Perspectives on the RNA polymerase II core promoter

Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis

Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.

Transcription factor IID parks and drives preinitiation complexes at sharp or broad promoters

Core promoters are sites where transcriptional regulatory inputs of a gene are integrated to direct the assembly of the preinitiation complex (PIC) and RNA polymerase II (Pol II) transcription output. Until now, core promoter functions have been investigated by distinct methods, including Pol II transcription initiation site mappings and structural characterization of PICs on distinct promoters. Here, we bring together these previously unconnected observations and hypothesize how, on metazoan TATA promoters, the precisely structured building up of transcription factor (TF) IID-based PICs results in sharp transcription start site (TSS) selection; or, in contrast, how the less strictly controlled positioning of the TATA-less promoter DNA relative to TFIID-core PIC components results in alternative broad TSS selections by Pol II.

Three-dimensional genome structure and function

Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.

N-Acetyltransferase 9 Inhibits Porcine Reproductive and Respiratory Syndrome Virus Proliferation by N-Terminal Acetylation of the Structural Protein GP5

Porcine reproductive and respiratory syndrome virus (PRRSV) is a serious threat to the global swine industry. As a typical immunosuppressive virus, PRRSV has developed a variety of complex mechanisms to escape the host innate immunity. In this study, we uncovered a novel immune escape mechanism of PRRSV infection. Here, we demonstrate for the first time that the endoplasmic reticulum (ER)-resident N-acetyltransferase Nat9 is an important host restriction factor for PRRSV infection. Nat9 inhibited PRRSV proliferation in an acetyltransferase activity-dependent manner. Mechanistically, glycoprotein 5 (GP5) of PRRSV was identified as interacting with Nat9 and being N-terminally acetylated by it, which generates a GP5 degradation signal, promoting the K27-linked-ubiquitination degradation of GP5 to decrease virion assembly. Meanwhile, the expression of Nat9 was inhibited during PRRSV infection. In detail, two transcription factors, ETV5 and SP1, were screened out as the key transcription factors binding to the core promoter region of Nat9, and the PRRSV nonstructural protein 1β (Nsp1β), Nsp4, Nsp9, and nucleocapsid (N) proteins were found to interfere significantly with the expression of ETV5 and SP1, thereby regulating the transcription activity of Nat9 and inhibiting the expression of Nat9. The findings suggest that PRRSV decreases the N-terminal acetylation of GP5 to support virion assembly by inhibiting the expression of Nat9. Taken together, our findings showed that PRRSV has developed complex mechanisms to inhibit Nat9 expression and trigger virion assembly. IMPORTANCE To ensure efficient replication, a virus must hijack or regulate multiple host factors for its own benefit. Understanding virus-host interactions and the molecular mechanisms of host resistance to PRRSV infection is necessary to develop effective strategies to control PRRSV. The N-acetyltransferase Nat9 plays important roles during virus infection. Here, we demonstrate that Nat9 exhibits an antiviral effect on PRRSV proliferation. The GP5 protein of PRRSV is targeted specifically by Nat9, which mediates GP5 N-terminal acetylation and degradation via a ubiquitination-dependent proteasomal pathway. However, PRRSV manipulates the transcription factors ETV5 and SP1 to inhibit the expression of Nat9 and promote virion assembly. Thus, we report a novel function of Nat9 in PRRSV infection and elucidate a new mechanism by which PRRSV can escape the host innate immunity, which may provide novel insights for the development of antiviral drugs.

PRRSV Non-Structural Proteins Orchestrate Porcine E3 Ubiquitin Ligase RNF122 to Promote PRRSV Proliferation

Ubiquitination plays a major role in immune regulation after viral infection. An alternatively spliced porcine E3 ubiquitin ligase RNF122 promoted PRRSV infection and upregulated in PRRSV-infected PAM cells was identified. We characterized the core promoter of RNF122, located between −550 to −470 bp upstream of the transcription start site (TSS), which displayed significant differential transcriptional activities in regulating the transcription and expression of RNF122. The transcription factor HLTF was inhibited by nsp1α and nsp7 of PRRSV, and the transcription factor E2F complex regulated by nsp9. Together, they modulated the transcription and expression of RNF122. RNF122 could mediate K63-linked ubiquitination to raise stability of PRRSV nsp4 protein and thus promote virus replication. Moreover, RNF122 also performed K27-linked and K48-linked ubiquitination of MDA5 to degrade MDA5 and inhibit IFN production, ultimately promoted virus proliferation. In this study, we illustrate a new immune escape mechanism of PRRSV that enhances self-stability and function of viral nsp4, thus, regulating RNF122 expression to antagonize IFNα/β production. The present study broadens our knowledge of PRRSV-coding protein modulating transcription, expression and modification of host protein to counteract innate immune signaling, and may provide novel insights for the development of antiviral drugs.

HOPX Exhibits Oncogenic Activity during Squamous Skin Carcinogenesis

Cutaneous squamous cell carcinomas (SCCs) are frequent heterogeneous tumors arising from sun-exposed regions of the skin and characterized by complex pathogenesis. HOPX is a member of the homeodomain-containing superfamily of proteins holding an atypical homeodomain unable to bind to DNA. First discovered in the heart as a regulator of cardiac development, in the skin, HOPX modulates the terminal differentiation of keratinocytes. There is a particular interest in studying HOPX in squamous skin carcinogenesis because it has the atypical structure and the functional duality as an oncogene and a tumor suppressor gene, reported in different malignancies. In this study, we analyzed the effects of HOPX knockdown and overexpression on SCC tumorigenicity in vitro and in vivo. Our data show that HOPX knockdown in SCC cells inhibits their proliferative and invasive activity through the acceleration of apoptosis. We established that methylation of two alternative HOPX promoters leads to differential expression of HOPX transcripts in normal keratinocytes and SCC cells. Importantly, we report that HOPX acts as an oncogene in the pathogenesis of SCC probably through the activation of the second alternative promoter and the modulation of apoptosis.

Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation

The core-promoter, a stretch of DNA surrounding the transcription start site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell-cycling behaviour between cells of different fates. The role promoter-associated gene-regulatory-networks play in development-associated transitions in cell-cycle-dynamics is poorly understood. This study demonstrates in a vertebrate embryo, how core-promoter variations define transcriptional output in cells transitioning from a proliferative to cell-lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo segmentation, using the FUCCI transgenic cell-cycle-phase marker, revealed a spatial and lineage-specific separation in cell-cycling behaviour. To investigate the role differential promoter usage plays in this process, cap-analysis-of-gene-expression (CAGE) was performed on cells segregated by cycling dynamics. This analysis revealed a dramatic increase in tissue-specific gene expression, concurrent with slowed cycling behaviour. We revealed a distinct sharpening in TSS utilization in genes upregulated in slowly cycling, differentiating tissues, associated with enhanced utilization of the TATA-box, in addition to Sp1 binding-sites. In contrast, genes upregulated in rapidly cycling cells carry broad distribution of TSS utilization, coupled with enrichment for the CCAAT-box. These promoter features appear to correspond to cell-cycle-dynamic rather than tissue/cell-lineage origin. Moreover, we observed genes with cell-cycle-dynamic-associated transitioning in TSS distribution and differential utilization of alternative promoters. These results demonstrate the regulatory role of core-promoters in cell-cycle-dependent transcription regulation, during embryo-development.

Enzymatic Protein Biopolymers as a Tool to Synthetize Eukaryotic Messenger Ribonucleic Acid (mRNA) with Uses in Vaccination, Immunotherapy and Nanotechnology

Multi-subunit enzymes are protein biopolymers that are involved in many cellular processes. The enzyme that carries out the process of transcription of mRNAs is RNA polymerase II (RNAPII), which is a multi-subunit enzyme in eukaryotes. This protein biopolymer starts the transcription from specific sites and is positioned by transcription factors, which form a preinitiation complex (PIC) on gene promoters. To recognize and position the RNAPII and the transcription factors on the gene promoters are needed specific DNA sequences in the gene promoters, which are named promoter elements. Those gene promoter elements can vary and therefore several kinds of promoters exist, however, it appears that all promoters can use a similar pathway for PIC formation. Those pathways are discussed in this review. The in vitro transcribed mRNA can be used as vaccines to fight infectious diseases, e.g., in immunotherapy against cancer and in nanotechnology to deliver mRNA for a missing protein into the cell. We have outlined a procedure to produce an mRNA vaccine against the SARS-CoV-2 virus, which is the causing agent of the big pandemic, COVID-19, affecting human beings all over the world. The potential advantages of using eukaryotic RNAPII to synthetize large transcripts are outlined and discussed. In addition, we suggest a method to cap the mRNA at the 5′ terminus by using enzymes, which might be more effective than cap analogs. Finally, we suggest the construction of a future multi-talented RNAPII, which would be able to synthetize large mRNA and cap them in the test tube.

Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae

BACKGROUND

The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function.

RESULTS

To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model.

CONCLUSIONS

Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.

Transcriptional Regulation of the Bovine Fatty Acid Transport Protein 1 Gene by Krüppel-Like Factors 15

Simple Summary

The nutritional value and qualities of beef are enhanced when the unsaturated fatty acid content is increased. Fatty acid transport protein 1 (FATP1), also called SLC27A1, an integral membrane protein that facilitates long-chain fatty acid influx, is involved in the genetic network for oleic acid synthesis in beef. Polymorphisms in bovine SLC27A1 gene are most significantly associated with oleic acid. Its expression exhibits significant positive correlations with bovine intramuscular fat content in the longissimus thoracis muscle. However, the transcription factors that contribute to the control and regulation of its expression have not been characterized extensively. In this study, we determined the tissue distribution of SLC27A1 mRNA and found that bovine SLC27A1 was highly expressed in subcutaneous adipose tissue and the longissimus thoracis muscle. Furthermore, we analyzed the molecular mechanisms involved in SLC27A1 regulation and found that the transcriptional activity of SLC27A1 gene was dependent on KLF15 transcription factor. These results may lead to an enhanced understanding of the regulation of SLC27A1 expression in other models, as well as provide new insights into the regulatory mechanism and biological functions of the SLC27A1 gene in determining the lipid composition in beef.

Abstract

Oleic acid is a major monounsaturated fatty acid, which accounts for about 33% of the fatty acid content in beef and is considered to have the least negative effect on serum cholesterol levels. Fatty acid transport protein 1 (FATP1), an integral membrane protein that facilitates long-chain fatty acid (LCFA) influx, is involved in the genetic network for oleic acid synthesis in beef. Its expression exhibits significant positive correlations with intramuscular fat (IMF) content in the longissimus thoracis. However, the expression mechanism of SLC27A1 or FATP1 is still unclear. To elucidate the molecular mechanisms involved in bovine SLC27A1 regulation, we cloned and characterized the promoter region of SLC27A1. By applying 5′-rapid amplification of cDNA end analysis, we identified two alternative splice variants of this gene. Using a series of 5′ deletion promoter plasmids in luciferase reporter assays, we found that the core promoter was 96 base pairs upstream from the transcription initiation site. Electrophoretic mobility shift assay combined with a site-directed mutation experiment demonstrated that KLF15 binding to the promoter region drives the SLC27A1 transcription. KLF15 plays an essential role in adipogenesis and skeletal muscle lipid flux. Thus, these results might provide further information on the regulatory roles of SLC27A1 gene in mediating the lipid composition in beef.

Evidence that alternative transcriptional initiation is largely nonadaptive

Alternative transcriptional initiation (ATI) refers to the frequent observation that one gene has multiple transcription start sites (TSSs). Although this phenomenon is thought to be adaptive, the specific advantage is rarely known. Here, we propose that each gene has one optimal TSS and that ATI arises primarily from imprecise transcriptional initiation that could be deleterious. This error hypothesis predicts that (i) the TSS diversity of a gene reduces with its expression level; (ii) the fractional use of the major TSS increases, but that of each minor TSS decreases, with the gene expression level; and (iii) cis-elements for major TSSs are selectively constrained, while those for minor TSSs are not. By contrast, the adaptive hypothesis does not make these predictions a priori. Our analysis of human and mouse transcriptomes confirms each of the three predictions. These and other findings strongly suggest that ATI predominantly results from molecular errors, requiring a major revision of our understanding of the precision and regulation of transcription.

The transcription of a gene may start from one of several transcription start sites, a phenomenon known as alternative transcriptional initiation. Contrary to common belief, this study shows that variation of the transcription start site of a given gene is nonadaptive and is largely attributable to transcriptional initiation error that is typically deleterious.

Multiple surveys of transcriptional initiation showed that mammalian genes typically have multiple transcription start sites such that transcription is initiated from any one of these sites. Many researchers believe that this phenomenon is adaptive because it allows production of multiple transcripts, from the same gene, that potentially vary in function or post-transcriptional regulation. Nevertheless, it is also possible that each gene has only one optimal transcription start site and that alternative transcriptional initiation arises primarily from molecular errors that are slightly deleterious. This error hypothesis makes a series of predictions about the amount of transcription start site diversity per gene, relative uses of the various start sites of a gene, among-tissue and across-species differences in start site usage, and the evolutionary conservation of cis-regulatory elements of various start sites, all of which are verified in our analyses of genome-wide transcription start site data from the human and mouse. These findings strongly suggest that alternative transcriptional initiation largely reflects molecular errors instead of molecular adaptations and require a rethink of the precision and regulation of transcription.

p53 Dynamically Directs TFIID Assembly on Target Gene Promoters

p53 is a central regulator that turns on vast gene networks to maintain cellular integrity in the presence of various stimuli. p53 activates transcription initiation in part by aiding recruitment of TFIID to the promoter. However, the precise means by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters remains elusive. To address this key issue, we have undertaken an integrated approach involving single-molecule fluorescence microscopy, single-particle cryo-electron microscopy, and biochemistry. Our real-time single-molecule imaging data demonstrate that TFIID alone binds poorly to native p53 target promoters. p53 unlocks TFIID's ability to bind DNA by stabilizing TFIID contacts with both the core promoter and a region within p53's response element. Analysis of single-molecule dissociation kinetics reveals that TFIID interacts with promoters via transient and prolonged DNA binding modes that are each regulated by p53. Importantly, our structural work reveals that TFIID's conversion to a rearranged DNA binding conformation is enhanced in the presence of DNA and p53. Notably, TFIID's interaction with DNA induces p53 to rapidly dissociate, which likely leads to additional rounds of p53-mediated recruitment of other basal factors. Collectively, these findings indicate that p53 dynamically escorts and loads TFIID onto its target promoters.

High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

Here, Curina et al. found that a subgroup of ETS family transcription factors (the ELF proteins) shows a strong bias in its genomic distribution by binding in very close proximity (<60 nt) to the transcription start sites of housekeeping genes. They show that a limited number of highly active transcription factors can equip cis-regulatory elements with disparate functional roles and cell type specificity with the ability to efficiently promote transcription.

Enhancers and promoters that control the transcriptional output of terminally differentiated cells include cell type-specific and broadly active housekeeping elements. Whether the high constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead also on shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 base pairs (bp) from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised, macrophage-specific enhancers and promoters. The role of ELFs in promoting high-level constitutive transcription was suggested by multiple evidence: ELF sites enabled robust transcriptional activation by endogenous and minimal synthetic promoters, ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data suggest that the co-optation of a limited number of highly active transcription factors represents a broadly adopted strategy to equip both cell type-specific and housekeeping cis-regulatory elements with the ability to efficiently promote transcription.

rAAV-compatible MiniPromoters for restricted expression in the brain and eye

BACKGROUND

Small promoters that recapitulate endogenous gene expression patterns are important for basic, preclinical, and now clinical research. Recently, there has been a promising revival of gene therapy for diseases with unmet therapeutic needs. To date, most gene therapies have used viral-based ubiquitous promoters-however, promoters that restrict expression to target cells will minimize off-target side effects, broaden the palette of deliverable therapeutics, and thereby improve safety and efficacy. Here, we take steps towards filling the need for such promoters by developing a high-throughput pipeline that goes from genome-based bioinformatic design to rapid testing in vivo.

METHODS

For much of this work, therapeutically interesting Pleiades MiniPromoters (MiniPs; ~4 kb human DNA regulatory elements), previously tested in knock-in mice, were "cut down" to ~2.5 kb and tested in recombinant adeno-associated virus (rAAV), the virus of choice for gene therapy of the central nervous system. To evaluate our methods, we generated 29 experimental rAAV2/9 viruses carrying 19 different MiniPs, which were injected intravenously into neonatal mice to allow broad unbiased distribution, and characterized in neural tissues by X-gal immunohistochemistry for icre, or immunofluorescent detection of GFP.

RESULTS

The data showed that 16 of the 19 (84 %) MiniPs recapitulated the expression pattern of their design source. This included expression of: Ple67 in brain raphe nuclei; Ple155 in Purkinje cells of the cerebellum, and retinal bipolar ON cells; Ple261 in endothelial cells of brain blood vessels; and Ple264 in retinal Müller glia.

CONCLUSIONS

Overall, the methodology and MiniPs presented here represent important advances for basic and preclinical research, and may enable a paradigm shift in gene therapy.

Promoter and Terminator Discovery and Engineering

Control of gene expression is crucial to optimize metabolic pathways and synthetic gene networks. Promoters and terminators are stretches of DNA upstream and downstream (respectively) of genes that control both the rate at which the gene is transcribed and the rate at which mRNA is degraded. As a result, both of these elements control net protein expression from a synthetic construct. Thus, it is highly important to discover and engineer promoters and terminators with desired characteristics. This chapter highlights various approaches taken to catalogue these important synthetic elements. Specifically, early strategies have focused largely on semi-rational techniques such as saturation mutagenesis to diversify native promoters and terminators. Next, in an effort to reduce the length of the synthetic biology design cycle, efforts in the field have turned towards the rational design of synthetic promoters and terminators. In this vein, we cover recently developed methods such as hybrid engineering, high throughput characterization, and thermodynamic modeling which allow finer control in the rational design of novel promoters and terminators. Emphasis is placed on the methodologies used and this chapter showcases the utility of these methods across multiple host organisms.

Molecular Cloning of a cDNA Encoding for Taenia solium TATA-Box Binding Protein 1 (TsTBP1) and Study of Its Interactions with the TATA-Box of Actin 5 and Typical 2-Cys Peroxiredoxin Genes

TATA-box binding protein (TBP) is an essential regulatory transcription factor for the TATA-box and TATA-box-less gene promoters. We report the cloning and characterization of a full-length cDNA that encodes a Taenia solium TATA-box binding protein 1 (TsTBP1). Deduced amino acid composition from its nucleotide sequence revealed that encodes a protein of 238 residues with a predicted molecular weight of 26.7 kDa, and a theoretical pI of 10.6. The NH₂-terminal domain shows no conservation when compared with to pig and human TBP1s. However, it shows high conservation in size and amino acid identity with taeniids TBP1s. In contrast, the TsTBP1 COOH-terminal domain is highly conserved among organisms, and contains the amino acids involved in interactions with the TATA-box, as well as with TFIIA and TFIIB. In silico TsTBP1 modeling reveals that the COOH-terminal domain forms the classical saddle structure of the TBP family, with one α-helix at the end, not present in pig and human. Native TsTBP1 was detected in T. solium cysticerci´s nuclear extract by western blot using rabbit antibodies generated against two synthetic peptides located in the NH₂ and COOH-terminal domains of TsTBP1. These antibodies, through immunofluorescence technique, identified the TBP1 in the nucleus of cells that form the bladder wall of cysticerci of Taenia crassiceps, an organism close related to T. solium. Electrophoretic mobility shift assays using nuclear extracts from T. solium cysticerci and antibodies against the NH₂-terminal domain of TsTBP1 showed the interaction of native TsTBP1 with the TATA-box present in T. solium actin 5 (pAT5) and 2-Cys peroxiredoxin (Ts2-CysPrx) gene promoters; in contrast, when antibodies against the anti-COOH-terminal domain of TsTBP1 were used, they inhibited the binding of TsTBP1 to the TATA-box of the pAT5 promoter gene.

DTIE, a novel core promoter element that directs start site selection in TATA-less genes

The transcription start site (TSS) determines the length and composition of the 5′ UTR and therefore can have a profound effect on translation. Yet, little is known about the mechanism underlying start site selection, particularly from promoters lacking conventional core elements such as TATA-box and Initiator. Here we report a novel mechanism of start site selection in the TATA- and Initiator-less promoter of miR-22, through a strictly localized downstream element termed DTIE and an upstream distal element. Changing the distance between them reduced promoter strength, altered TSS selection and diminished Pol II recruitment. Biochemical assays suggest that DTIE does not serve as a docking site for TFIID, the major core promoter-binding factor. TFIID is recruited to the promoter through DTIE but is dispensable for TSS selection. We determined DTIE consensus and found it to be remarkably prevalent, present at the same TSS downstream location in ≈20.8% of human promoters, the vast majority of which are TATA-less. Analysis of DTIE in the tumor suppressor p53 confirmed a similar function. Our findings reveal a novel mechanism of transcription initiation from TATA-less promoters.

Co-occurrence of transcription and translation gene regulatory features underlies coordinated mRNA and protein synthesis

Background

Variability in protein levels is generated through intricate control of the different gene decoding phases. Presently little is known about the links between the various gene expression stages. Here we investigated the relationship between transcription and translation regulatory properties encoded in mammalian genes.

Results

We found that the TATA-box, a core promoter element known to enhance transcriptional output, is associated not only with higher mRNA levels but also with positive translation regulatory features and elevated translation efficiency. Further investigation revealed general association between transcription and translation regulatory trends. Specifically, translation inhibitory features such as the presence of upstream AUG (uAUG) and increased lengths of the 5′UTR, the coding sequence and the 3′UTR, are strongly associated with lower translation as well as lower transcriptional rate.

Conclusions

Our findings reveal that co-occurrence of several gene-encoded transcription and translation regulatory features with the same trend substantially contributes to the final mRNA and protein expression levels and enables their coordination.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-688) contains supplementary material, which is available to authorized users.

Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing

Chinese hamster ovary (CHO) cell lines are one of the major production tools for monoclonal antibodies, recombinant proteins, and therapeutics. Although many efforts have significantly improved the availability of sequence information for CHO cells in the last years, forthcoming draft genomes still lack the information depth known from the mouse or human genomes. Many genes annotated for CHO cells and the Chinese hamster reference genome still are in silico predictions, only insufficiently verified by biological experiments. The correct annotation of transcription start sites (TSSs) is of special interest for CHO cells, as these directly define the location of the eukaryotic core promoter. Our study aims to elucidate these largely unexplored regions, trying to shed light on promoter landscapes in the Chinese hamster genome. Based on a 5' enriched dual library RNA sequencing approach 6547 TSSs were identified, of which over 90% were assigned to known genes. These TSSs were used to perform extensive promoter studies using a novel, modular bioinformatics pipeline, incorporating analyses of important regulatory elements of the eukaryotic core promoter on per-gene level and on genomic scale.

Distinct role of core promoter architecture in regulation of light-mediated responses in plant genes

In the present study, we selected four distinct classes of light-regulated promoters. The light-regulated promoters can be distinctly grouped into either TATA-box-containing or TATA-less (initiator-containing) promoters. Further, using either native promoters or their swapped versions of core promoter elements, we established that TATA-box and Inr (Initiator) elements have distinct mechanisms which are involved in light-mediated regulation, and these elements are not swappable. We identified that mutations in either functional TATA-box or Inr elements lead to the formation of nucleosomal structure. The nucleotide diversity in either the TATA-box or Inr element in Arabidopsis ecotypes proposes that the nucleotide variation in core promoters can alter the gene expression. We show that motif overrepresentation in light-activated promoters encompasses different specific regulatory motifs present downstream of TSS (transcription start site), and this might serve as a key factor in regulating light promoters which are parallel with these elements. Finally, we conclude that the TATA-box or Inr element does not act in isolation, but our results clearly suggests the probable involvement of other distinct core promoter elements in concurrence with the TATA-box or Inr element to impart selectivity to light-mediated transcription.

Disparity between microRNA levels and promoter strength is associated with initiation rate and Pol II pausing

MicroRNAs are transcribed by RNA polymerase II but the transcriptional features influencing their synthesis are poorly defined. Here we report that a TATA box in microRNA and protein-coding genes is associated with increased sensitivity to slow RNA polymerase II. Promoters driven by TATA box or NF-κB elicit high re-initiation rates, but paradoxically lower microRNA levels. MicroRNA synthesis becomes more productive by decreasing the initiation rate, but less productive when the re-initiation rate increases. This phenomenon is associated with a delay in miR-146a induction by NF-κB. Finally, we demonstrate that microRNAs are remarkably strong pause sites. Our findings suggest that lower efficiency of microRNA synthesis directed by TATA box or NF-κB is a consequence of frequent transcription initiations that lead to RNA polymerase II crowding at pause sites, thereby increasing the chance of collision and premature termination. These findings highlight the importance of the transcription initiation mechanism for microRNA synthesis, and have implications for TATA-box promoters in general.

Regulation of gene expression in the genomic context

Metazoan life is dependent on the proper temporal and spatial control of gene expression within the many cells-essentially all with the identical genome-that make up the organism. While much is understood about how individual gene regulatory elements function, many questions remain about how they interact to maintain correct regulation globally throughout the genome. In this review we summarize the basic features and functions of the crucial regulatory elements promoters, enhancers, and insulators and discuss some of the ways in which proper interactions between these elements is realized. We focus in particular on the role of core promoter sequences and propose explanations for some of the contradictory results seen in experiments aimed at understanding insulator function. We suggest that gene regulation depends on local genomic context and argue that more holistic in vivo investigations that take into account multiple local features will be necessary to understand how genome-wide gene regulation is maintained.

A new paradigm for transcription factor TFIIB functionality

Experimental and bioinformatic studies of transcription initiation by RNA polymerase II (RNAP2) have revealed a mechanism of RNAP2 transcription initiation less uniform across gene promoters than initially thought. However, the general transcription factor TFIIB is presumed to be universally required for RNAP2 transcription initiation. Based on bioinformatic analysis of data and effects of TFIIB knockdown in primary and transformed cell lines on cellular functionality and global gene expression, we report that TFIIB is dispensable for transcription of many human promoters, but is essential for herpes simplex virus-1 (HSV-1) gene transcription and replication. We report a novel cell cycle TFIIB regulation and localization of the acetylated TFIIB variant on the transcriptionally silent mitotic chromatids. Taken together, these results establish a new paradigm for TFIIB functionality in human gene expression, which when downregulated has potent anti-viral effects.

Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots

Transcription initiation, essential to gene expression regulation, involves recruitment of basal transcription factors to the core promoter elements (CPEs). The distribution of currently known CPEs across plant genomes is largely unknown. This is the first large scale genome-wide report on the computational prediction of CPEs across eight plant genomes to help better understand the transcription initiation complex assembly. The distribution of thirteen known CPEs across four monocots (Brachypodium distachyon, Oryza sativa ssp. japonica, Sorghum bicolor, Zea mays) and four dicots (Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera, Glycine max) reveals the structural organization of the core promoter in relation to the TATA-box as well as with respect to other CPEs. The distribution of known CPE motifs with respect to transcription start site (TSS) exhibited positional conservation within monocots and dicots with slight differences across all eight genomes. Further, a more refined subset of annotated genes based on orthologs of the model monocot (O. sativa ssp. japonica) and dicot (A. thaliana) genomes supported the positional distribution of these thirteen known CPEs. DNA free energy profiles provided evidence that the structural properties of promoter regions are distinctly different from that of the non-regulatory genome sequence. It also showed that monocot core promoters have lower DNA free energy than dicot core promoters. The comparison of monocot and dicot promoter sequences highlights both the similarities and differences in the core promoter architecture irrespective of the species-specific nucleotide bias. This study will be useful for future work related to genome annotation projects and can inspire research efforts aimed to better understand regulatory mechanisms of transcription.

Chromatin and epigenetic features of long-range gene regulation

The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. Developments in chromosome conformation capture technologies have revealed that interactions between regions of chromatin are pervasive and highly cell-type specific. The movement of enhancers and promoters in and out of higher-order chromatin structures within the nucleus are associated with changes in expression and histone modifications. However, the factors responsible for mediating these changes and determining enhancer:promoter specificity are still not completely known. In this review, we summarize what is known about the patterns of epigenetic and chromatin features characteristic of elements involved in long-range interactions. In addition, we review the insights into both local and global patterns of chromatin interactions that have been revealed by the latest experimental and computational methods.

Two novel positive cis-regulatory elements involved in green tissue-specific promoter activity in rice (Oryza sativa L ssp.)

In plant genetic engineering, using tissue-specific promoters to control the expression of target gene is an effective way to avoid potential negative effects of using constitutive promoter, such as metabolic burden and so on. However, until now, there are few tissue-specific promoters with strong and reliable expression that could be used in crop biotechnology application. In this study, based on microarray and RT-PCR data, we identified a rice green tissue-specific expression gene DX1 (LOC_Os12g33120). The expression pattern of DX1 gene promoter was examined by using the β-glucuronidase (GUS) reporter gene and analyzed in transgenic rice plants in different tissues. Histochemical assays and quantitative analyses of GUS activity confirmed that P (DX1):GUS was highly expressed in green tissues. To identify the regulatory elements controlling the expression of the DX1 gene, a series of 5' and 3' deletions of DX1 promoter were fused to GUS gene and stably introduced into rice plants. In addition, gel mobility shift assays and site-directed mutagenesis studies were used, allowing for the identification of two novel tissue-specific cis-acting elements (GSE1 and GSE2) within P(DX1). GSE1 acted as a positive regulator in all green tissues (leaf, sheath, stem and panicle). Compared with GSE1, GSE2 acted as a positive regulator only in sheath and stem tissue, and had a weaker effect on gene expression. In addition, P(DX1):GUS was not expressed in anther and seed, this characteristic reduced the potential ecological risk and potential food safety issues. Taken together, our results strongly suggest that the identified promoter, P(DX1), and its cis regulatory elements, GSE1 and GSE2, are potentially useful in the field of rice transgenic breeding.

KEY MESSAGE

We have isolated and characterized the rice green tissue-specific promoter P(DX1), and identified two novel positive cis-acting elements in P(DX1).

The unexpected traits associated with core promoter elements

The core promoter of eukaryotic coding and non-coding genes that are transcribed by RNA polymerase II (RNAP II) is composed of DNA elements surrounding the transcription start site. These elements serve as the docking site of the basal transcription machinery and have an important role in determining the position and directing the rate of transcription initiation. This review summarizes the current knowledge about core promoter elements and focuses on several unexpected links between core promoter structure and certain gene features. These include the association between the presence or absence of a TATA-box and gene length, gene structure, gene function, evolution rate and transcription elongation.

Mechanisms elevating ORMDL3 expression in recurrent wheeze patients: role of Ets-1, p300 and CREB

The first genetic factor identified for childhood asthma by genome-wide association study (GWAS) is the locus on chromosome 17q21, harboring the Orosomucoid 1-like 3 (ORMDL3) gene. ORMDL3 is implicated in facilitation of endoplasmic reticulum-mediated inflammatory responses, believed to underlie its association with asthma. In the present study, we demonstrated that mRNA expression of ORMDL3 is significantly increased in the peripheral blood of recurrent wheeze patients compared with normal control subjects by real-time RT-PCR. To elucidate the molecular mechanisms involved in human ORMDL3 regulation, we cloned and characterized the promoter region of ORMDL3. Applying 5'-rapid amplification of cDNA end analysis (RACE), we revealed that ORMDL3 gene used multiple transcriptional start sites (TSSs). Using a series of 5' deletion promoter plasmids in luciferase reporter assays, we identified that the proximal minimal promoter of ORMDL3 was located within the region -84/+58 relative to the TSS. Mutational analysis, RNA interference experiments and sequential chromatin immunoprecipitation (ChIP) assay demonstrated that transcriptional activity of the ORMDL3 gene was cooperatively regulated by multiple transcription factors, including Ets-1, p300 and CREB. The expression levels of Ets-1, p300 and CREB were increased in the peripheral blood of recurrent wheeze patients compared with normal control subjects and showed a strong linear correlation with the expression of ORMDL3. Our findings indicate that Ets-1, p300 and CREB binding to the promoter region drive the ORMDL3 transcription.

Cloning and characterization of human Golgi phosphoprotein 2 gene (GOLPH2/GP73/GOLM1) promoter

Human Golgi phosphoprotein 2 gene (also known as GOLPH2, GP73 or GOLM1) encodes an epithelial-specific Golgi membrane protein which can be induced by virus infection. It is also overexpressed in a number of tumors and is currently considered as an early diagnosis marker for hepatocellular carcinoma. However, little is known about how GOLPH2 is dysregulated in these disease conditions and the functional implications of its overexpression. The aim of this study is to investigate human GOLPH2 regulation mechanisms. We cloned a 2599 bp promoter fragment of GOLPH2 and found it maintained epithelial specificity. By deletion analysis, a repressive region (-864 to -734 bp), a positive regulatory region (-734 to -421 bp) and a core promoter region (-421 to -79 bp) were identified. Sequence analysis revealed that GOLPH2 core promoter was devoid of canonical TATA element and classified as a TATA-less promoter. Adenoviral early region 1A (E1A) was able to activate GOLPH2 and the CtBP interaction domain of E1A was sufficient but not required for activation. A GC-box motif (-89 to -83 bp) in GOLPH2 core promoter region partly mediated E1A transactivation. These results delineated regulatory regions and functional element in GOLPH2 promoter, elucidated adenoviral E1A stimulation mechanisms and provided insight into GOLPH2 functions.

Identification of cis-Regulatory Elements in the dmyc Gene of Drosophila Melanogaster

Myc is a crucial regulator of growth and proliferation during animal development. Many signals and transcription factors lead to changes in the expression levels of Drosophila myc, yet no clear model exists to explain the complexity of its regulation at the level of transcription. In this study we used Drosophila genetic tools to track the dmyc cis-regulatory elements. Bioinformatics analyses identified conserved sequence blocks in the noncoding regions of the dmyc gene. Investigation of lacZ reporter activity driven by upstream, downstream, and intronic sequences of the dmyc gene in embryonic, larval imaginal discs, larval brain, and adult ovaries, revealed that it is likely to be transcribed from multiple transcription initiation units including a far upstream regulatory region, a TATA box containing proximal complex and a TATA-less downstream promoter element in conjunction with an initiator within the intron 2 region. Our data provide evidence for a modular organization of dmyc regulatory sequences; these modules will most likely be required to generate the tissue-specific patterns of dmyc transcripts. The far upstream region is active in late embryogenesis, while activity of other cis elements is evident during embryogenesis, in specific larval imaginal tissues and during oogenesis. These data provide a framework for further investigation of the transcriptional regulatory mechanisms of dmyc.

Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis

A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5' untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif.

Nucleotide composition-linked divergence of vertebrate core promoter architecture

Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists; however for most of these motifs, the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements, we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independently of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both the conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation.

Genome-wide detection of a TFIID localization element from an initial human disease mutation

Eukaryotic core promoters are often characterized by the presence of consensus motifs such as the TATA box or initiator elements, which attract and direct the transcriptional machinery to the transcription start site. However, many human promoters have none of the known core promoter motifs, suggesting that undiscovered promoter motifs exist in the genome. We previously identified a mutation in the human Ankyrin-1 (ANK-1) promoter that causes the disease ankyrin-deficient Hereditary Spherocytosis (HS). Although the ANK-1 promoter is CpG rich, no discernable basal promoter elements had been identified. We showed that the HS mutation disrupted the binding of the transcription factor TFIID, the major component of the pre-initiation complex. We hypothesized that the mutation identified a candidate promoter element with a more widespread role in gene regulation. We examined 17,181 human promoters for the experimentally validated binding site, called the TFIID localization sequence (DLS) and found three times as many promoters containing DLS than TATA motifs. Mutational analyses of DLS sequences confirmed their functional significance, as did the addition of a DLS site to a minimal Sp1 promoter. Our results demonstrate that novel promoter elements can be identified on a genome-wide scale through observations of regulatory disruptions that cause human disease.

Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation

The eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence now indicates that core promoter recognition complexes together with 'non-prototypical' subunits may have a vital regulatory function in driving cell-specific programmes of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions.

Conserved short sequences in promoter regions of human genome

Recognition of promoter elements by the transcription factors is one of the early initial and crucial steps in gene expression and regulation. In prokaryotes, there are clear signals to identify the promoter regions like TATAAT at around -10 and TTGACA at -35 positions from transcription start site (TSS). In eukaryotes the promoter regions are structurally more complex and there are no conserved or consensus sequences similar to the ones found in prokaryotic promoters. We have located a set of GC rich short sequences (< 8 nt) that are relatively common in human promoter sequences around the TSS (+/- 100 relative to TSS). These sequences were sorted based on their frequency of occurrence in the database and the most common 50 sequences were used for further studies. Sigmoidal behavior of the high end of the frequency distribution of these sequences suggests presence of some internal co-operativity. These short sequences are distributed on both sides of TSS, suggesting that probably the transcription factors recognize these sequences on both upstream and downstream of TSS. As eukaryotic promoters lack any conserved sequences, we expect that these short sequences may help in recognition of promoter regions by relevant transcription factors prior to the initiation of transcription process. We postulate that a cluster of genes with common short sequences in the promoter region can be recognized by a particular transcription factor. We also found that most of these short sequences are fairly common within miRNA (both mature and stem-loop sequences). Our studies indicate that eukaryotic transcription is more complex than currently believed.

Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility

Background

Alternative Promoter (AP) usages have been shown to enable diversified transcriptional regulation of individual gene in a context-specific (e.g., pathway, cell lineage, tissue type, and development stage et. ac.) way. Aberrant uses of APs have been directly linked to mechanism of certain human diseases. However, whether or not there exists a general link between a gene's AP repertoire and its expression diversity is currently unknown. The general relation between a gene's AP repertoire and its disease susceptibility also remains largely unexplored.

Methodology/Principal Findings

Based on the differential expression ratio inferred from all human microarray data in NCBI GEO and the list of disease genes curated in public repositories, we systemically analyzed the general relation of AP repertoire with expression diversity and disease susceptibility. We found that genes with APs are more likely to be differentially expressed and/or disease associated than those with Single Promoter (SP), and genes with more APs are more likely differentially expressed and disease susceptible than those with less APs. Further analysis showed that genes with increased number of APs tend to have increased length in all aspects of gene structure including 3′ UTR, be associated with increased duplicability, and have increased connectivity in protein-protein interaction network.

Conclusions

Our genome-wide analysis provided evidences that increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility.

Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes

Marijuana cannabinoids, the endocannabinoids, and cannabinoid cell receptors have been shown to play important roles in immune regulation particularly as potent modulators of anti-inflammatory cytokines. The predominant cannabinoid receptor involved in this immune regulation is cannabinoid receptor 2 (CB(2)), which is predominantly expressed in B lymphocytes. However, the promoter region and mechanisms of CB(2) gene regulation are unknown in this immune cell type. Utilizing a combination of bioinformatics, 5' rapid amplification of cDNA ends (5' RACE), real-time reverse transcription-polymerase chain reaction, DNA sequencing, and luciferase reporter assays, we show that human B cells express one CB(2) transcript while mouse B cells express three CB(2) transcripts, with specific transcript selection occurring during B cell activation by lipopolysaccharide. Alignment of our sequenced RACE products to either the mouse or human genome, along with the GenBank submitted mRNA sequences, revealed that the transcripts we isolated contained previously unidentified transcriptional start sites (TSS). In addition, expression construct testing of the genomic region containing the TSSs of the mouse CB(2) exon 1 transcripts showed an eightfold increase of promoter activity over baseline. These data show for the first time that human B cells use only one TSS for CB(2) while mouse B cells use multiple TSSs and that the mouse TSSs are in a genomic area with promoter activity, thus suggesting the location of the gene promoter region. Defining these TSSs also provides clues to the various gene regulatory factors involved in the expression of CB(2) during B cell activation.

Regulation of gene expression via the core promoter and the basal transcriptional machinery

The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional regulatory element. There are two main strategies for transcription initiation - focused and dispersed initiation. In focused initiation, transcription starts from a single nucleotide or within a cluster of several nucleotides, whereas in dispersed initiation, there are several weak transcription start sites over a broad region of about 50 to 100 nucleotides. Focused initiation is the predominant means of transcription in simpler organisms, whereas dispersed initiation is observed in approximately two-thirds of vertebrate genes. Regulated genes tend to have focused promoters, and constitutive genes typically have dispersed promoters. Hence, in vertebrates, focused promoters are used in a small but biologically important fraction of genes. The properties of focused core promoters are dependent upon the presence or absence of sequence motifs such as the TATA box and DPE. For example, Caudal, a key regulator of the homeotic gene network, preferentially activates transcription from DPE- versus TATA-dependent promoters. The basal transcription factors, which act in conjunction with the core promoter, are another important component in the regulation of gene expression. For instance, upon differentiation of myoblasts to myotubes, the cells undergo a switch from a TFIID-based transcription system to a TRF3-TAF3-based system. These findings suggest that the core promoter and basal transcription factors are important yet mostly unexplored components in the regulation of gene expression.

TAF4/4b x TAF12 displays a unique mode of DNA binding and is required for core promoter function of a subset of genes

The major core promoter-binding factor in polymerase II transcription machinery is TFIID, a complex consisting of TBP, the TATA box-binding protein, and 13 to 14 TBP-associated factors (TAFs). Previously we found that the histone H2A-like TAF paralogs TAF4 and TAF4b possess DNA-binding activity. Whether TAF4/TAF4b DNA binding directs TFIID to a specific core promoter element or facilitates TFIID binding to established core promoter elements is not known. Here we analyzed the mode of TAF4b.TAF12 DNA binding and show that this complex binds DNA with high affinity. The DNA length required for optimal binding is approximately 70 bp. Although the complex displays a weak sequence preference, the nucleotide composition is less important than the length of the DNA for high affinity binding. Comparative expression profiling of wild-type and a DNA-binding mutant of TAF4 revealed common core promoter features in the down-regulated genes that include a TATA-box and an Initiator. Further examination of the PEL98 gene from this group showed diminished Initiator activity and TFIID occupancy in TAF4 DNA-binding mutant cells. These findings suggest that DNA binding by TAF4/4b-TAF12 facilitates the association of TFIID with the core promoter of a subset of genes.

Activation and repression domains within the promoter of the rat cathepsin L gene orchestrate sertoli cell-specific and stage-specific gene transcription in transgenic mice

In murine testes, only Sertoli cells express the cathepsin L (Ctsl) gene, and this expression is restricted to stages V-VIII of the cycle. Our previous transgenic analysis of Tg (-2065/+977) demonstrated that this expression is regulated by a approximately 2-kb promoter. To begin to elucidate this regulation, we analyzed the in vivo expression of two new transgenes, Tg (-935/+977) and Tg (-451/+977). Tg (-935/+977) was expressed by Sertoli cells but, in contrast to Tg (-2065/+977), was expressed at all stages of the cycle, by spermatocytes, by the vascular endothelium, and by seven other organs. Tg (-451/+977) was not expressed by Sertoli cells but by spermatogenic cells and by the brain. Lack of expression of Tg (-451/+977) by Sertoli cells was not due to a lack of essential cis-acting elements. Transient transfection analysis of primary cultures of mature rat Sertoli cells demonstrated that in mature Sertoli cells, most of the activity of the Ctsl promoter is accounted for by one of two redundant upstream GC motifs and an Initiator that are within 100 bp of the transcription start site. We conclude that transcriptional repressors upstream from nucleotide -935 of the rat Ctsl gene restrict testicular expression of this gene to Sertoli cells at stages V-VIII. At these stages, transcriptional activators located between nucleotides -935 and -452 promote access of the transcriptional machinery to the two GC boxes and to the Initiator. Thus, upstream repressors and activators as well as cis-acting elements near the transcription start site control stage-specific Ctsl transcription by Sertoli cells.

Characterization of sINR, a strict version of the Initiator core promoter element

The proximal promoter consists of binding sites for transcription regulators and a core promoter. We identified an overrepresented motif in the proximal promoter of human genes with an Initiator (INR) positional bias. The core of the motif fits the INR consensus but its sequence is more strict and flanked by additional conserved sequences. This strict INR (sINR) is enriched in TATA-less genes that belong to specific functional categories. Analysis of the sINR-containing DHX9 and ATP5F1 genes showed that the entire sINR sequence, including the strict core and the conserved flanking sequences, is important for transcription. A conventional INR sequence could not substitute for DHX9 sINR whereas, sINR could replace a conventional INR. The minimal region required to create the major TSS of the DHX9 promoter includes the sINR and an upstream Sp1 site. In a heterologous context, sINR substituted for the TATA box when positioned downstream to several Sp1 sites. Consistent with that the majority of sINR promoters contain at least one Sp1 site. Thus, sINR is a TATA-less-specific INR that functions in cooperation with Sp1. These findings support the idea that the INR is a family of related core promoter motifs.

A motif within a complex promoter from the oomycete Phytophthora infestans determines transcription during an intermediate stage of sporulation

Sporulation in Phytophthora infestans is associated with a major remodeling of the transcriptome. To better understand promoter structure and how sporulation-specific expression is determined in this organism, the Pks1 gene was analyzed. Pks1 encodes a protein kinase that is induced at an intermediate stage of sporulation, prior to sporangium maturation. Major and minor transcription start sites mapped throughout the promoter, which contains many T-rich stretches and Inr-like elements. Within the T-rich region are several motifs which bound nuclear proteins in EMSA. Tests of modified promoters in transformants implicated a CCGTTG located 110-nt upstream of the transcription start point as a major regulator of sporulation-specific transcription. The motif also bound a sporulation-specific nuclear protein complex. A bioinformatics analysis indicated that the motif is highly over-represented within co-expressed promoters, in which it predominantly resides 100-300-nt upstream of transcription start sites. Other sequences, such as a CATTTGTT motif, also bound nuclear proteins but did not play an essential role in spore-specific expression.