The "initiator" as a transcription control element

Genomic organization and functional analysis of the gene encoding the Krüppel-like transcription factor KLF6

The Krüppel-like transcription Factor 6 (KLF6) is regulated during cell proliferation and differentiation events like mammalian development and tissue regeneration, while its aberrant expression is associated with tumor formation. To investigate KLF6 transcriptional control, the genomic organization of human KLF6 together with its cis-regulatory region was analyzed. A high sequence homology of KLF6 regulatory regions was found in mammals, which in turn predicts a high degree of evolutionary conserved transcriptional mechanisms. A transcription start site was identified at the first nucleotide downstream of a potential initiator element. Also, the role of KLF6 regulatory regions was determined by transfection experiments. A minimal promoter region lacking a TATA-box yet containing an Initiator was identified and found to be active in all cells analyzed. In addition, two strong activating sequences were located between positions -407/-344 and -307/-207, where the latter contained Sp1 and CAAT-box sites. Furthermore, ectopic expression of Sp1 increased the transcriptional activity of the KLF6 promoter. In conclusion, our data revealed that KLF6 gene transcription is under control of a TATA-box independent initiation mechanism together with an evolutionary conserved array of positive cis-acting elements.

Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator

Downstream core promoter elements are an expanding class of regulatory sequences that add considerable diversity to the promoter architecture of RNA polymerase II-transcribed genes. We set out to determine the factors necessary for downstream promoter element (DPE)-dependent transcription and find that, against expectations, TFIID and the GTFs are not sufficient. Instead, the protein kinase CK2 and the coactivator PC4 establish DPE-specific transcription in an in vitro transcription system containing TFIID, Mediator, and the GTFs. Chromatin immunoprecipitation analyses using the DPE-dependent IRF-1 and TAF7 promoters demonstrated that CK2, and PC4 are present on these promoters in vivo. In contrast, neither PC4 nor CK2 were detected on the TAF1-dependent cyclin D promoter, which contains a DCE type of downstream element. Our findings also demonstrate that CK2 activity alters TFIID-dependent recognition of DCE sequences. These data establish that CK2 acts as a switch, converting the transcriptional machinery from functioning on one type of downstream element to another.

Spacing requirements for simultaneous recognition of the adenovirus major late promoter TATAAAAG box and initiator element

The distance between the TATAAAAG box and initiator element of the strong adenovirus major late promoter was systematically altered to determine the optimal spacing for simultaneous recognition of both elements. We find that the TATAAAAG element is strongly dominant over the initiator for specification of the start site. The wild type spacing of 23 base pairs between TATAAAAG and +1A is optimal for promoter strength and selective recognition of the A-start. Initiation is constrained to a window spaced 19-26 base pairs downstream of (-31)-TATAAAAG-(-24), and A-starts are favored over alternate starts only when spaced between 21 and 25 base pairs downstream of TATAAAAG. We report an expanded TATAAAAG and initiator promoter consensus for vertebrates and plants. Plant promoters of this class are (A-T)-rich and have an A-rich (non-template strand) core promoter sequence element downstream of +1A.

Cloning and characterization of the human CD200 promoter region

CD200 is a type I membrane glycoprotein which is expressed on a number of cell types uniquely relevant to the inflammatory and immune cascade; included in those are dendritic cells, endothelial cells and activated T cells. Previous studies have shown that CD200 plays an important role in prevention of graft rejection, autoimmune diseases and spontaneous abortion. The molecular mechanism(s) controlling expression of CD200 are yet to be defined. We report below the cloning and characterization of the 5'-flanking region of the human CD200 gene, including an exon1/intron1 boundary region and various transcriptional initiation sites. Serial deletion analysis revealed a 169 bp region responsible for constitutive expression of CD200. Positive regulatory domains (PRDs) were identified in the core promoter using linker-scanning mutagenesis. EMSA documented clear evidence for C/EBPbeta as being important in transcriptional regulation of CD200.

cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis

Promoters, including neither TATA box nor initiator, have been frequently found in testicular germ cell-specific genes in mice. These investigations imply that unique forms of the polymerase II transcription initiation machinery play a role in selective activation of germ cell-specific gene expression programs during spermatogenesis. However, there is little information about testis-specific core promoters, because useful germ cell culture system is not available. In this study, we characterize the regulatory region of the haploid-specific Oxct2b gene in detail by using in vivo transient transfection assay in combination with a transgenic approach, with electrophoretic mobility shift and chromatin immunoprecipitation assays. Expression studies using mutant constructs demonstrate that a 34 bp region, which extends from -49 to -16, acts as a core promoter in an orientation-dependent manner. This promoter region includes the cAMP-responsive element (CRE)-like sequence TGACGCAG, but contains no other motifs, such as a TATA box or initiator. The CRE-like element is indispensable for the core promoter activity, but not for activator in testicular germ cells, through the binding of a testis-specific CRE modulator transcription factor. These results indicate the presence of alternative transcriptional initiation machinery for cell-type-specific gene expression in testicular germ cells.

Cloning, sequencing, structural and molecular biological characterization of placental protein 20 (PP20)/human thiamin pyrophosphokinase (hTPK)

Full-length cDNAs of placental protein 20 (PP20) were cloned by screening a human placental cDNA library, which encode a 243 amino acid protein, identical to human thiamin pyrophosphokinase (hTPK) as confirmed by protein sequence analysis. Genomic alignment showed that the PP20/hTPK gene contains 9 exons. It is abundantly expressed in placenta, as numerous EST clones were identified. As thiamine metabolism deficiencies have been seen in placental infarcts previously, these indicate that PP20/hTPK may have a role in placental diseases. Analysis of the 1kb promoter region showed numerous putative transcription factor binding sites, which might be responsible for the ubiquitous PP20/hTPK expression. This may also be in accordance with the presence of the protein in tissues responsible for the regulation of the exquisite balance between cell division, differentiation and survival. TPK activity of the purified and recombinant protein was proved by mass spectrometry with electrospray ionization. By Western blot, PP20/hTPK was found in all human normal and tumorous adult and fetal tissues in nearly equal amounts, but not in sera. By immunohistochemical and immunofluorescent confocal imaging methods, diffuse labelling in the cytoplasm of the syncytiotrophoblasts and weak staining of the trophoblasts were observed, and the amount of PP20/hTPK decreased from the first trimester to the end of gestation. A 3D model of PP20/hTPK was computed (PDB No.: 1OLY) by homology modelling. A high degree of structural homology showed that the thiamin binding site was highly similar to that of the mouse enzyme, but highly different from the bacterial ones. Comparison of the catalytic centre sequences revealed differences, raising the possibility of designing new drugs which specifically inhibit bacterial and fungal enzymes without affecting PP20/hTPK and offering the possibility for safe antimicrobial therapy during pregnancy.

Transcription of macrophage IGF-I exon 1 is positively regulated by the 5′-untranslated region and negatively regulated by the 5′-flanking region

Idiopathic pulmonary fibrosis (IPF) is an insidious lung disease with no known cure or effective therapy. Macrophage-derived insulin-like growth factor-I (IGF-I) is thought to play a role in the pathogenesis of IPF; however, little is known about the control of IGF-I expression in macrophages. In this report we investigated the cis-regulatory elements that control basal expression using luciferase reporter constructs in RAW 264.7 macrophages. We show that the +95 to +329 region contains elements necessary to direct maximal promoter activity, whereas the +251 to +329 region contains the minimal promoter. Mapping transcriptional start sites for endogenous IGF-I in primary macrophages revealed that the major transcriptional start site is centered at +150, whereas the most 3′-transcriptional start site is centered at +255. Nuclear proteins from primary and RAW 264.7 macrophages bind specifically to the region required for maximal promoter activity (+134 to +173) and to the region required for minimal promoter activity (+267 to +299). Antibody supershift assays indicate that Sp3 bound to the +267 to +299 region. Moreover, mutation of the putative binding site reduced Sp3 binding in EMSAs and increased promoter activity in luciferase reporter gene assays. We also found that the regions from −1711 to −855 and −855 to −337 contain putative macrophage-specific suppressor elements that do not function in HeLa or COS-7 epithelial cell lines. These data support the view that macrophage IGF-I expression is positively regulated by elements located in the 5′-untranslated region and negatively regulated by elements in the 5′-flanking region of the IGF-I gene.

Characterization of promoter elements of the human HYAL-2 gene

The regulated catabolism of hyaluronan is critical to the function of many connective tissues. In cartilage, hyaluronan catabolism occurs locally by resident chondrocytes. To determine whether the expression of lysosomal hyaluronidases contributes to this regulation, the promoter elements associated with HYAL-2 gene expression were characterized. Human articular chondrocytes were found to express all three lysosomal hyaluronidases, HYAL-1, HYAL-2, and HYAL-3. HYAL-2 was the predominant gene product. Using 5' RACE (rapid amplification of cDNA ends) analysis, multiple transcription initiation sites were identified including a novel initiation site located within intron 1 of the gene expressed by human articular chondrocytes. The presence of multiple transcriptional initiation sites is a typical feature of TATA-less promoter regions, such as those of HYAL-2. Approximately 4000 bp of 5' flanking sequence of the HYAL-2 gene was characterized. Transient transfection of C-28/I2 cells with various 5' deletion constructs indicated that the region between +959 to +1158 (within intron 1) contains the basal promoter for HYAL-2 in chondrocytes. In addition, the region +224 to +958 contained a negative modulator that could control the basal expression level of HYAL-2. Treatment of human articular chondrocytes or C-28/I2 cells with various catabolic cytokines did not alter HYAL-2 mRNA expression, luciferase promoter expression, or hyaluronidase enzymatic activity. Thus, in chondrocytes HYAL-2 appears to be constitutively expressed and not inducibly regulated by catabolic agents. As such, it appears that the expression of lysosomal hyaluronidase participates little in the overall regulation of hyaluronan catabolism.

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE

A minimally addressed area in Saccharomyces cerevisiae research is the mapping of transcription start sites (TSS). Mapping of TSS in S.cerevisiae has the potential to contribute to our understanding of gene regulation, transcription, mRNA stability and aspects of RNA biology. Here, we use 5' SAGE to map 5' TSS in S.cerevisiae. Tags identifying the first 15-17 bases of the transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Each clone sequenced from this library identifies 10-20 TSS. We have identified 13,746 unique, unambiguous sequence tags from 2231 S.cerevisiae genes. TSS identified in this study are consistent with published results, with primer extension results described here, and are consistent with expectations based on previous work on transcription initiation. We have aligned the sequence flanking 4637 TSS to identify the consensus sequence A(A(rich))5NPyA(A/T)NN(A(rich))6, which confirms and expands the previous reported PyA(A/T)Pu consensus pattern. The TSS data allowed the identification of a previously unrecognized gene, uncovered errors in previous annotation, and identified potential regulatory RNAs and upstream open reading frames in 5'-untranslated region.

Stimulation of Myc transactivation by the TATA binding protein in promoter-reporter assays

Background

The c-Myc oncogenic transcription factor heterodimerizes with Max, binds specific DNA sites and regulates transcription. The role of Myc in transcriptional activation involves its binding to TRRAP and histone acetylases; however, Myc's ability to activate transcription in transient transfection assays is remarkably weak (2 to 5 fold) when compared to other transcription factors. Since a deletion Myc mutant D106-143 and a substitution mutant W135E that weakly binds TRRAP are still fully active in transient transfection reporter assays and the TATA binding protein (TBP) has been reported to directly bind Myc, we sought to determine the effect of TBP on Myc transactivation.

Results

We report here a potent stimulation of Myc transactivation by TBP, allowing up to 35-fold transactivation of reporter constructs. Although promoters with an initiator (InR) element briskly responded to Myc transactivation, the presence of an InR significantly diminished the response to increasing amounts of TBP. We surmise from these findings that promoters containing both TATA and InR elements may control Myc responsive genes that require brisk increased expression within a narrow window of Myc levels, independent of TBP. In contrast, promoters driven by the TATA element only, may also respond to modulation of TBP activity or levels.

Conclusion

Our observations not only demonstrate that TBP is limiting for Myc transactivation in transient transfection experiments, but they also suggest that the inclusion of TBP in Myc transactivation assays may further improve the characterization of c-Myc target genes.

Promoter features related to tissue specificity as measured by Shannon entropy

BACKGROUND

The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanisms.

RESULTS

We introduce a definition of tissue specificity based on Shannon entropy to rank human genes according to their overall tissue specificity and by their specificity to particular tissues. We apply our definition to microarray-based and expressed sequence tag (EST)-based expression data for human genes and use similar data for mouse genes to validate our results. We show that most genes show statistically significant tissue-dependent variations in expression level. We find that the most tissue-specific genes typically have a TATA box, no CpG island, and often code for extracellular proteins. As expected, CpG islands are found in most of the least tissue-specific genes, which often code for proteins located in the nucleus or mitochondrion. The class of genes with no CpG island or TATA box are the most common mid-specificity genes and commonly code for proteins located in a membrane. Sp1 was found to be a weak indicator of less-specific expression. YY1 binding sites, either as initiators or as downstream sites, were strongly associated with the least-specific genes.

CONCLUSIONS

We have begun to understand the components of promoters that distinguish tissue-specific from ubiquitous genes, to identify associations that can predict the broad class of gene expression from sequence data alone.

Evidence that the Dictyostelium STAT protein Dd-STATa plays a role in the differentiation of inner basal disc cells and identification of a promoter element essential for expression in these cells

Dd-STATa, a Dictyostelium homolog of the metazoan STAT (signal transducers and activators of transcription) proteins, is necessary in the slug for correct entry into culmination. Dd-STATa-null mutant fails to culminate and its phenotype correlates with the loss of a funnel-shaped core region, the pstAB core region, which expresses both the ecmA and ecmB genes. To understand how the differentiation of pstAB core cells is regulated, we identified an EST that is expressed in the core cells of normal slugs but down-regulated in the Dd-STATa-null mutant. This EST, SSK348, encodes a close homolog of the Dictyostelium acetyl-CoA synthetase (ACS). A promoter fragment of the cognate gene, aslA (acetyl-CoA synthetase-like A), was fused to a lacZ reporter and the expression pattern determined. As expected from the behavior of the endogenous aslA gene, the aslA::lacZ fusion gene is not expressed in Dd-STATa-null slugs. In parental cells, the aslA promoter is first activated in the funnel-shaped core cells located at the slug anterior, the "pstAB core." During culmination, the pstAB core cells move down, through the prespore cells, to form the inner part of the basal disc. As the spore mass climbs the stalk, the aslA gene comes to be expressed in cells of the upper and lower cups, structures that cradle the spore head. Deletion and point mutation analyses of the promoter identified an AT-rich sequence that is necessary for expression in the pstAB core. This acts in combination with repressor regions that prevent ectopic aslA expression in the pre-stalk regions of slugs and the stalks of culminants. Thus, this study confirms that Dd-STATa is necessary for the differentiation of pstAB core cells, by showing that it is needed for the activation of the aslA gene. It also identifies aslA promoter elements that are likely to be regulated, directly or indirectly, by Dd-STATa.

Identification of Transcriptional Regulatory Elements in Chemosensory Receptor Genes by Probabilistic Segmentation

Genome sequencing has allowed many gene regulatory elements to be identified through cross-species comparisons . However, the expression of genes in multigene families can diverge rapidly between related species . An alternative approach to characterizing multigene families utilizes the fact that genes within the group are likely to share aspects of their regulation. Here, we use a statistical approach, probabilistic segmentation , to identify sequences that are overrepresented in the regions upstream of C. elegans chemosensory receptor genes. Although each of these elements is present in only a subset of the genes, their distribution across and within the promoters of chemosensory receptor genes makes it possible to detect them. Many of the motifs show positional preference with respect to the translational start site and correspond to the binding sites of known families of transcription factors. We verified one motif, the E-box sequence WWYCACSTGYY, by showing that it directs expression of reporter genes to the ADL chemosensory neurons. Thus, probabilistic segmentation can be used to identify functional regulatory elements with no previous knowledge of gene expression or regulation. This approach may be of particular value for rapidly evolving genes in the immune system and the nervous system.

Murine glypican-4 gene structure and expression; Sp1 and Sp3 play a major role in glypican-4 expression in 3T3-F442A cells

In this report we describe the genomic organization of the mouse glypican-4 (Gpc4), an analysis of its promoter and its transcriptional regulation in the 3T3-F442A adipocyte cell line. The Gpc4 gene consists of nine exons separated by eight introns. A series of deletion mutants and 4391 bp of the 5'-flanking region were cloned into pGL3-BASIC upstream of the luciferase reporter gene and transfected into 3T3-F442A adipocytes. Analysis of a 4.3-kb DNA fragment at the 5'-flanking region of this gene revealed that the Gpc4 promoter is a TATA-less promoter with a large cluster of GC boxes. Competitive electrophoretic mobility shift and supershift assays identified a cluster of nine functional GC boxes binding Sp1 and Sp3 in this region. Transactivation experiments in insect cells showed that both Sp1 and Sp3 are major activators of the Gpc4 promoter. Gpc4 is expressed in adipocytes where its expression is highest in confluent 3T3-F442A adipoblasts and decreases dramatically as cells differentiate. Sp protein analyses demonstrated a major decrease in Sp3 protein in differentiated adipocytes as compared to undifferentiated adipoblasts. These experiments show that Gpc4 is developmentally regulated in 3T3-F442A adipocytes and suggest that Sp transcription factors play a significant role in the regulated expression of Gpc4.

The role of TFIID, the initiator element and a novel 5' TFIID binding site in the transcriptional control of the TATA-less human cytosolic phospholipase A2-alpha promoter

Human cytosolic phospholipase A2-alpha (cPLA2-alpha) is a critical enzyme in the liberation of arachidonic acid (AA) from cellular membranes and the subsequent formation of prostaglandins (PGs), leukotrienes (LTs), hydroxyeicosatetraenoic acids (HETEs) and platelet activating factor in many different cell types. Much is known of the effect of posttranslational phosphorylation and calcium binding events on the enzymatic activity of cPLA2-alpha, but to date little is known about its specific transcriptional control. Through the use of reporter gene constructs and eletrophoretic mobility shift assays (EMSAs), this study determined the minimal promoter required for basal transcriptional activity of the human cPLA2-alpha promoter to include base pairs -40 through the transcription start site (TSS). In addition, it confirms the importance of an initiator (Inr) element at the TSS by deletion reporter gene analysis, and further identifies bases -3 (C) and -2 (T) as critical bases in the Inr function by mutation reporter gene analysis. Finally, this study describes a novel AAGGAG motif at -30 to -35 which is bound by TATA-box binding protein (TBP) and is critical for basal transcriptional activity.

Identification of polymorphisms in the promoter region of the human NRF2 gene

Transcription factor Nrf2 regulates the basal and inducible expression of detoxifying and antioxidant genes. Recent studies using nrf2-null mice suggest that Nrf2 dysfunction might be involved in the pathogenesis of human diseases. To gain insight into the relationship between impairment in the NRF2 gene and human diseases, we attempted to identify polymorphisms in the human NRF2 gene. We determined the structure of the NRF2 gene and found three single nucleotide polymorphisms and one triplet repeat polymorphism in its regulatory region. These results provide a molecular basis for the genetic analysis of the NRF2 gene. The frequency of each polymorphism was examined in two groups of patients with systemic lupus erythematosus and chronic obstructive pulmonary disease. This study did not reveal a close connection between the risk of these diseases and the polymorphisms. However, available lines of evidence suggest the importance of examining the link between NRF2 polymorphisms and other oxidative stress-related diseases.

Multiple novel transcription initiation sites for NRG1

The large neuregulin 1 gene (NRG1) has been mapped to a 1.125 Mb region on chromosome 8p11-21. Three major forms of NRG1 (types I-III), all with distinct amino-termini encoded by unique 5'-exons, have been described. We report here the discovery of nine novel NRG1 exons, including six alternative 5'-exons, increasing the number of potential promoters in NRG1 from three to nine. The novel transcripts of NRG1 described here use the novel 5'-exons which are either coding or non-coding. The functional relevance of the predicted proteins they encode has not been evaluated. Three of the novel 5'-exons are well conserved in syntenic rat and mouse sequences; they encode proteins with novel amino-termini, here termed types IV-VI. NRG1 plays a central role in neural development and is most likely involved in regulation of synaptic plasticity, or how the brain responds or adapts to the environment. The unusually complex gene structure may facilitate spatial and temporal regulation of NRG1 expression, fine-tune NRG1 protein function at different stages during development of the nervous system, and adapt responses to the environment in the adult brain.

Core promoter structure in the oomycete Phytophthora infestans

We have investigated the core promoter structure of the oomycete Phytophthora infestans. The transcriptional start sites (TSS) of three previously characterized P. infestans genes, Piexo1, Piexo3, and Piendo1, were determined by primer extension analyses. The TSS regions were homologous to a previously identified 16-nucleotide (nt) core sequence that overlaps the TSS in most oomycete genes. The core promoter regions of Piexo1 and Piendo1 were investigated by using a transient protoplast expression assay and the reporter gene beta-glucuronidase. Mutational analyses of the promoters of Piexo1 and Piendo1 showed that there is a putative core promoter element encompassing the TSS (-2 to +5) that has high sequence and functional homology to a known core promoter element present in other eukaryotes, the initiator element (Inr). Downstream and flanking the Inr is a highly conserved oomycete promoter region (+7 to +15), hereafter referred to as FPR (flanking promoter region), which is also important for promoter function. The importance of the 19-nt core promoter region (Inr and FPR) in Piexo1 and Piendo1 was further investigated through electrophoretic mobility shift assays (EMSA). The EMSA studies showed that (i) both core promoters were able to specifically bind a protein or protein complex in a P. infestans whole-cell protein extract and (ii) the same mutations that reduced binding of the EMSA complex also reduced beta-glucuronidase (GUS) levels in transient expression assays. The consistency of results obtained using two different assays (GUS transient assays [in vivo] and EMSA studies [in vitro]) supports a convergence of inference about the relative importance of specific nucleotides within the 19-nt core promoter region.

Isolation and characterization of the 5'-flanking region of the growth hormone secretagogue receptor gene from black seabream Acanthopagrus schlegeli

Ghrelin, the recently discovered endogenous ligand for growth hormone secretagogue receptor (GHSR), is widely expressed and involved in regulating diverse physiological functions in addition to stimulation of growth hormone (GH) secretion. Previous studies have demonstrated the functional significance of the ghrelin/GHSR system, yet the transcriptional regulation of the ghrelin and GHSR genes are poorly understood. We have recently cloned the GHSR cDNA from the pituitary of black seabream Acanthopagrus schlegeli. In the present study, we have isolated a 2.1 kb 5'-flanking region of the GHSR gene from the same species and have investigated, for the first time, the transcriptional regulation of GHSR from a non-human species. The 5'-flanking region of the seabream GHSR gene was found to contain a number of unique putative transcription factor-binding sites different from the human counterpart. Functional characterization of the 5'-flanking region in several cell lines indicates that the region between -1423 and +19 contains sufficient elements for promoter function. Moreover, progressive 3'-deletion analysis suggests the presence of negative regulatory element(s) and essential cis-acting element(s) at -514/+19 and -928/-515, respectively. Furthermore, we have shown that the promoter activity is significantly enhanced by a GHSR agonist in a cell line stably expressing the seabream GHSR, and this stimulatory effect could be completely blocked by a GHSR antagonist. These results suggest that homologous up-regulation plays an important role in the transcriptional control of the teleostean GHSR gene. This is in big contrast to the human situation in which a homologous down-regulation of the GHSR gene transcription by its own ligand has been previously demonstrated.

The MTE, a new core promoter element for transcription by RNA polymerase II

The core promoter is the ultimate target of the vast network of regulatory factors that contribute to the initiation of transcription by RNA polymerase II. Here we describe the MTE (motif ten element), a new core promoter element that appears to be conserved from Drosophila to humans. The MTE promotes transcription by RNA polymerase II when it is located precisely at positions +18 to +27 relative to A(+1) in the initiator (Inr) element. MTE sequences from +18 to +22 relative to A(+1) are important for basal transcription, and a region from +18 to +27 is sufficient to confer MTE activity to heterologous core promoters. The MTE requires the Inr, but functions independently of the TATA-box and DPE. Notably, the loss of transcriptional activity upon mutation of a TATA-box or DPE can be compensated by the addition of an MTE. In addition, the MTE exhibits strong synergism with the TATA-box as well as the DPE. These findings indicate that the MTE is a novel downstream core promoter element that is important for transcription by RNA polymerase II.

Zebrafish cellular nucleic acid-binding protein: gene structure and developmental behaviour

Here we analyse the structural organisation and expression of the zebrafish cellular nucleic acid-binding protein (zCNBP) gene and protein. The gene is organised in five exons and four introns. A noteworthy feature of the gene is the absence of a predicted promoter region. The coding region encodes a 163-amino acid polypeptide with the highly conserved general structural organisation of seven CCHC Zn knuckle domains and an RGG box between the first and the second Zn knuckles. Although theoretical alternative splicing is possible, only one form of zCNBP is actually detected. This form is able to bind to single-stranded DNA and RNA probes in vitro. The analysis of zCNBP developmental expression shows a high amount of CNBP-mRNA in ovary and during the first developmental stages. CNBP-mRNA levels decrease while early development progresses until the midblastula transition (MBT) stage and increases again thereafter. The protein is localised in the cytoplasm of blastomeres whereas it is mainly nuclear in developmental stages after the MBT. These findings suggest that CNBP is a strikingly conserved single-stranded nucleic acid-binding protein which might interact with maternal mRNA during its storage in the embryo cell cytoplasm. It becomes nuclear once MBT takes place possibly in order to modulate zygotic transcription and/or to associate with newly synthesised transcripts.

Characterization of a novel postacrosomal perinuclear theca-specific protein, CYPT1

The perinuclear theca (PT) is a unique cytoskeletal structure that surrounds the nucleus of the sperm. The posterior acrosome segment of the PT (postacrosomal PT) is thought to play roles in shaping the nucleus during differentiation of the spermatid and in activating the oocyte during fertilization. We isolated a cDNA clone that encoded a novel haploid germ cell-specific cysteine-rich perinuclear theca protein, CYPT1. The transcripts were expressed exclusively in testicular germ cells after meiotic division. Sequence analysis revealed that CYPT1 comprised 168 amino acids and that the N-terminal was rich in basic amino acids, including cysteine clusters. Immunohistochemical and biochemical analyses localized CYPT1 to the postacrosomal PT of elongated spermatids and mature sperm. The cypt1 had three paralogs that were expressed in adult testis. A comparison of genomic structure suggested that two of the three cypt1 paralogs were generated by gene triplication on the X chromosome, while one paralog was retrotransposed to an autosome. Interestingly, the 5'-flanking regions of these genes were highly homologous with the promoter region of the spermatid-specific gene Zfy-2. CYPT1 and the proteins of the paralogous genes constitute a novel, basic cysteine-rich sperm protein family that may contribute to the function of the postacrosomal PT during nuclear shaping.

Transcriptional regulation of the mouse gene encoding the alpha-4 subunit of the GABAA receptor

The gamma-aminobutyric acid type A receptors (GABAA-Rs) mediate fast inhibitory synaptic transmission in the brain. The alpha4 subunit of the GABAA-R confers distinct pharmacological properties on the receptor and its expression pattern exhibits plasticity in response to physiological and pharmacological stimuli, including withdrawal from progesterone and alcohol. We have analyzed the promoter region of the mouse GABRA4 gene that encodes the alpha4 subunit and found that the promoter has multiple transcriptional initiation sites and lacks a TATA box. The minimal promoter for GABRA4 spans the region between -444 to -19 bp relative to the coding ATG and shows high activity in cultured mouse cortical neurons. Both Sp3 and Sp4 transcription factors can interact with the two Sp1 binding sites within the minimal promoter and are critical for maximal activity of the promoter in neurons.

Inflammatory mediators and growth factors in obstructive renal injury

Obstruction of the upper urinary tract poses a significant clinical challenge to the urologist, and the cascade of renal cellular and molecular events triggered by upper urinary tract obstruction result in a progressive, and eventually permanent, loss in renal function. These pathological changes include the development of renal fibrosis, tubular atrophy, interstitial inflammation, and apoptotic renal cell death. A myriad of cytokines and growth factors have been identified as major contributors to obstruction-induced renal fibrosis and apoptotic cell death, including transforming growth factor-beta1, angiotensin II, nuclear factor-kappaB, and tumor necrosis factor-alpha. This review examines the role of these mediators in obstruction-induced renal injury.

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.

Characterization of the human renal Na(+)-sulphate cotransporter gene ( NAS1) promoter

Sulphate (SO(4)(2-)) plays an essential role during growth, development, and cellular metabolism. Recently, we have isolated the human renal Na(+)-SO(4)(2-) cotransporter (hNaSi-1) that is implicated in the regulation of serum SO(4)(2-) levels. To gain an insight into hNaSi-1 regulation, our aims were to clone and characterize functionally the hNaSi-1 gene ( NAS1) promoter. We PCR-amplified 3742 bp of the NAS1 5'-flanking region, which is 64% AT-rich and contains numerous putative cis-acting elements. The NAS1 transcription start site was mapped to 25 bp upstream from the translation start site. NAS1 promoter truncations fused to luciferase gene constructs transfected into renal LLC-PK1, MDCK and OK cells allowed us to establish that the first 169 bp of the NAS1 promoter are sufficient for basal transcription. Furthermore, the NAS1 promoter conferred responsiveness to the polycyclic aromatic hydrocarbon 3-methylcholanthrene (3-MC), but not to thyroid hormone (T(3)) or vitamin D [1,25-(OH)(2)D(3)]. Site-directed mutagenesis of the NAS1 promoter identified a functional xenobiotic response element at -2,052, which conferred 3-MC responsiveness. The human NAS1 gene promoter is not responsive to Vitamin D or T(3), unlike the mouse Nas1 promoter with which it shares approximately 40% sequence similarity, but is transactivated by 3-MC, suggesting that the control of renal SO(4)(2-) reabsorption via the regulation of NAS1 transcription may be important for maintaining the sulphation potential for kidney polycyclic aromatic hydrocarbon metabolism.

Differential cellular requirements for activation of herpes simplex virus type 1 early (tk) and late (gC) promoters by ICP4

The herpes simplex virus type 1 immediate-early protein, ICP4, activates the transcription of viral early and late genes and is essential for viral growth. It has been shown to bind DNA and interact with components of the general transcription machinery to activate or repress viral transcription, depending upon promoter context. Since early and late gene promoters have different architectures and cellular metabolism may be very different at early and late times after infection, the cellular requirements for ICP4-mediated activation of early and late genes may differ. This hypothesis was tested using tk and gC as representative early and late promoters, respectively. Nuclear extracts and phosphocellulose column fractions derived from nuclear extracts were able to reconstitute basal and ICP4-activated transcription of both promoters in vitro. When examining the contribution of the general transcription factors on the ability of ICP4 to activate transcription, the fraction containing the general transcription factor TFIIA was not essential for ICP4 activation of the gC promoter, but it was required for efficient activation of the tk promoter. The addition of recombinant TFIIA restored the ability of ICP4 to efficiently activate the tk promoter, but it had no net effect on activation of the gC promoter. The dispensability of TFIIA for ICP4 activation of the gC promoter required an intact INR element. In addition, microarray and Northern blot analysis indicated that TFIIA abundance may be reduced at late times of infection. This decrease in TFIIA expression during infection and its dispensability for activation of late but not early genes suggest one of possibly many mechanisms for the transition from viral early to late gene expression.

Terminal deoxynucleotidyl transferase is down-regulated by AP-1-like regulatory elements in human lymphoid cells

Terminal deoxynucleotidyl transferase (TdT) is a template-independent DNA polymerase that catalyses the incorporation of deoxyribonucleotides into the 3'-hydroxyl end of DNA templates and is thought to increase junctional diversity of antigen receptor genes. TdT is expressed only on immature lymphocytes and acute lymphoblastic leukaemia cells and its transcriptional expression is tightly regulated. We had previously found that protein kinase C (PKC) activation down-regulates TdT expression. PKC-activation induces the synthesis of the Fos and Jun proteins, known as the major components of activation protein 1 (AP-1) transcriptional factor implicated in transcriptional control. Here we report the identification of several DNA-protein interactions within the TdT promoter region in non-TdT expressing human cells. Sequence analysis revealed the presence of a putative AP-1-like DNA-binding site, suggesting that AP-1 may play a relevant role in TdT transcriptional regulation. Using a different source of nuclear extracts and the AP-1-TdT motif as a probe we identified several DNA-protein retarded complexes in electrophoretic mobility shift assays. Super-band shifting analysis using an antibody against c-Jun protein confirmed that the main interaction is produced by a nuclear factor that belongs to the AP-1 family transcription factors. Our findings suggest that the TdT gene expression is down-regulated, at least in part, through AP-1-like transcription factors.

Mouse prostasin gene structure, promoter analysis, and restricted expression in lung and kidney

Human prostasin is a membrane-anchored serine peptidase hypothesized to regulate lung epithelial sodium transport. It belongs to a unique family of genes on chromosome 16p11.2/13.3. Here we describe genomic cloning, promoter analysis, and expression of prostasin's mouse ortholog. The 4.3-kb mouse prostasin gene (prss8) has a six-exon organization identical to human prostasin. Prss8 spans two signal tagged-sites localized to chromosome 7. Multiple mRNA transcripts arise from two consensus initiator elements of a TATA-less promoter and an alternatively spliced, 5' untranslated region intron. Reporter assay establishes that the initiator elements and a GC-rich domain comprise the core promoter and identifies 5' flanking regions with strong enhancer and repressor activity. The 3' untranslated region overlaps the 3' untranslated region of the Myst1 gene oriented tail-to-tail at this locus. Prss8 is highly transcribed in pancreas, kidney, submaxillary gland, lung, thyroid, prostate, and epididymis, and is developmentally regulated. Using selective riboprobes and antibodies to mouse prostasin, we localized its expression to lung airway epithelial and alveolar type II cells and kidney cortical tubule epithelium. Mouse prostasin highly resembles its human ortholog in gene organization and tissue specificity, including strong expression in pulmonary epithelium, suggesting that mice will be useful for probing prostasin's functions in vivo.

Genomic organization and promoter analysis of the gene encoding the mouse chemoattractant-like receptor, CMKLR1

Chemoattractant-like receptor 1 (CMKLR1) is a functionally unknown ("orphan") G-protein coupled receptor. It has been implicated in osseous and cartilage development, and it also has a pathophysiological role as one of the minor coreceptors involved in human immunodeficiency virus type I (HIV-1)/simian immunodeficiency virus (SIV) infection of CD4(+) immune cells. Here we report the cloning of the mouse cmklr1 gene, the characterization of its genomic structure for comparison with the human gene, and the mapping and functional analysis of its 5' flanking sequence. The gene was found to contain three exons intercepted by one larger and one smaller intron. The overall structure resembles the human orthologue. The promoter lacks classical TATA and CCAAT boxes but contains several GC-rich regions as well as AP-4 elements, C/EBP motifs, and GATA-1 and GATA-2 binding sites. Promoter function was analyzed in mouse neuroblastoma (NB4 1A3) cells, endogenously expressing CMKLR1, as well as in mouse embryonic fibroblastic (3T3 clone A31) cells not expressing CMKLR1. 5' Deletion analysis and luciferase reporter gene assays of the promoter indicated that a 280-bp sequence adjacent to the transcription start site (established through 5'-RACE) is essential for initiating transcription. Within this region it was possible to identify four potential Sp1-binding sites that may be active in the transcription of the gene. Thus, we show that the mcmklr1 gene has several conserved features in common with its human counterpart, which suggests that they are regulated in a similar manner. The promoter does not seem to be tissue specific but other elements or enhancers may be missing. The results provide a necessary basis for further studies of the gene regulation and function of this chemoattractant-like receptor and will be useful when manipulating the gene in the development of transgenic animal models.

Genomic structure and promoter characterization of the human Sprouty4 gene, a novel regulator of lung morphogenesis

The expression of Sprouty4 (Spry4), an intracellular FGF receptor antagonist, shows a temporally and spatially restricted pattern in embryonic lung and is induced by ERK signaling. To clarify the molecular mechanisms regulating Spry4 transcription, the genomic structure of the human Sprouty4 (hSpry4) gene was first determined by using the GenomeWalker kit. The hSpry4 gene spans > 14 kb and is organized in three exons and two introns. Multiple transcription start sites were subsequently mapped by 5'-rapid amplification of cDNA ends. Analysis of up to 4 kb of sequence in the 5'-flanking region of the gene showed the presence of multiple potential transcription factor binding sites but no TATA or CAAT boxes. Transient transfection using luciferase reporter gene constructs with progressive deletions of the hSpry4 5'-flanking region revealed that the core promoter activity is located within the proximal 0.4-kb region, whereas the minimal ERK-inducible promoter activity is between -69 and -31. Homology analysis further showed that the core promoter region of the hSpry4 gene exhibits significant similarity to the 5'-flanking region of the mouse gene.

Functional analysis of the human Sprouty2 gene promoter

Sprouty2 plays a key role in negatively modulating the fibroblast growth factor signaling pathway, which is required for early branching events in embryonic development. The expression of the murine Sprouty2 gene shows a temporally and spatially restricted pattern in developing lung. In order to clarify the molecular mechanisms governing the transcription of the Sprouty2 gene, we first characterized the genomic organization of the human Sprouty2 (hSpry2) gene and mapped its transcription start sites by 5'-rapid amplification of cDNA ends. Subsequently, a 4-kb sequence from the 5'-flanking region of the gene was cloned and determined to contain promoter activity. Detailed truncation analysis of the hSpry2 promoter revealed the presence of context-specific suppressor activity in the distal upstream region. More importantly, we demonstrated that all the elements necessary to achieve strong basal transcription activity were located within the proximal 0.4-kb region. Sequence analysis revealed that this functionally important proximal region contains neither TATA nor CAAT box but an initiator element around the transcription start site. Several cis-acting elements (including AP2, CREB, SP1 and Ets-1) were found to be present in the proximal region, and their interactions with specific nuclear proteins were confirmed by electrophoretic mobility shift assays. To our knowledge, this is the first promoter study of any mammalian Sprouty gene. We propose that the high-level basal expression of hSpry2 is controlled by multiple transcription factors binding to its proximal promoter.

Structural Basis of Transcription: An RNA Polymerase II-TFIIB Cocrystal at 4.5 Angstroms

The structure of the general transcription factor IIB (TFIIB) in a complex with RNA polymerase II reveals three features crucial for transcription initiation: an N-terminal zinc ribbon domain of TFIIB that contacts the "dock" domain of the polymerase, near the path of RNA exit from a transcribing enzyme; a "finger" domain of TFIIB that is inserted into the polymerase active center; and a C-terminal domain, whose interaction with both the polymerase and with a TATA box-binding protein (TBP)-promoter DNA complex orients the DNA for unwinding and transcription. TFIIB stabilizes an early initiation complex, containing an incomplete RNA-DNA hybrid region. It may interact with the template strand, which sets the location of the transcription start site, and may interfere with RNA exit, which leads to abortive initiation or promoter escape. The trajectory of promoter DNA determined by the C-terminal domain of TFIIB traverses sites of interaction with TFIIE, TFIIF, and TFIIH, serving to define their roles in the transcription initiation process.

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.

Structural basis of core promoter recognition in a primitive eukaryote

Transcription start site selection in eukaryotes is mediated through combinations of the TATA, initiator (Inr), and downstream promoter elements (DPE). In Trichomonas vaginalis, a parabasalian flagellate thought to represent an ancient eukaryote lineage, the Inr appears to be solely responsible for start site selection and is recognized by the initiator binding protein 39 kDa (IBP39). IBP39 contains an N-terminal Inr binding domain (IBD) connected via a flexible linker to a C-terminal domain (C domain). Here we present crystal structures of the apoIBD and IBD-Inr complexes and the C domain. The IBD structures reveal a winged-helix motif with prokaryotic and eukaryotic features and a scaffold similar to that of ETS-family proteins. The C domain structure and biochemical studies indicate that it interacts with the T. vaginalis RNAP II large subunit C-terminal domain. These data suggest that binding of IBP39 to the Inr directly recruits RNAP II and in this way initiates transcription.

The clustered olfactory receptor gene family 262: genomic organization, promotor elements, and interacting transcription factors

For six mouse olfactory receptor genes from family 262 which are expressed in clustered populations of olfactory sensory neurons, the genomic as well as cDNA structures were deciphered. All genes contained several exons which in some cases were alternatively spliced. Immediately upstream of the transcription start sites, sequence motif blocks were identified that are highly conserved among olfactory receptor (OR) genes which are expressed in clustered neuronal populations. By means of electrophoretic mobility shift assays, it was demonstrated that segments of the motif block region interact with proteins extracted from nuclear fractions of the olfactory epithelium. Yeast one-hybrid screenings of an olfactory cDNA library led to the identification of a set of transcription factors that specifically bind to particular elements of the motif block region. The identified factors can be categorized into two types: One group is known to be involved in transcriptional initiation, and the second group represents factors involved in pattern formations. The identified components may contribute to govern the precise topographic expression pattern of olfactory receptor genes.

Promoter analysis of the human translation termination factor 1 gene

The human translation termination factor 1 (ETF1) gene encodes a class-1 release factor, eRF1, which catalyses termination of protein synthesis at all three stop codons. In this report, we describe the functional organization of the 5'-region of the gene. Primer extension and ribonuclease protection mapping revealed three transcription start sites clustered within approximately 10 bp. DNase I-hypersensitive site analysis identified five hypersensitive sites, one of which was located downstream of the initiation start sites. We used transient expression assays to define the 5'-regulating regions and in vivo and in vitro footprinting analysis to identify potential cis-acting regulatory elements. A basal promoter, spanning nucleotides -210/+117, contained no TATA box but a putative initiator element (Inr) and multiple potential Sp1/Sp3 binding sites, and thus displayed some of the features of a housekeeping gene. An additional upstream promoter containing positive and negative regulatory elements also regulated ETF1 gene expression. Real-time quantitative RT-PCR analysis showed tissue-specific expression of ETF1 transcripts in mouse tissues. Our results are suggestive of a constitutive expression of the human ETF1 gene but with possible cell- and tissue-specific regulation.

Template switches during plus-strand DNA synthesis of duck hepatitis B virus are influenced by the base composition of the minus-strand terminal redundancy

Two template switches are necessary during plus-strand DNA synthesis of the relaxed circular (RC) form of the hepadnavirus genome. The 3' end of the minus-strand DNA makes important contributions to both of these template switches. It acts as the donor site for the first template switch, called primer translocation, and subsequently acts as the acceptor site for the second template switch, termed circularization. Circularization involves transfer of the nascent 3' end of the plus strand from the 5' end of the minus-strand DNA to the 3' end, where further elongation can lead to production of RC DNA. In duck hepatitis B virus (DHBV), a small terminal redundancy (5'r and 3'r) on the ends of the minus-strand DNA has been shown to be important, but not sufficient, for circularization. We investigated what contribution, if any, the base composition of the terminal redundancy made to the circularization process. Using a genetic approach, we found a strong positive correlation between the fraction of A and T residues within the terminal redundancy and the efficiency of the circularization process in those variants. Additionally, we found that the level of in situ priming increases, at the expense of primer translocation, as the fraction of A and T residues in the 3'r decreases. Thus, a terminal redundancy rich in A and T residues is important for both plus-strand template switches in DHBV.

The RNA polymerase II core promoter

The events leading to transcription of eukaryotic protein-coding genes culminate in the positioning of RNA polymerase II at the correct initiation site. The core promoter, which can extend ~35 bp upstream and/or downstream of this site, plays a central role in regulating initiation. Specific DNA elements within the core promoter bind the factors that nucleate the assembly of a functional preinitiation complex and integrate stimulatory and repressive signals from factors bound at distal sites. Although core promoter structure was originally thought to be invariant, a remarkable degree of diversity has become apparent. This article reviews the structural and functional diversity of the RNA polymerase II core promoter.

The rise of DNA methylation and the importance of chromatin on multidrug resistance in cancer

In recent years, the different classes of drugs and regimens used clinically have provided an improvement in tumour management. However, treatment is often palliative for the majority of cancer patients. Transformed cells respond poorly to chemotherapy mainly due to the development of the multidrug resistance (MDR) phenotype. Response to treatment does not generally result in complete remission and disease cure is uncommon for patients presenting with advanced stage cancer. Successful treatment of cancer requires a clearer understanding of chemotherapeutic resistance. Here, we examine what is known of one of the most extensively studied mechanisms of cellular drug resistance. The human multidrug resistance gene 1 (MDR1) is associated with expression of p-glycoprotein (Pgp). A transmembrane protein, Pgp acts as an efflux pump and reduces intracellular drug levels and thus its effectiveness as an antitumor agent. The precise mechanism of transcriptional regulation has been unclear due to the complex regulatory nature of the gene. It has become increasingly apparent that trans-activation or genetic amplification is by no means the only mechanism of activation. Consequently, alternative pathways have received more attention in the area of epigenetics to help explain transcriptional competence at a higher level of organization. The goal of this article is to highlight important findings in the field of methylation and explain how they impinge on MDR1 gene regulation. In this review, we cover the current information and postulate that epigenetic modification of MDR1 chromatin influences gene transcription in leukaemia. Finally, we explore transcriptional regulation and highlight recent progress with engineered ZFP's (zinc finger proteins).

The murine G+C-rich promoter binding protein mGPBP is required for promoter-specific transcription

The archetypal TATA-box deficient G+C-rich promoter of the murine adenosine deaminase gene (Ada) requires a 48-bp minimal self-sufficient promoter element (MSPE) for function. This MSPE was used to isolate a novel full-length cDNA clone that encodes a 66-kDa murine G+C-rich promoter binding protein (mGPBP). The mGPBP mRNAs are ubiquitously expressed as either 3.0- or 3.5-kb forms differing in 3' polyadenylation site usage. Purified recombinant mGPBP, in the absence of any other mammalian cofactors, binds specifically to both the murine Ada gene promoter's MSPE and the nonhomologous human Topo IIalpha gene's G+C-rich promoter. In situ binding assays, immunoprecipitation, and Western blot analyses demonstrated that mGPBP is a nuclear factor that can form complexes with TATA-binding protein, TFIIB, TFIIF, RNA polymerase II, and P300/CBP both in vitro and in intact cells. In cotransfection assays, increased mGPBP expression transactivated the murine Ada gene's promoter. Sequestering of GPBP present in HeLa cell nuclear extract by immunoabsorption completely and reversibly suppressed extract-dependent in vitro transcription from the murine Ada gene's G+C-rich promoter. However, transcription from the human Topo IIalpha gene's TATA box-containing G+C-rich promoter was only partially suppressed and the adenovirus major late gene's classical TATA box-dependent promoter is totally unaffected under identical assay conditions. These results implicate GPBP as a requisite G+C-rich promoter-specific transcription factor and provide a mechanistic basis for distinguishing transcription initiated at a TATA box-deficient G+C-rich promoter from that initiated at a TATA box-dependent promoter.

Expression of nonclassical MHC class Ib genes: comparison of regulatory elements

Peptide binding proteins of the major histocompatibility complex consist of the "classical" class Ia and "nonclassical" class Ib genes. The gene organization and structure/function relationship of the various exons comprising class I proteins are very similar among the class Ia and class Ib genes. Although the tissue-specific patterns of expression of these two gene families are overlapping, many class Ib genes are distinguished by relative low abundance and/or limited tissue distribution. Further, many of the class Ib genes serve specialized roles in immune responses. Given that the coding sequences of the class Ia and class Ib genes are highly homologous we sought to examine the promoter regions of the various class Ib genes by comparison to the well characterized promoter elements regulating expression of the class Ia genes. This analysis revealed a surprising complexity of promoter structures among all class I genes and few instances of conservation of class Ia promoter regulatory elements among the class Ib genes.

Cloning and characterization of the human UDP-glucuronosyltransferase 1A8, 1A9, and 1A10 gene promoters: differential regulation through an interior-like region

The human UDP-glucuronosyltransferases, UGT1A8, 1A9, and 1A10, are closely related in sequence and have a major role in the elimination of lipophilic chemicals by glucuronidation. UGT1A8 and 1A10 are expressed exclusively in the gastrointestinal tract, whereas UGT1A9 is expressed mainly in the liver and kidneys. To determine the factors contributing to the extrahepatic expression of these UDP-glucuronosyltransferases, we have cloned and characterized the promoters of the UGT1A8, 1A9, and 1A10 genes and studied their regulation in the colon cell line, Caco2. Their transcription start sites were mapped, and a functional overlapping Sp1/initiator-like site was identified which strongly contributed to UGT1A8 and 1A10 promoter activity. The high promoter activity of UGT1A8 and 1A10 correlated with the binding of nuclear proteins (complex B) to this region. Two-bp differences in the corresponding site in the UGT1A9 promoter prevented the binding of complex B and reduced promoter activity. Although Sp1 was able to bind to the Sp1/initiator-like site, its binding was dispensable for promoter activity. However, the binding of Sp1 to a second Sp1 site 30 bp 5' to the Sp1/initiator-like site greatly enhanced the activity of the UGT1A8 and 1A10 promoters. These results provide evidence that the UGT1A8, 1A9, and 1A10 genes are differentially regulated through an initiator element in their 5'-flanking regions.

Architecture and transcriptional activity of the initiator element of the TATA-less RPL21 gene

The nuclear RPL21 gene coding for the plastid ribosomal protein L21 is a TATA-less gene that is overexpressed in a leaf-dependent manner by the specific usage of a strong initiator called P1. We have previously shown that the RPL21 core promoter spanning from -23 to +104 relative to P1 start site activates transcription in the same manner as does the full promoter. Here, we present results of experiments aimed at deciphering the RPL21 core promoter architecture. Results of transient expression using various 5' deletions of the core promoter fused to a chloramphenicol acetyl transferase (CAT) reporter gene show that 34 bp encompassing the P1 initiation site (from -23 to +11) are required for full transcription activation. Gel-shift analysis shows that five DNA/protein complexes (C1-C5) are formed on this 34-bp fragment with protein extracts from green tissues. C1 is the major complex present during seed germination. The other complexes are present in young leaf tissues suggesting a role in transcription activation. Linker scanning mutagenesis experiments show that the five complexes form two independent groups: I (C1-C3) and II (C4 and C5), with a common binding site located on P1. Using transgenic plants, we show that three nucleotides encompassing the P1 start site and three trinucleotides necessary for group I binding are determinant for RPL21 activation. These results identify an unusually compact core structure, which is centred on P1 initiation site and is responsible for transcription activation. A model of the architecture of this region is presented.

Identification of upstream cis-acting regulatory elements controlling lineage-specific expression of the mouse NK cell activation receptor, NKR-P1C

Mouse NKR-P1C (NK1.1) is a homodimeric type II transmembrane protein expressed on natural killer (NK) cells, NKT cells, and on CD117+ progenitor thymocytes capable of giving rise to cells of the T and NK lineages. Although its physiological ligands remain unknown, NKR-P1C engagement with a monoclonal antibody (mAb) leads to interferon-gamma (IFN-gamma) production and the directed release of cytotoxic granules from NK cells. We have cloned and sequenced a approximately 10-kb genomic fragment corresponding to the 5'-flanking region of the C57Bl/6 mouse NKR-P1C gene. A transcriptional initiation site has been mapped in NK cells and an NK1.1+ T cell line by primer extension and rapid amplification of 5'-cDNA ends (5'-RACE) techniques. Although the 5'-flanking region of NKR-P1C is TATA-less, we have identified an initiator region and a downstream promoter element, which together constitute the principal minimal functional promoter. Computational analysis of the 10-kb 5'-flanking region revealed potential regulatory factor binding sites. DNaseI hypersensitivity assays identified a single hypersensitive site (HS) about a 9-kb upstream of the transcriptional initiation site. This site, termed HS1, was able to act as a transcriptional enhancer element in an NK cell line, while minimally affecting transcription in non-NK cell lines. Moreover, the HS1 element was shown to function as a promoter, with a transcript detected only in fetal NK1.1+ cells. An additional promoter and two non-coding exons were also characterized. These results identify the minimal upstream cis-acting elements, and point to a complex regulatory mechanism involved in the lineage-specific control of NKR-P1C expression in NK lymphocytes.