, required for intragenic or 5'-located pol III promoters, are composed of unique or different components. We show here that two different forms of hTFIIIB can be separated physically by ion exchange chromatography. hTFIIIB-alpha shows strong preference for transcription of the U6 over the VAI gene and does not contain TATA binding protein (TBP). After SDS-PAGE and renaturation of proteins, the transcriptional activity of hTFIIIB-alpha can be reconstituted by fractions corresponding to a mean M(r) of 25, 60 and 90 kDa. Upon gradient centrifugation or gel filtration, the activity of hTFIIIB-alpha is associated with an M(r) of 60 +/- 10 kDa, indicating that the components of the complex tend to dissociate. In contrast, hTFIIIB-beta is predominantly active on intragenic pol III promoters. It reveals an M(r) of 300 +/- 30 kDa upon gel filtration and, besides TBP, it contains several associated factors (TAFs). Two of these proteins reveal an M(r) of 60 kDa and 90 kDa, and it is conceivable that they are related to polypeptides of similar mass functionally identified in hTFIIIB-alpha. These protein are probably required for the recruitment of pol III to the initiation site at 5'-located and intragenic promoters.

The activity of transcription factor PBP, which binds to the proximal sequence element of mammalian U6 genes, is regulated during differentiation of F9 cells.

Mouse F9 embryonic carcinoma (EC) cells differentiate in culture to parietal endoderm (PE) cells upon induction with retinoic acid and cyclic AMP. In the course of this process, the expression of polymerase III transcripts, e.g., 5S rRNA and U6 small nuclear RNA, is dramatically reduced. This reduction of endogenous RNA content is accompanied by a loss of transcriptional capacity in cell extracts from PE cells. Partial purification of such extracts reveals that the DNA-binding activity of transcription factor PBP, binding specifically to the proximal sequence element (PSE) sequence of vertebrate U6 genes, is significantly reduced. This finding is corroborated by a loss in the transcriptional activity of this factor in reconstitution assays with partially purified polymerase III transcription components. In contrast, the activity of TFIIIA and TFIIIB and the amount of free TATA-binding protein remain unchanged during the differentiation process analyzed here. These data show for the first time that the PSE-binding protein PBP is essentially involved in the differential regulation of polymerase III genes governed by external promoters.

Human TFIIIA alone is sufficient to prevent nucleosomal repression of a homologous 5S gene.

Plasmid DNA harbouring the human 5S rRNA gene was assembled into nucleosomes using either Xenopus S150 extracts or purified core histones in the presence of pectin. In both cases reconstitution of nucleosomes led to a complete repression of transcription. This repression could be efficiently counteracted by preincubating the template DNA with highly purified hTFIIIA which allowed the protein to bind to the ICR of the 5S gene. By using an efficient and well-defined in vitro reconstitution system based on isolated core histones in the presence of pectin, which is devoid of endogenous transcription factors, we demonstrate here for the first time that human TFIIIA alone is sufficient to prevent nucleosomal repression of h5S gene transcription and that additional pol III transcription factors are not required to achieve this effect. Additionally, we investigated the binding of hTFIIIA to a mononucleosome reconstituted on the human 5S gene. DNAse I footprinting experiments reveal that the entire ICR of the human 5S gene is covered by the nucleosome, thereby precluding the subsequent binding of human TFIIIA to the promoter of the 5S gene.

Isolation of transcription factor IIIC from Dictyostelium discoideum.

Transcription factor IIIC (TFIIIC) binds in a sequence-specific manner to RNA-polymerase-III-transcribed genes (e.g. tRNA genes). It sequesters other transcription factors into the preformed complex, thereby activating transcription by RNA polymerase III. The Dictyostelium discoideum homologue of TFIIIC was highly purified by affinity chromatography based on its tDNA-binding activity. This TFIIIC homologue is a multicomponent factor (molecular mass 380 kDa), which binds to the B-box element of the internal tRNA gene promoter without significant A-box interaction. Partially purified D. discoideum TFIIIC is able to functionally complement a human RNA polymerase III in vitro transcription system depleted of human TFIIIC. We provide evidence that partially purified D. discoideum TFIIIC interacts in vitro with gene-external B-box elements present down-stream of many D. discoideum tRNA genes.

Transcription factors required for the expression of Xenopus laevis selenocysteine tRNA in vitro.

It has previously been reported that transcription in vivo of the tRNA(Sec) gene requires three promoter elements, a PSE and a TATA-box upstream of the coding region which are functionally interchangeable with the U6 snRNA gene counterparts and an internal B-block, resembling that of classical tRNA genes (1). We have established an in vitro transcription system from HeLa cells in which three factors, which are either essential for or stimulate transcription were identified. Apart from the TATA-binding protein TBP, the PSE-binding protein PBP was found to be essentially required for expression of the gene. Depletion of PBP from cell extracts by PSE-oligonucleotides abolished tRNA(Sec) transcription, which could be reconstituted by readdition of partially purified PBP. Addition of increasing amounts of recombinant human TBP to an S100 extract stimulated transcription of the tRNA(Sec), the mouse U6 snRNA and the human Y3 genes, an effect which was not observed in the case of a TATA-less tRNA gene. Purified human TFIIA strongly stimulated tRNA(Sec) transcription in a fashion depending on the concentration of TBP. Surprisingly, partially purified TFIIIC was shown to be dispensable for transcription in vitro and unable to bind the B-block of this gene in vitro, although its sequence matches the consensus for this element. Collectively, these data suggest that the mechanism by which transcription complexes are formed on the tRNA(Sec) gene is dramatically different from that observed for classical tRNA genes and much more resembles that observed for externally controlled pol III genes.

Mammalian transcription factor PBP. Characterization of its binding properties to the proximal sequence element of U6 genes.

The DNA binding properties of human transcription factor PBP, which specifically binds to the proximal sequence element of mammalian U6 genes and which plays a pivotal role during their transcription, were analyzed both qualitatively and quantitatively. As a prerequisite, we analyzed the optimal conditions for DNA binding of the PBP by assaying the stability of the interaction against increasing concentrations of salt, dithiothreitol, and heparin. The protein, which does not induce DNA bending, has a characteristic sensitivity against elevated temperatures and precipitously loses activity between 41 and 43 degrees C, a property which can be used for selective inactivation of the protein. Subjection of the PBP to limited proteinase K treatment showed that the protein consists of at least two functional domains, one of which is required for DNA binding. The PBP binds to the PSE with a much higher specific equilibrium constant (Ks = 1.33 x 10(11) M-1) than to nonspecific DNA (Kn = 1.18 x 10(5) M-1). The association and dissociation rates of PBP.PSE interactions were quantitatively determined by kinetic analyses. The pronounced lag phase during the initiation reaction of mammalian U6 transcription in vitro is probably correlated with the slow binding of the PBP to its target sequence. Once formed, however, the PBP.PSE complex is very stable and has a much lower dissociation (kd = 1.84 x 10(-5) s-1) than association rate constant (ka = 0.18 x 10(6) M-1 s-1). Collectively, the results demonstrate that the PSE binding protein stably associates with a high affinity to its cognate promoter sequence, and this process represents one of the primary events in the formation of the preinitiation complex on the U6 gene. Finally, we analyzed the effect of individual base pair mutations within mammalian U6 PSE sequences on the binding of the PBP.

Transcription factor IIA stimulates the expression of classical polIII-genes.

Protein fractions containing TFIIA, a transcription factor known to be involved in transcription initiation by RNA polymerase II and 5'-regulated polymerase III genes (e.g. U6), were tested for their role in in vitro transcription of classical pol III genes. These fractions were shown to stimulate a basal transcription system, reconstituted from highly purified fractions hTFIIIB and hTFIIIC. We demonstrate that this stimulating activity isolated from HeLa cells coelutes over at least six chromatographic steps with hTFIIA. Moreover the native molecular mass and the stability of this activity against heat treatment are comparable to those of hTFIIA. Finally we show that recombinant TFIIA from Saccharomyces cerevisiae can substitute for the human factor in pol III transcription in vitro which proves that TFIIA is also involved in the efficient expression of classical pol III genes.

Transcription factor IIA is inactivated during terminal differentiation of avian erythroid cells.

Avian histone H5 and alpha A-globin genes are transcribed much more efficiently in whole cell extracts derived from immature polychromatic erythrocytes than in extracts from mature duck erythrocytes. We found that these differential activities are detectable only if assayed with promoters containing a functional TATA box. The addition of either highly purified human or recombinant yeast transcription factor IIA (TFIIA) to extracts from mature erythrocytes resulted in a significant increase in transcription from TATA-containing promoters, whereas transcription from TATA-less promoters remained unaffected. Moreover, the activity of TFIIA was found to be reduced in extracts from mature erythrocytes. These data support the proposition that inactivation of TFIIA may contribute to a general repression of gene activity in avian erythrocytes, and only those genes with alternative mechanisms of initiation complex formation continue to be expressed in these cells. In the case of the histone H5 gene, such an alternative mechanism could be mediated via the interaction between duck erythrocyte upstream stimulating factor and TFIID.

TFIIA is required for in vitro transcription of mammalian U6 genes by RNA polymerase III.

Transcription factor TFIIA, defined by its role in transcription by RNA polymerase II, is also involved in RNA polymerase III transcription of mammalian U6 small nuclear RNA genes. This finding was substantiated by experimental evidence including (i) extensive copurification of an activity required for U6 transcription with TFIIA, (ii) the comparable molecular dimensions of this activity and TFIIA, (iii) the identical heat stability of both activities, and (iv) functional analyses revealing that TFIIA facilitates the interaction of TFIID with the TATA box of the U6 gene. As was shown previously for TFIID, TFIIA is the second basal transcription factor which could be demonstrated to be involved in gene expression by two different RNA polymerases.

Proximal sequence element factor binding and species specificity in vertebrate U6 snRNA promoters.

The Xenopus tropicalis U6 gene is very poorly transcribed both when introduced into human cells by transfection, and in human cell-free extracts. By analysis of hybrid promoters constructed from human and Xenopus sequences in various combinations, we show that species specificity is mediated by the proximal sequence elements (PSEs) of the promoters. We demonstrate the PSE-dependence of U6 transcription in a fractionated extract of HeLa cells. One of the fractions required for transcription contains an activity designated PSE-binding protein (PBP), previously shown to bind to the PSE of the mouse U6 gene. Binding of PBP to various wild-type and hybrid U6 PSE sequences correlates with their activity in transcription in HeLa cell extracts. This provides strong evidence that PBP is the PSE-binding factor involved in U6 transcription. In addition, it suggests that the differential affinities of the promoters for PBP is responsible for the observed species specificity. The divergence between U snRNA promoters in different species contrasts with the relatively strong conservation of other families of RNA polymerase II and III transcribed gene promoters. Possible mechanisms by which this diversity could be generated are discussed.

Transcription factor eUSF is an essential component of isolated transcription complexes on the duck histone H5 gene and it mediates the interaction of TFIID with a TATA-deficient promoter.

We analysed the formation of transcription complexes on the H5 gene of the duck which is efficiently transcribed in HeLa cell extracts in vitro. Upon deletion of its TATA-box, the fidelity of transcription of the H5 gene is maintained, although the efficiency of this process is significantly reduced. Selective inactivation of TFIID in whole cell extracts and reconstitution experiments either with human recombinant TFIID or a protein fraction from duck erythrocytes enriched in TFIID show that transcription of the TATA-less H5 promoter nevertheless requires the protein TFIID. Screening of promoter elements which could indirectly mediate the interaction of TFIID with a TATA-less H5 promoter led to the identification of a sequence element located about 40 base-pairs downstream from the H5 initiation site that shows partial homology to the USF consensus sequence. In electrophoretic mobility shift and footprinting studies we demonstrated a specific interaction of the erythroid factor USF (eUSF) with this downstream element. By isolating active transcription complexes we found that all components required for correct initiation remain stably associated with the H5 promoter irrespective of the presence or absence of the TATA box. Moreover, the reconstitution of eUSF and TFIID-depleted transcription complexes with purified protein fractions demonstrate that not only TFIID but also eUSF essentially participates in complex formation even on H5 promoter mutations lacking the TATA-box. Mutual interactions between eUSF and TFIID appear to stabilize the binding of TFIID in the presence or absence of its proper binding site.

Identification of transcription factors required for the expression of mammalian U6 genes in vitro.

Transcription factors, required for the basal expression of the mouse U6 gene were identified in extracts from HeLa cells. This gene is transcribed at least four times more efficiently than its human counterpart in extracts from mouse or HeLa cells and hence provides an excellent in vitro system for the identification of transcription factors involved in the basal expression of mammalian U6 genes. At least four separate protein components were found to be required in addition to RNA polymerase III for correct synthesis of U6 RNA in vitro. These correspond to: (i) TFIIIB; (ii) a heat labile activity contained in a protein fraction enriched in TFIID; (iii) an, as yet, uncharacterized component contained in the flow-through upon rechromatography on phosphocellulose, and finally; (iv) a protein specifically binding to the mouse U6 gene promoter and transactivating its expression. Transcription factors IIIA and IIIC are not involved in mammalian U6 transcription in vitro. The U6-specific transcription factor has a molecular mass of approximately 90 +/- 10 kDa. It specifically binds to the U6 gene from bp -42 to -78 on the coding and from bp -37 to -79 on the non-coding strand thereby centrally encompassing the PSE motif of the mouse U6 promoter. The binding activity of this protein is correlated with the efficiency with which the U6 gene is transcribed in vitro, thereby indicating a crucial role of the PSE-binding protein for U6 transcription.

Human transcription factor IIIC binds to its cognate promoter sequences in a metal coordinated fashion.

Transcription factor IIIC from human cells (hTFIIIC) contains a 55 kDa polypeptide which specifically binds to the promoter of the VAI and 5S gene. This interaction can be abolished by depleting divalent metal cations from the free protein through chelation with EDTA. Prior association of the protein with its DNA-binding sequence renders the complex refractory to chelation by EDTA. Specific binding of hTFIIIC to its cognate promoter sequences--shown by electrophoretic mobility shift and DNase I protection assays--can be restored by the addition of zinc ions. In contrast to the binding of hTFIIIA to the 5S gene, which was monitored in parallel and which exclusively requires Zn2+, the binding of hTFIIIC to the VAI and 5S gene can also be reconstituted--albeit with a lower efficiency--by the transition metals Co2+, Fe2+ and Mn2+ but not by Ni2+ or Cu2+. These results show that hTFIIIC binds to its promoter sequences in a metal coordinated fashion which differs from that observed for the binding of hTFIIIA to the 5S gene.