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TBP-TAF complexes: selectivity factors for eukaryotic transcription.

Recent evidence indicates that the TATA-binding protein (TBP) is central to transcription by all three eukaryotic RNA polymerases (I, II, and III). Interestingly, the majority of the TBP does not appear to be free protein in vivo. Instead, it is found associated with other factors (TAFs) in multisubunit complexes. The past year has brought significant advances in our understanding of the subunit compositions and biochemical functions of these complexes. In addition, the crystal structures of the TBP core domain and the TBP-TATA box DNA complex provide new insights into how this small protein might interact with many different partners.

Animals↗

Characterization of cis-regulating elements and trans-activating factors of the rat cardiac troponin T gene.

To study the transcriptional regulation of the rat cardiac troponin T (cTnT) gene, chimeric genes composed of the upstream region (-757 to +193 base pairs (bp) relative to the transcription initiation site) of the cTnT gene and the bacterial chloramphenicol acetyltransferase (CAT) gene were constructed and transfected into primary cultures of neonatal cardiomyocytes and cardiac fibroblasts. Deletion analysis showed that a 41-bp fragment (-249 to -209 bp) containing the MEF-2-like motif is an essential element for minimal cardiac-specific expression of the rat cTnT gene. The proximal promoter (-208 to -1 bp) contains two consensus CArG boxes, one M-CAT motif, one AP2 site, and one TATA box. The construct (cTNT-208) composed of the CAT reporter gene driven by this proximal promoter did not show cardiac muscle-specific expression. Ligation of consensus MEF-2-like sequence into the upstream of this chimera only partially increased its ability to express in cardiomyocytes. These results suggest that the spacing among MEF-2-like motif and proximal promoter and/or the flanking sequences of the MEF-2-like motif are important in determining cardiac muscle-specific expression. By footprint analysis with a DNA fragment (-303 to +6 bp), we identified three novel regions (called A, B, and C) protected by protein extract from rat hearts, in addition to the known motifs such as MEF-2, M-CAT, and CArG. Gel retardation with the probe (-235 to -141 bp), containing the MEF-2-like motif, one of the CArG boxes, and the C region, or the 41-bp probe (-249 to -209 bp), containing the MEF-2-like motif, revealed different DNA-protein complexes formed by heart, skeletal muscle, and liver extracts. By using DNA affinity purification, DNA-binding proteins with apparent molecular masses of 22-26 kDa were identified from rat heart extract but not from skeletal and liver extracts, suggesting the involvement of cardiac-specific proteins in regulating the cTnT gene expression.

Animals↗

Promoter structure of the mouse TATA-binding protein (TBP) gene.

5'-RACE and genomic cloning were used to determine that the mouse TBP (mTBP) gene consists of one 5'-terminal non-coding exon followed by seven protein-coding exons. The region upstream of the first exon lacks a TATA-box. Hence, as with the case of other genes carrying TATA-less promoter, transcription starts from a cluster of sites which are located at the restricted region of mTBP gene. Interestingly, sequences of this region are well conserved between human and mouse TBP genes, suggesting that both mouse and human TBP genes drive mRNA synthesis in a similar way, and the sequence homology between two genes was used to assign a putative start point for the human TBP gene. Mouse, human, and Trimersurus gramineus (green habu snake) TBP genes share two GC-rich regions in their promoter regions. Thus, it is probable that diverse species of vertebrates commonly use TATA-less promoter bearing GC-rich regions to direct ubiquitous TBP expression.

Amino Acid Sequence↗

Structural and functional characterization on the interaction of yeast TFIID subunit TAF1 with TATA-binding protein.

General transcription factor TFIID, consisting of TATA-binding protein (TBP) and TBP-associated factors (TAFs), plays a central role in both positive and negative regulation of transcription. The TAF N-terminal domain (TAND) of TAF1 has been shown to interact with TBP and to modulate the interaction of TBP with the TATA box, which is required for transcriptional initiation and activation of TATA-promoter operated genes. We have previously demonstrated that the Drosophila TAND region of TAF1 (residues 11-77) undergoes an induced folding from a largely unstructured state to a globular structure that occupies the DNA-binding surface of TBP thereby inhibiting the DNA-binding activity of TBP. In Saccharomyces cerevisiae, the TAND region of TAF1 displays marked differences in the primary structure relative to Drosophila TAF1 (11% identity) yet possesses transcriptional activity both in vivo and in vitro. Here we present structural and functional studies of yeast TAND1 and TAND2 regions (residues 10-37, and 46-71, respectively). Our NMR data show that, in yeast, TAND1 contains two alpha-helices (residues 16-23, 30-36) and TAND2 forms a mini beta-sheet structure (residues 53-56, 61-64). These TAND1 and TAND2 structured regions interact with the concave and convex sides of the saddle-like structure of TBP, respectively. Present NMR, mutagenesis and genetic data together elucidate that the minimal region (TAND1 core) required for GAL4-dependent transcriptional activation corresponds to the first helix region of TAND1, while the functional core region of TAND2, involved in direct interaction with TBP convex alpha-helix 2, overlaps with the mini beta-sheet region.

Amino Acid Sequence↗

Comparative analysis of the pig BAC sequence involved in the regulation of myostatin gene.

Myostatin (GDF8, MSTN) is a member of the transforming growth factor beta superfamily that is essential for proper regulation of skeletal muscle mass. In order to study its expression and regulatory mechanism deeply, we have presented a comparative analysis of about 170-kb pig BAC sequence containing the myostatin gene among pig, human and mouse. The genomic region is characterized by high interspersed repeats and low G+C content. As for the myostatin gene, a higher sequence similarity is found between human and pig than between these species and the mouse. One striking feature is that the structure of two TATA-boxes in the nearby downstream of CCAAT-box is identified in the promoter. Further analysis reveals that the TATA-box1 is responsible for the transcription in pig and human, but the TATA-box2 acts on the transcription in mouse. The other interesting feature is that two polyadenylation signal sequences (AATAAA) exist in 3'UTR of the pig myostatin gene. Moreover, a large number of potential transcription factor-binding sites are also identified in evolutionary conserved regions (ECRs), which may be associated with the regulation of myostatin. Many putative transcription factors play an important role in the muscle development, and the complex interaction between myostatin and these factors may be required for proper muscle development.

3' Flanking Region↗

Transcription initiation is controlled by three core promoter elements in the hgl5 gene of the protozoan parasite Entamoeba histolytica.

Entamoeba histolytica is a single cell eukaryote that is the etiologic agent of amoebic colitis. Core promoter elements of E. histolytica protein encoding genes include a TATA-like sequence (GTATTTAAAG/C) at -30, a novel element designated GAAC (GAACT) that has a variable location between TATA and the site of transcription initiation, and a putative initiator (Inr) element (AAAAATTCA) overlying the site of transcription initiation. The presence of three separate conserved sequences in a eukaryotic core promoter is unprecedented and prompted examination of their roles in regulating transcription initiation. Alterations of all three regions in the hgl5 gene decreased reporter gene activity with the greatest effect seen by mutation of the GAAC element. Positional analysis of the TATA box demonstrated that transcription initiated consistently 30-31 bases downstream of the TATA region. Mutation of either the TATA or GAAC elements resulted in the appearance of new transcription start sites upstream of +1 in the promoter of the hgl5 gene. Mutation of the Inr element resulted in no change in the site of transcription initiation; however, in the presence of a mutated TATA and GAAC regions, the Inr element controlled the site of transcription initiation. We conclude that all three elements play a role in determining the site of transcription initiation. The variable position of the GAAC element relative to the site of transcription initiation, and the multiple transcription initiations that resulted from its mutation, indicate that the GAAC element has an important and apparently novel role in transcriptional control in E. histolytica.

Animals↗

Simian virus 40 large T antigen interacts with human TFIIB-related factor and small nuclear RNA-activating protein complex for transcriptional activation of TATA-containing polymerase III promoters.

The TATA-binding protein (TBP) is common to the basal transcription factors of all three RNA polymerases, being associated with polymerase-specific TBP-associated factors (TAFs). Simian virus 40 large T antigen has previously been shown to interact with the TBP-TAFII complexes, TFIID (B. Damania and J. C. Alwine, Genes Dev. 10:1369-1381, 1996), and the TBP-TAFI complex, SL1 (W. Zhai, J. Tuan, and L. Comai, Genes Dev. 11: 1605-1617, 1997), and in both cases these interactions are critical for transcriptional activation. We show a similar mechanism for activation of the class 3 polymerase III (pol III) promoter for the U6 RNA gene. Large T antigen can activate this promoter, which contains a TATA box and an upstream proximal sequence element but cannot activate the TATA-less, intragenic VAI promoter (a class 2, pol III promoter). Mutants of large T antigen that cannot activate pol II promoters also fail to activate the U6 promoter. We provide evidence that large T antigen can interact with the TBP-containing pol III transcription factor human TFIIB-related factor (hBRF), as well as with at least two of the three TAFs in the pol III-specific small nuclear RNA-activating protein complex (SNAPc). In addition, we demonstrate that large T antigen can cofractionate and coimmunoprecipitate with the hBRF-containing complex TFIIIB derived from HeLa cells infected with a recombinant adenovirus which expresses large T antigen. Hence, similar to its function with pol I and pol II promoters, large T antigen interacts with TBP-containing, basal pol III transcription factors and appears to perform a TAF-like function.

Animals↗

The TBP-like factor: an alternative transcription factor in metazoa?

Protein sequence analysis has revealed a family of TATA-binding-protein (TBP)-like factors (TLFs) in metazoan organisms. Modelling of the three-dimensional structure of these TLFs suggests that they form an asymmetric saddle-like structure and that, unlike TBP, TLFs might bind to DNA sequences other than classical TATA boxes. Thus, the existence of TLFs presents a challenge to the doctrine that TBP is a universal regulator of transcription in metazoans.

Amino Acid Sequence↗

Specific repression of TATA-mediated but not initiator-mediated transcription by wild-type p53.

The p53 protein is apparently central to the development of human cancers because both alleles are often found to be mutated in different tumour types. In addition, wild-type p53 can inhibit transformation by viral and cellular oncogenes in vitro, so p53 has been classified as a tumour suppressor. Investigations of the normal function of p53 have indicated that at least one of its functions could involve the activation of gene expression through the binding of specific DNA-regulatory sequences. Also, overexpression of p53 can mediate growth arrest and repress transcription from a variety of promoters. We demonstrate here both in vivo and in vitro that expression of wild-type p53 specifically represses the activity of promoters whose initiation is dependent on the presence of a TATA box. Promoters whose accurate transcription is directed by a pyrimidine-rich initiator element, however, are immune to the effects of p53. Furthermore, we observe that repression is mediated by an interaction of p53 with basal transcription factor(s). Thus, p53 appears to repress the activity of certain promoters through direct communication with TATA box-dependent basal transcription machinery.

3T3 Cells↗

Cloning of the Xenopus laevis cdk2 promoter and functional analysis in oocytes and during early development.

CDK2 (cyclin-dependent kinase 2) is a serine/threonine kinase which is involved in regulating S-phase entry in higher eukaryotes. To investigate the transcriptional control of this gene, a 13-kb Xenopus laevis genomic clone containing the 5' flanking sequences was isolated. A 2.7-kb fragment containing the promoter region was sequenced and the transcription start point (tsp) was determined by primer extension. Several putative regulatory elements, such as the E2F-binding site, Y box and octamer-binding site, were localized in this region, but no TATA box was found. When fused to cat, a reporter gene encoding chloramphenicol acetyltransferase, the 5' flanking sequences were shown to function in oocytes and an enhancer activity was found in this region. During early embryogenesis, cdk2 promoter activity was tested and de novo transcription was detected at the mid-blastula transition.

Animals↗

DNA-protein interactions in the proximal zeta-globin promoter: identification of novel CCACCC- and CCAAT-binding proteins.

The human zeta-globin gene is expressed in a tissue- and developmental-specific pattern, with expression confined to primitive erythroid cells of the embryonic yolk sac blood islands. Transgenic mouse studies have shown that the proximal zeta-globin promoter contains sequences that contribute to the stage-specificity of expression, but no systematic functional studies of the cis elements in the proximal zeta-globin promoter have been reported. In this paper, we show that a number of conserved sequence elements in the zeta-globin promoter are important for promoter activity in transiently transfected K562 erythroleukemia cells, which constitutively express zeta-globin. These include a GATA site at -105, a CCACC site at -93, a CCAAT box at -65, and a TATA box at -29. A highly conserved CCTCC sequence at -78 is not important for zeta-globin promoter activity in this system. Mutations at these sites do not result in increased promoter activity in OCIM1 cells, an erythroid line that does not express zeta-globin, suggesting none of these sites is a developmental silencer. Electrophoretic mobility shift assays show that K562 and OCIM1 nuclear extracts contain DNA-binding activities that interact with the -105 GATA, -65 CCAAT, and -29 TATA sites. In addition K562 cells, but not OCIM1 cells, have an activity that binds the -93 CCACC site. GATA-1 interacts with the GATA site. The K562 CCACC-binding protein is distinct from Sp1, Sp2, Sp3, Sp4, EKLF, and BKLF. A specific -65 CCAAT-binding activity is present in K562 and OCIM1 nuclear extracts that is distinct from other CCAAT-binding proteins including CBF/NF-Y, C/EBP, NF-1, and CP2. Thus, we have identified two novel factors that may contribute to the tissue or developmental stage-specific expression of zeta-globin.

Animals↗

Repression of RNA polymerase II and III transcription during M phase of the cell cycle.

Nuclear transcription is repressed when eukaryotic cells enter mitosis. Using Xenopus egg extracts shifted to the mitotic state with recombinant cyclin B1 protein, we have been able to reproduce mitotic repression of transcription in vitro. Active RNA polymerase III transcription is observed in interphase extracts in the absence of added cyclin, but is strongly repressed by the induction of cdc2/cyclin B (maturation/mitosis promoting factor, MPF) kinase activity in the mitotic extract. Studies with protein kinase inhibitors show that protein phosphorylation is required for repression. Add-back experiments indicate that repression of class III gene transcription is due to inactivation of the transcription factor TFIIIB. TFIIIB is composed of the TATA-box binding protein (TBP) and TBP-associated factors of 75 and 92 kDa. In the present study, we show that TBP and a polypeptide of 92 kDa are substrates of the mitotic kinase in highly purified TF- IIIB fractions. We also show that a phosphatase present in the Xenopus egg extract can reactivate transcription after repression by the mitotic kinases. This result suggests a mechanism for reactivation of transcription after exit from mitosis into the G1 phase of the cell cycle. As for pol III genes, purified cdc2/cyclin B kinase is sufficient to inhibit transcription by RNA polymerase II in a reconstituted transcription system containing the basal transcription factors and polymerase.

Animals↗

New potent agents binding to a poly(dT) sequence in double-stranded DNA: bis(Zn(2+)-cyclen) and tris(Zn(2+)-cyclen) complexes.

In an effort to search for mechanistically new and more potent agents than conventional drugs that target AT-rich sequences in double-stranded DNA, we have tested multi(Zn(2+)-cyclen) complexes. Indeed, they selectively bound to poly(dT) sequences to melt the A-T hydrogen bonds; only 2.5 microM or 4 microM of the p-tris(Zn(2+)-cyclen) complex were required to completely melt a 50 microM nucleobase of double-stranded poly(dA) x poly(dT) or poly(dA-dT)(2) at 25 degrees C. The region with seven consecutive T's in native DNA (150 bp) was protected from micrococcal nuclease hydrolysis, as revealed by footprinting assays, with IC(50) values of 2 microM for p-bis(Zn(2+)-cyclen) and 0.5 microM for p-tris(Zn(2+)-cyclen). The high affinity to AT-rich sequences of these Zn(2+)-cyclen complexes matches or surpasses those of the conventional AT-binding drugs distamycin A (IC(50)=2 microM) and DAPI (5 microM). Moreover, the p-tris(Zn(2+)-cyclen) complex selectively binds to the TATA box sequence of the SV40 early promoter to inhibit the binding of the TATA binding protein as effectively as distamycin A, with an IC(50) value of 0.4 microM. In vitro transcription of poly(dA) x poly(dT) using Escherichia coli RNA polymerase was effectively inhibited by p-tris(Zn(2+)-cyclen). The [(3)H]-ATP incorporation into RNA was more strongly blocked (IC(50)=0.8 microM) than the [(3)H]-UTP incorporation (IC(50)=40 microM), a fact indicating that the p-tris(Zn(2+)-cyclen) complex interacts only with the poly(dT) strand in the double-stranded DNA template.

Base Sequence↗

Transcription from TATA-less promoters: dihydrofolate reductase as a model.

The promoters of many of the genes encoding the so-called "housekeeping" enzymes, oncogenes, growth factors and their receptors, and transcription factors, do not contain a canonical TATA box, which is known to direct transcription initiation. The mechanisms through which TATA-less promoters are regulated, and their transcription start sites selected, have begun to yield to investigation. Using the dihydrofolate reductase (DHFR) gene as a model, recent work on this group of genes has been reviewed. Control of transcription initiation and the role of "initiator" sequences, as well as their binding factors, in particular YY1 and E2F, are addressed. In the DHFR gene, neither the E2F site at the major initiation region nor the upstream Sp1 sites can alone produce wild-type initiation, despite the fact that each of these sites has certain properties of initiators. Many TATA-less genes are growth regulated, that is, transcription is increased in response to stimulation of cell proliferation. Although both Sp1 and E2F have been implicated in growth regulation, our recent studies suggest that Sp1 sites alone can confer a growth-dependent increase in transcription in the late G1 and early S phases of the cell cycle. The regulatory role of E2F, which binds to many TATA-less promoters and mediates viral stimulation of transcription, is also reviewed.

Animals↗

Regulated expression of TATA-binding protein-related factor 3 (TRF3) during early embryogenesis.

RNA polymerase (Pol) II transcription persists in TATA-box-binding protein (TBP)(-/-) mutant mouse embryos, indicating TBP-independent mechanisms for Pol II transcription in early development. TBP-related factor 3 (TRF3) has been proposed to substitute for TBP in TBP(-/-) mouse embryos. We examined the expression of TRF3 in maturing oocytes and early embryos and found that TRF3 was co-expressed with TBP in the meiotic oocytes and early embryos from the late one-cell stage onward. The amounts of TBP and TRF3 changed dynamically and correlated well with transcriptional activity. Chromatin immunoprecipitation (ChIP) assay revealed that different gene promoters in mouse embryonic stem (ES) cells recruited TRF3 and TBP selectively. Comparative analyses of TRF3 and TBP during cell cycle showed that both factors proceeded through cell cycle in a similar pace, except that TRF3 was slightly delayed than TBP in entering the nucleus when cells were exiting the M-phase. Data from expression and biochemical analyses therefore support the hypothesis that TRF3 plays a role in early mouse development. In addition, results from co-localization study suggest that TRF3 may be also involved in Pol I transcription.

Animals↗

Requirement of distal and proximal promoter sequences for chromatin organization of the osteocalcin gene in bone-derived cells.

The osteocalcin (OC) gene encodes a 10 Kda bone-specific protein which is expressed with the onset of mineralization during the differentiation of normal diploid osteoblasts. We have previously reported that transcriptional activation of this gene is accompanied by the presence of two DNase I hypersensitive sites, both located in the promoter region spanning key basal (proximal site, -170 to -70) and steroid-dependent enhancer (distal site, -600 to -400) elements. Here, we have examined stably transfected ROS 17/2.8 cell lines carrying OC promoter-reporter transgenes which contain a series of 5'-deletions and determined the effects of these truncations on the chromatin organization. It has been found that: (1) DNase I hypersensitivity at -600 is not a requirement for vitamin D-dependent transcriptional upregulation; (2) basal transcriptional activity and proximal nuclease hypersensitivity depend exclusively on protein-DNA interactions occurring within the proximal promoter region, and (3) within the chromatin context, the proximal 100 bp promoter fragment, containing essential elements such as the OC box (-99 to -76) and TATA box (-44 to -31), is insufficient to support formation of the proximal nuclease hypersensitive site and transcriptional activity.

Animals↗

Sequence of the 5'-flanking region of CYP3A5: comparative analysis with CYP3A4 and CYP3A7.

Two genomic clones containing the 3'-end of CYP3A7, the whole 5'-flanking region plus the first exon of CYP3A5 were isolated from two different human genomic banks and sequenced. The 5'-flanking region of CYP3A5, from nucleotide -1 to -1434, was 60% and 59% similar with the corresponding regions of CYP3A4 and CYP3A7, respectively. However, the similarity increased to 74% when regions from nucleotide -1 to -700 were compared and dropped to less than 42% for regions upstream from -700. The CYP3A5 promoter contains a CATA box instead of the typical TATA box and a basic transcription element (BTE). Other consensus sequences previously found in CYP3A4 and CYP3A7 were also identified in the 5'-flanking of CYP3A5 from -1 to -700. Both CYP3A5 and CYP3A7 genes appear to be tandemly associated and transcribed in the same direction on chromosome 7.

Aryl Hydrocarbon Hydroxylases↗

Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man.

We have isolated 8 different long terminal repeat (LTR) sequences of the ERV-H family of endogenous retrovirus-like elements from human chromosome 18, 9 from African green monkey, and 28 from marmoset. Human ERV-H LTRs have been divided into three types designated Type I, Type Ia, and Type II. Comparative analyses of the 45 isolated LTRs and 60 human ERV-H LTRs enabled a further subdivision into 13 subtypes. Type I elements were widely distributed in all three species. Their average evolutionary age (40 MYr), estimated by a consensus sequence approach, suggests that they first expanded in the genomes at the time New- and Old World monkeys diverged. The occurence of some very old Type I sequences indicate that ERV-H elements may have integrated even before prosimians and primates diverged. Type Ia and - II elements were found in both monkey species. Promoter active Type I and Type Ia LTRs were found while Type II LTRs were inactive. Promoter active Type I LTRs generally contained a functional GC/GT box immediately 3' to the TATA box, providing strong binding of Sp1 family proteins, while the highly promoter active Type Ia element H6 contained synergistically acting Sp1 binding sites located in the U3 enhancer region.

Animals↗