TATA Element Research Articles

Epigenetic Silencing Mechanisms in Budding Yeast and Fruit Fly: Different Paths, Same Destinations

Transcriptional silencing in budding yeast and fruit fly is mediated by fundamentally unrelated proteins that assemble very different chromatin structures. Surprisingly, the repressive mechanisms evolved from these very different materials have similar features, including an epigenetic mode of inheritance and a block to transcription based on interference with the assembly or function of the promoter complex rather than with the binding of gene-specific activators.

Interdependent Recruitment of SAGA and Srb Mediator by Transcriptional Activator Gcn4p

Transcriptional activation by Gcn4p is enhanced by the coactivators SWI/SNF, SAGA, and Srb mediator, which stimulate recruitment of TATA binding protein (TBP) and polymerase II to target promoters. We show that wild-type recruitment of SAGA by Gcn4p is dependent on mediator but independent of SWI/SNF function at three different promoters. Recruitment of mediator is also independent of SWI/SNF but is enhanced by SAGA at a subset of Gcn4p target genes. Recruitment of all three coactivators to ARG1 is independent of the TATA element and preinitiation complex formation, whereas efficient recruitment of the general transcription factors requires the TATA box. We propose an activation pathway involving interdependent recruitment of SAGA and Srb mediator to the upstream activation sequence, enabling SWI/SNF recruitment and the binding of TBP and other general factors to the promoter. We also found that high-level recruitment of Tra1p and other SAGA subunits is independent of the Ada2p/Ada3p/Gcn5p histone acetyltransferase module but requires Spt3p in addition to subunits required for SAGA integrity. Thus, while Tra1p can bind directly to Gcn4p in vitro, it requires other SAGA subunits for efficient recruitment in vivo.

Genome wide analysis of Arabidopsis core promoters

BackgroundCore promoters are the gene regulatory regions most proximal to the transcription start site (TSS), central to the formation of pre-initiation complexes and for combinatorial gene regulation. The DNA elements required for core promoter function in plants are poorly understood. To establish the sequence motifs that characterize plant core promoters and to compare them to the corresponding sequences in animals, we took advantage of available full-length cDNAs (FL-cDNAs) and predicted upstream regulatory sequences to carry out the analysis of 12,749 Arabidopsis core promoters.ResultsUsing a combination of expectation maximization and Gibbs sampling methods, we identified several motifs overrepresented in Arabidopsis core promoters. One of them corresponded to the TATA element, for which an in-depth analysis resulted in the generation of robust TATA Nucleotide Frequency Matrices (NFMs) capable of predicting Arabidopsis TATA elements with a high degree of confidence. We established that approximately 29% of all Arabidopsis promoters contain TATA motifs, clustered around position -32 with respect to the TSS. The presence of TATA elements was associated with genes represented more frequently in EST collections and with shorter 5' UTRs. No cis-elements were found over-represented in TATA-less, compared to TATA-containing promoters.ConclusionOur studies provide a first genome-wide illustration of the composition and structure of core Arabidopsis promoters. The percentage of TATA-containing promoters is much lower than commonly recognized, yet comparable to the number of Drosophila promoters containing a TATA element. Although several other DNA elements were identified as over-represented in Arabidopsis promoters, they are present in only a small fraction of the genes and they represent elements not previously described in animals, suggesting a distinct architecture of the core promoters of plant and animal genes.

The Repressor Element Silencing Transcription Factor (REST)-mediated Transcriptional Repression Requires the Inhibition of Sp1

The terminal differentiation of neuronal and pancreatic beta-cells requires the specific expression of genes that are targets of an important transcriptional repressor named RE-1 silencing transcription factor (REST). The molecular mechanism by which these REST target genes are expressed only in neuronal and beta-cells and are repressed by REST in other tissues is a central issue in differentiation program of neuronal and beta-cells. Herein, we showed that the transcriptional factor Sp1 was required for expression of most REST target genes both in insulin-secreting cells and neuronal-like cells where REST is absent. Inhibition of REST in a non-beta and a non-neuronal cell model restored the transcriptional activity of Sp1. This activity was also restored by trichostatin A indicating the requirement of histone deacetylases for the REST-mediated silencing of Sp1. Conversely, exogenous introduction of REST blocked Sp1-mediated transcriptional activity. The REST inhibitory effect was mediated through its C-terminal repressor domain, which could interact with Sp1. Taken together, these data show that the inhibition of Sp1 by REST is required for the silencing of its target genes expression in non-neuronal and in non-beta-cells. We conclude that the interplay between REST and Sp1 determines the cell-specific expression of REST target genes.

Deciphering the Contribution of Knowncis-Elements in the Mouse Cone Arrestin Gene to its Cone-Specific Expression

Cone arrestin (CAR) is highly expressed in all cone photoreceptors of the retina and a subset of pinealocytes in the pineal gland. This study was initiated to examine the cis-elements responsible for the cell-specific expression pattern of CAR. Mutagenesis and specific deletions of known cis-elements in the proximal promoter of the mouse CAR (mCAR) gene were introduced and analyzed in vitro and in vivo. A series of mCAR promoter-luciferase reporter constructs were transiently transfected into COS-7 or Weri-Rb-1 retinoblastoma cells and tested in in vitro promoter assays. Transgenic Xenopus laevis were created with deletional or mutated promoter fragments driving an enhanced green fluorescent protein (EGFP) reporter gene. The resultant EGFP expression pattern in the transgenic animals was analyzed by fluorescence microscopy and immunocytochemistry. A significant decrease in in vitro transcriptional activities was observed when the minimal 215-bp promoter fragment was mutated in each of the four cone-rod homeobox (CRX)-binding elements (CBEs) or in either of the two TATA-elements. The 215-bp mCAR proximal promoter drove EGFP expression to cone photoreceptors and pinealocytes in transgenic Xenopus laevis; however, the truncated 147-bp fragment drove expression to both cone and rod photoreceptors. Transgenic tadpoles carrying a single mutation in either the TATA-box, the TATA-element or the proximal CBE had undetectable EGFP expression in the retina. However, when one of the other three CBEs was mutated, EGFP expression was observed in muscle and brain tissues, in addition to the eyes. Also, when both TATA elements were mutated, transgenic animals had EGFP expression in all photoreceptors. Because no reporter activity was observed when either a 3.2-kb 5' extended region or the first intron of the mCAR gene was tested in Weri-Rb-1 cells, neither construct was examined in vivo. The data demonstrate that the regulatory functions of the known cis-elements in the mCAR promoter are highly dependent on location and nucleotide sequence conservation. The TATA elements and CBEs are crucial for driving both basal transcriptional activity and tissue specificity to cone photoreceptors and pinealocytes.

Characterization of the promoter of the mouse c-Jun NH 2-terminal/stress-activated protein kinase alpha gene

We report the isolation of the mouse JNK/SAPKα gene, the determination of its exon/intron organization and the characterization of its promoter region. The mouse JNK/SAPKα gene spans a region of 36 kbp and contains 13 exons, which represent about 8% of the gene sequence. Major JNK/SAPKα splice variants (I and II) are generated by alternative splicing of exons 7 and 8, respectively, whereas minor variants (III and IV) are generated using cryptic sites located inside exon 9. The regulatory elements of the JNK/SAPKα gene are located in a 400-bp region placed upstream of the first exon. The gene lacks a TATA element and the initiation of transcription is located inside a 1-kbp CG island. Two regulatory regions located at −98/−69 and −69/−30 were defined by deletion analysis of the promoter.

Functional analysis of the mouse Fcgrt 5′ proximal promoter

The Brambell receptor (FcRB, FcRn) mediates transmission of immunity from mother to young perinatally and plays a central role in IgG protection and homeostasis throughout life. Developmental and tissue specific expression is via transcriptional regulation of the gene for the receptor heavy chain, Fcgrt. In neonatal mouse intestine, expression is high to absorb IgG from mother's milk, but then nearly absent in adult intestine and in most other tissues. In this initial functional characterization, reporter gene assays revealed at least two upstream promoter regions (−372/−140 and −105/−1), each with repressor and activator functions, and a downstream activator domain (+1/+78). The gene carries no upstream TATA element or Inr sequence, and an apparent downstream promoter feature (DPE) lacks typical context for an active element, rendering uncertain the nature of the organizing feature for the transcription initiation complex. Electrophoretic mobility shift analysis of the proximal upstream region identified transcription factor (TF) binding to motifs for NF1, Sp1 (GT box) and Ets. Binding to the GT box and Ets motif was observed only with mature cell sources, and not with neonatal enterocyte extracts. Site-directed mutagenesis confirmed that TF binding to the GT box up-regulates promoter activity in adult (NIH3T3) cells, whereas binding to the Ets motif represses activity. Binding of NF1 protein to the Fcgrt promoter was confirmed in nuclear extracts of NIH3T3 cells and in adult mouse enterocytes, whereas an apparently different TF bound uniquely to the NF1 site in neonatal enterocyte extracts as the sole identified candidate for an expected developmental-specific high-level activator in this tissue. These data indicate regions of potential importance in the Fcgrt proximal promoter and additionally suggest that the selective temporal and spatial availability of specific TFs may contribute to the developmental and tissue-specific regulation of Fcgrt expression.

The DNA element controlling expression of the varicella-zoster virus open reading frame 28 and 29 genes consists of two divergent unidirectional promoters which have a common USF site.

The mechanism of the divergent expression of the varicella-zoster virus (VZV) ORF 28 and ORF 29 genes from a common intergenic DNA element, the ORF 28/29 promoter, is of interest based on the observation that both genes are expressed during VZV lytic infection but only the ORF 29 gene is expressed in latently infected neurons. In the work presented here, expression driven by the ORF 28/29 intergenic region was examined. We found that the promoter activity towards the ORF 29 direction is more responsive to activation by the major viral transactivator IE62 than that towards the ORF 28 direction in the context of our experimental system. Analysis of the functional DNA elements involved in IE62 activation of the bidirectional ORF 28/29 regulatory element revealed that in both transfected and VZV-superinfected cells it is a fusion of two unidirectional promoters overlapping an essential USF binding site but with distinct TATA elements. A single TATA element directs expression in the ORF 28 direction, whereas the two TATA elements directing ORF 29 gene expression are alternatively and differentially utilized for transcription initiation. We also identified an Sp1 site localized proximal to the ORF 28 gene which functions as an activator element for expression in both directions. These results indicate that the ORF 28 and ORF 29 genes can be expressed either coordinately or independently and that the observed expression of only the ORF 29 gene during VZV latency may involve neuron-specific cellular factors and/or structural aspects of the latent viral genome.

Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles.

The recruitment of TATA box-binding protein (TBP) to promoters is one of the rate-limiting steps during transcription initiation. However, the global importance of TBP recruitment in determining the absolute and changing levels of transcription across the genome is not known. We used a genomic approach to explore the relationship between TBP recruitment to promoters and global gene expression profiles in Saccharomyces cerevisiae. Our data indicate that first, RNA polymerase III promoters are the most prominent binding targets of TBP in vivo. Second, the steady-state transcript levels of genes throughout the genome are proportional to the occupancy of their promoters by TBP, and changes in the expression levels of these genes are closely correlated with changes in TBP recruitment to their promoters. Third, a consensus TATA element does not appear to be a major determinant of either TBP binding or gene expression throughout the genome. Our results indicate that the recruitment of TBP to promoters in vivo is of universal importance in determining gene expression levels in yeast, regardless of the nature of the core promoter or the type of activator or repressor that may mediate changes in transcription. The primary data reported here are available at http://www.iyerlab.org/tbp.

Truncation and mutagenesis analysis of the human X-arrestin gene promoter

X-arrestin (arrestin-3) is an arrestin present specifically in the outer segments of red-, green-, and blue-cone photoreceptors. The X-arrestin gene is on Xcen-q22, and consists of 17 exons with a promoter containing a TATA box and elements important for photoreceptor expression, including three CRX and one PCE-1-like element. In order to delineate the promoter structure necessary for the pan-cone-specific expression of X-arrestin, the expression of the gene in retinoblastoma cell lines was investigated, and a structure–function analysis of the promoter was conducted in the appropriate cellular substrate. Expression of X-arrestin was detected at a low level in the Y79 retinoblastoma cell line but not in the WERI retinoblastoma cell line. Truncation and expression analysis of the X-arrestin promoter in Y79 showed maximal activity in the proximal 378-bp region containing the CRX and PCE-1-like elements upstream of the TATA and CAAT boxes and a negative regulator in the distal 1–2-kbp region. Mutagenesis of the three CRX and PCE-1-like elements and expression analysis demonstrated complete elimination of the promoter activity. Mutagenesis of the TATA box and PCE-1-like element individually resulted in similar decrease in promoter activity, but the decrease in the promoter activity was greater when the CRX elements were mutagenized with a 5′ to 3′ spatial gradient in the negative effect, suggesting a cooperative effect of the three CRX elements. The regulation of expression from this promoter may involve the binding of a multi-protein enhanceosome complex at the CRX triplet and the PCE-1-like element, resulting in the recruitment and activation of the RNA polymerase II complex at the downstream TATA box.

Molecular characterization of the Japanese flounder, Paralichthys olivaceus, CD3ɛ and evolution of the CD3 cluster

A second CD3 gene, i.e. CD3ɛ, has been cloned and sequenced in Japanese flounder. The full length cDNA is 1006 bp and encodes 164 amino acids. When compared with other known CD3ɛ peptide sequences, the most conserved region of the Japanese flounder CD3ɛ chain peptide is the cytoplasmic domain and the least conserved is the extracellular domain. A phylogenetic analysis based on the deduced amino acid sequence grouped the two Japanese flounder CD3 sequences with CD3ɛ and CD3γ(δ, respectively. The Japanese flounder CD3ɛ gene has Lyf-1, GATAs, Oct-1, CEBPs, AP-1, and NF-AT but lacks TATA and CCAAT elements in the 5′ flanking region. The Japanese flounder CD3 cluster (consisting of CD3ɛ and CD3γ(δ) spans only 10.4 kb. The two genes are oppositely transcribed only 3.8 kb apart. Both Japanese flounder CD3 genes have five exons. The two Japanese flounder CD3 genes were predominantly expressed in PBLs, kidney, spleen, and gills. A polyclonal rabbit antiserum that reacts with the CD3 marker on human T cells also reacted with Japanese flounder CD3ɛ. The epitope highly conserved between mammalian and non-mammalian CD3ɛs, this antibody bound to a single 15 kDa peptide.

The SANT Domain of Human MI-ER1 Interacts with Sp1 to Interfere with GC Box Recognition and Repress Transcription from Its Own Promoter

To gain insight into the regulation of hmi-er1 expression, we cloned a human genomic DNA fragment containing one of the two hmi-er1 promoters and consisting of 1460 bp upstream of the translation initiation codon of hMI-ER1. Computer-assisted sequence analysis revealed that the hmi-er1 promoter region contains a CpG island but lacks an identifiable TATA element, initiator sequence and downstream promoter element. This genomic DNA was able to direct transcription of a luciferase reporter gene in a variety of human cell lines, and the minimal promoter was shown to be located within-68/+144 bp. Several putative Sp1 binding sites were identified, and we show that Sp1 can bind to the hmi-er1 minimal promoter and increase transcription, suggesting that the level of hmi-er1 expression may depend on the availability of Sp1 protein. Functional analysis revealed that hMI-ER1 represses Sp1-activated transcription from the minimal promoter by a histone deacetylase-independent mechanism. Chromatin immunoprecipitation analysis demonstrated that both Sp1 and hMI-ER1 are associated with the chromatin of the hmi-er1 promoter and that overexpression of hMI-ER1 in cell lines that allow Tet-On-inducible expression resulted in loss of detectable Sp1 from the endogenous hmi-er1 promoter. The mechanism by which this occurs does not involve binding of hMI-ER1 to cis-acting elements. Instead, we show that hMI-ER1 physically associates with Sp1 and that endogenous complexes containing the two proteins could be detected in vivo. Furthermore, hMI-ER1 specifically interferes with binding of Sp1 to the hmi-er1 minimal promoter as well as to an Sp1 consensus oligonucleotide. Deletion analysis revealed that this interaction occurs through a region containing the SANT domain of hMI-ER1. Together, these data reveal a functional role for the SANT domain in the action of co-repressor regulatory factors and suggest that the association of hMI-ER1 with Sp1 represents a novel mechanism for the negative regulation of Sp1 target promoters.

Multiple transcripts of a gene for a leucine-rich repeat receptor kinase from morning glory (Ipomoea nil) originate from different TATA boxes in a tissue-specific manner.

TATA boxes are the most common regulatory elements found in the promoters of eukaryotic genes because they are associated with basal transcription initiation by RNA polymerase II. Often only a single TATA element is found in a given promoter, and tissue-, stage- and/or stimulus-specific expression occurs because the TATA box is associated with other cis -acting elements that enhance or repress transcription. We used software tools for gene analysis to assist in locating potential TATA box(es) in an AT-rich region of the promoter of a gene, inrpk1, which codes for a leucine-rich receptor protein kinase in morning glory (Ipomoea nil). Through the use of RT-PCR and various combinations of forward primers bracketing most of the promoter region we were able to define the 5'-ends of transcripts in this region. The region was then targeted for analysis by RNA Ligase-Mediated-5' Rapid Amplification of cDNA Ends (RLM-5' RACE) to identify the transcript initiation site(s). Positioning of initiation sites with respect to TATA boxes identified by gene analysis tools allowed us to identify three operational TATA elements which regulate basal transcription from this gene. Two TATA boxes were responsible for all of the inrpk1 transcripts found in leaves and cotyledons, and about 25-30% of the transcripts in roots. A third TATA box was involved only in expression in roots and accounted for the remaining 50-70% of root transcripts. RNAs expressed from this element lack two potentially functional upstream AUG codons, and may be translated more efficiently than transcripts originating from the other TATA boxes.

The minimal promoter plays a major role in silencing of the galago γ-globin gene in adult erythropoiesis

The human gamma-globin gene and its orthologous galago gamma-globin gene evolved from an ancestral epsilon-globin gene. In galago, expression of the gamma-gene remained restricted to the embryonic stage of development, whereas in humans, expression of the gamma-gene was recruited to the fetal stage. To localize the cis-elements responsible for this developmentally distinct regulation, we studied the expression patterns of the human gamma-gene driven by either the human or the galago gamma-promoters in transgenic mice. gamma-gene transcription driven by either promoter reached similar levels in embryonic erythropoiesis. In adult erythropoiesis the gamma-gene was silenced when controlled by the galago gamma-promoter, but it was expressed at a high level when it was linked to the human gamma-promoter. By a series of gamma-promoter truncations the sequences required for the down-regulation of the galago gamma-globin gene were localized to the minimal promoter. Furthermore, by interchanging the TATA, CCAAT, and CACCC elements between the human and galago minimal promoters we found that whereas each box made a developmentally distinctive contribution to gamma-globin gene expression, the CACCC box was largely responsible for the down-regulation of the gamma-gene in adult erythropoiesis.

Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes.

The TATA-binding protein (TBP) is a critical general transcription factor that associates with the core promoter and acts as a nexus for gene regulation through its interactions with other factors. A large number of proteins recognize the relatively small yet highly conserved C-terminal domain of TBP. One subset of these proteins (general transcription factors) interacts with the TBP.TATA complex and RNA polymerase II to create the preinitiation complex. To study TBP functions in preinitiation complex and other complexes, we generated a set of RNA aptamers with high affinity to yeast TBP. These aptamers act on TBP in different ways: all of them bind TBP competitively with DNA bearing the TATA element, and some can actively disrupt the TBP.TATA interaction in preformed, higher-order complexes containing the additional general transcription factors TFIIB and TFIIA. In crude cell extracts, the aptamers inhibit transcription in ways that reveal the dynamic nature of TBP interactions during initiation and reinitiation.

Regulation and Autoregulation of the Promoter for the Latency-associated Nuclear Antigen of Kaposi's Sarcoma-associated Herpesvirus

Kaposi's sarcoma-associated herpesvirus (KSHV) or human herpesvirus 8 has been established as the etiological agent of Kaposi's sarcoma and certain AIDS-associated lymphomas. KSHV establishes latent infection in these tumors, invariably expressing high levels of the viral latency-associated nuclear antigen (LANA) protein. LANA is necessary and sufficient to maintain the KSHV episome. It also modulates viral and cellular transcription and has been implicated directly in oncogenesis because of its ability to bind to the p53 and pRb tumor suppressor proteins. Previously, we identified the LANA promoter (LANAp) and showed that it was positively regulated by LANA itself. Here, we present a detailed mutational analysis and define cis-acting elements and trans-acting factors for the core LANAp. We found that a downstream promoter element, TATA box, and GC box/Sp1 site at -29 are all individually required for activity. This architecture places LANAp into the small and unusual group of eukaryotic promoters that contain both the downstream promoter element and TATA element but lack a defined initiation site. Furthermore, we demonstrate that LANA regulates its own promoter via its C-terminal domain and does bind to a defined site within the core promoter.

Androgen receptor coregulators in prostate cancer: mechanisms and clinical implications.

The transcriptional activity of androgen receptor (AR) is modulated by coregulators that have a significant influence on a number of functional properties of AR, including the ligand specificity as well as the DNA binding capacity. Because androgens and AR have pivotal roles in the development and

Sequence and Spacing of TATA Box Elements Are Critical for Accurate Initiation from the β-Phaseolin Promoter

The beta-phaseolin (phas) gene, which encodes one of the major seed storage proteins of P. vulgaris, is tightly regulated at the transcription level resulting in strict tissue-specific and spatial expression during embryonic development. The phas proximal promoter contains a complex arrangement of core promoter elements including three TATA boxes as well as several putative initiator elements. To delineate the respective contributions of the core promoter elements to transcription initiation we have performed site-directed mutagenesis of the phas promoter. In vivo expression studies were performed on transgenic Arabidopsis harboring phas promoter mutants driving expression of the beta-glucuronidase (gus) reporter gene. Quantitative assessment of GUS activity in seeds bearing the promoter mutants indicated that both sequence and spacing of the TATA elements influenced the efficiency of transcription. Substitution, insertion or deletion mutations had no effect on histochemical staining patterns indicating that strict spacing requirements are not essential for correct spatial expression of phas during embryogenesis. Further evaluation of the phas promoter by in vitro transcription analysis revealed the presence of multiple TATA-dependent transcription initiation start sites. The distance between TATA elements and transcription start sites was maintained in insertion and deletion mutants through the creation of novel initiation sites, indicating that positioning of the TATA elements rather than DNA sequence was the primary determinant of start site location. We conclude that, while dispensable for proper spatial distribution, the complex architecture of the phas promoter is required to ensure high levels of accurate phas transcription initiation in the developing embryo.

Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms.

The topological organization of a TATA binding protein-TFIIB-TFIIF-RNA polymerase II (RNAP II)-TFIIE-promoter complex was analyzed using site-specific protein-DNA photo-cross-linking of gel-purified complexes. The cross-linking results for the subunits of RNAP II were used to determine the path of promoter DNA against the structure of the enzyme. The results indicate that promoter DNA wraps around the mobile clamp of RNAP II. Cross-linking of TFIIF and TFIIE both upstream of the TATA element and downstream of the transcription start site suggests that both factors associate with the RNAP II mobile clamp. TFIIE alpha closely approaches promoter DNA at nucleotide -10, a position immediately upstream of the transcription bubble in the open complex. Increased stimulation of transcription initiation by TFIIE alpha is obtained when the DNA template is artificially premelted in the -11/-1 region, suggesting that TFIIE alpha facilitates open complex formation, possibly through its interaction with the upstream end of the partially opened transcription bubble. These results support the central roles of the mobile clamp of RNAP II and TFIIE in transcription initiation.

Genetic insights into the clinical diversity of beta thalassaemia.

Genetic insights into the clinical diversity of beta thalassaemia.