Kinetic and mechanistic analysis of the RNA polymerase II transcrption reaction at the human interleukin-2 promoter

Analytic delay distributions for a family of gene transcription models

Models intended to describe the time evolution of a gene network must somehow include transcription, the DNA-templated synthesis of RNA, and translation, the RNA-templated synthesis of proteins. In eukaryotes, the DNA template for transcription can be very long, often consisting of tens of thousands of nucleotides, and lengthy pauses may punctuate this process. Accordingly, transcription can last for many minutes, in some cases hours. There is a long history of introducing delays in gene expression models to take the transcription and translation times into account. Here we study a family of detailed transcription models that includes initiation, elongation, and termination reactions. We establish a framework for computing the distribution of transcription times, and work out these distributions for some typical cases. For elongation, a fixed delay is a good model provided elongation is fast compared to initiation and termination, and there are no sites where long pauses occur. The initiation and termination phases of the model then generate a nontrivial delay distribution, and elongation shifts this distribution by an amount corresponding to the elongation delay. When initiation and termination are relatively fast, the distribution of elongation times can be approximated by a Gaussian. A convolution of this Gaussian with the initiation and termination time distributions gives another analytic approximation to the transcription time distribution. If there are long pauses during elongation, because of the modularity of the family of models considered, the elongation phase can be partitioned into reactions generating a simple delay (elongation through regions where there are no long pauses), and reactions whose distribution of waiting times must be considered explicitly (initiation, termination, and motion through regions where long pauses are likely). In these cases, the distribution of transcription times again involves a nontrivial part and a shift due to fast elongation processes.

Structural visualization of transcription initiation in action

Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.

Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology

Transcription factors (TFs) control gene expression, often acting synergistically. Classical thermodynamic models offer a biophysical explanation for synergy based on binding cooperativity and regulated recruitment of RNA polymerase. Because transcription requires polymerase to transition through multiple states, recent work suggests that "kinetic synergy" can arise through TFs acting on distinct steps of the transcription cycle. These types of synergy are not mutually exclusive and are difficult to disentangle conceptually and experimentally. Here, we model and build a synthetic circuit in which TFs bind to a single shared site on DNA, such that TFs cannot synergize by simultaneous binding. We model mRNA production as a function of both TF binding and regulation of the transcription cycle, revealing a complex landscape dependent on TF concentration, DNA binding affinity, and regulatory activity. We use synthetic TFs to confirm that the transcription cycle must be integrated with recruitment for a quantitative understanding of gene regulation.

A local regulatory T cell feedback circuit maintains immune homeostasis by pruning self-activated T cells

A fraction of mature T cells can be activated by peripheral self-antigens, potentially eliciting host autoimmunity. We investigated homeostatic control of self-activated T cells within unperturbed tissue environments by combining high-resolution multiplexed and volumetric imaging with computational modeling. In lymph nodes, self-activated T cells produced interleukin (IL)-2, which enhanced local regulatory T cell (Treg) proliferation and inhibitory functionality. The resulting micro-domains reciprocally constrained inputs required for damaging effector responses, including CD28 co-stimulation and IL-2 signaling, constituting a negative feedback circuit. Due to these local constraints, self-activated T cells underwent transient clonal expansion, followed by rapid death ("pruning"). Computational simulations and experimental manipulations revealed the feedback machinery's quantitative limits: modest reductions in Treg micro-domain density or functionality produced non-linear breakdowns in control, enabling self-activated T cells to subvert pruning. This fine-tuned, paracrine feedback process not only enforces immune homeostasis but also establishes a sharp boundary between autoimmune and host-protective T cell responses.

Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity

Transcription by RNA polymerase II (Pol II) is a complex process that requires general transcription factors and Pol II to assemble on DNA into preinitiation complexes that can begin RNA synthesis upon binding of NTPs (nucleoside triphosphate). The pathways by which preinitiation complexes form, and how this impacts transcriptional activity are not completely clear. To address these issues, we developed a single molecule system using TIRF (total internal reflection fluorescence) microscopy and purified human transcription factors, which allows us to visualize transcriptional activity at individual template molecules. We see that stable interactions between polymerase II (Pol II) and a heteroduplex DNA template do not depend on general transcription factors; however, transcriptional activity is highly dependent upon TATA-binding protein, TFIIB and TFIIF. We also found that subsets of general transcription factors and Pol II can form stable complexes that are precursors for functional transcription complexes upon addition of the remaining factors and DNA. Ultimately we found that Pol II, TATA-binding protein, TFIIB and TFIIF can form a quaternary complex in the absence of promoter DNA, indicating that a stable network of interactions exists between these proteins independent of promoter DNA. Single molecule studies can be used to learn how different modes of preinitiation complex assembly impact transcriptional activity.

NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription

Transcription of interleukin-2 (IL-2), a pivotal cytokine in the mammalian immune response, is induced by NFAT and AP-1 transcriptional activators in stimulated T cells. NFATc2 and cJun drive high levels of synergistic human IL-2 transcription, which requires a unique interaction between the C-terminal activation domain of NFATc2 and cJun homodimers. Here we studied the mechanism by which this interaction contributes to synergistic activation of IL-2 transcription. We found that NFATc2 can recruit cJun homodimers to the -45 NFAT element, which lacks a neighboring AP-1 site. The bZip domain of cJun is sufficient to interact with the C-terminal activation domain of NFATc2 in the absence of DNA and this interaction is inhibited by AP-1 DNA. When the -45 NFAT site was replaced by either an NFAT/AP-1 composite site or a single AP-1 site the specificity for cJun homodimers in synergistically activating IL-2 transcription was lost, and cJun/cFos heterodimers strongly activated transcription. These studies support a model in which IL-2 transcriptional synergy is mediated by the unique recruitment of a cJun homodimer to the -45 NFAT site by NFATc2, where it acts as a co-activator for IL-2 transcription.

The C-terminal region of human NFATc2 binds cJun to synergistically activate interleukin-2 transcription

At eukaryotic promoters, multi-faceted protein-protein and protein-DNA interactions can result in synergistic transcriptional activation. NFAT and AP-1 proteins induce interleukin-2 (IL-2) transcription in stimulated T cells, but the contributions of individual members of these activator families to synergistically activating IL-2 transcription is not known. To investigate the combinatorial regulation of IL-2 transcription we tested the ability of different combinations of NFATc2, NFATc1, cJun, and cFos to synergistically activate transcription from the IL-2 promoter. We found that NFATc2 and cJun are exclusive in their ability to synergistically activate human IL-2 transcription. Protein-protein interaction assays revealed that in the absence of DNA, NFATc2, but not NFATc1, bound directly to cJun/cJun dimers, but not to cFos/cJun heterodimers. A region of NFATc2 C-terminal of the DNA binding domain was necessary and sufficient for interaction with cJun in the absence of DNA, and this same region of NFATc2 was required for the synergistic activation of IL-2 transcription in T cells. Moreover, expression of this C-terminal region of NFATc2 specifically repressed the synergistic activation of IL-2 transcription. These studies show that a previously unidentified interaction between human NFATc2 and cJun is necessary for synergistic activation of IL-2 transcription in T cells.

RNA polymerase II and TAFs undergo a slow isomerization after the polymerase is recruited to promoter-bound TFIID

Transcription of mRNA genes requires that RNA polymerase II (Pol II) and the general transcription factors assemble on promoter DNA to form an organized complex capable of initiating transcription. Biochemical studies have shown that Pol II and TFIID (transcription factor IID) contact overlapping regions of the promoter, leading to the question of how these large factors reconcile their promoter interactions during complex assembly. To investigate how the TAF (TATA-binding protein-associated factor) subunits of TFIID alter the kinetic mechanism by which complexes assemble on promoters, we used a highly purified human transcription system. We found that TAFs sharply decrease the rate at which Pol II, TFIIB, and TFIIF assemble on promoter-bound TFIID-TFIIA. Interestingly, the slow step in this process is not recruitment of these factors to the DNA, but rather a postrecruitment isomerization of protein-DNA contacts that occurs throughout the core promoter. Our findings support a model in which Pol II and the general transcription factors rapidly bind promoter-bound TFIID-TFIIA, after which complexes undergo a slow isomerization in which the TAFs reorganize their contacts with the promoter to allow Pol II to properly engage the DNA. In this manner, TAFs kinetically repress basal transcription.

A TATA binding protein regulatory network that governs transcription complex assembly

BACKGROUND

Eukaryotic genes are controlled by proteins that assemble stepwise into a transcription complex. How the individual biochemically defined assembly steps are coordinated and applied throughout a genome is largely unknown. Here, we model and experimentally test a portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome.

RESULTS

Biochemical knowledge was used to formulate a series of coupled TBP regulatory reactions involving TFIID, SAGA, NC2, Mot1, and promoter DNA. The reactions were then linked to basic segments of the transcription cycle and modeled computationally. A single framework was employed, allowing the contribution of specific steps to vary from gene to gene. Promoter binding and transcriptional output were measured genome-wide using ChIP-chip and expression microarray assays. Mutagenesis was used to test the framework by shutting down specific parts of the network.

CONCLUSION

The model accounts for the regulation of TBP at most transcriptionally active promoters and provides a conceptual tool for interpreting genome-wide data sets. The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale.

Characterization of the sequence and architectural constraints of the regulatory and core regions of the human interleukin-2 promoter

The cytokine interleukin-2 (IL-2) is produced by T cells when they recognize a foreign antigen. Transcription of the IL-2 gene is tightly controlled by the combined actions of multiple transcriptional activators. However, the contribution of sequences in the IL-2 core promoter and the architecture of the IL-2 regulatory region to setting levels of IL-2 transcription are not understood. We have probed these properties of the human IL-2 promoter to understand how the regulatory and core promoter regions cooperate in response to T cell stimulation, thereby setting high levels of inducible transcription. We found that the IL-2 core promoter contains a TATA box that is critical for inducible expression. Moreover, the spacing and orientation between the IL-2 regulatory and core promoter regions is important for setting the level of transcription. The regulatory region of the IL-2 promoter is capable of mediating high levels of expression even when the helical phasing between transcription factor binding sites is perturbed. Although long considered an enhancer, our studies indicate that the regulatory region in the IL-2 promoter is better considered as a proximal regulatory element, since it lacks multiple properties associated with enhancer elements.

An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch

Glucose and galactose are two alternative carbon sources in yeast for energy production, producing CO2 and alcohol. The yeast needs to switch from glucose to galactose metabolism as required, by transcriptional regulation of the respective metabolic enzymes. This regulation is achieved mainly through the GAL genetic switch, in addition to glucose repression mechanism. This study integrates the two metabolic pathways with the genetic regulatory circuit using the GEPASI 3.30 simulation environment, and investigates the model behavior under various nutrient conditions. Our system is successful in achieving transcriptional upregulation of the galactose metabolizing enzymes as required. Under high glucose and high galactose concentrations, the in silico yeast chooses to metabolize glucose first, after which it resorts to using the galactose available. We also show what the preferred storage macromolecules are in different metabolic pathways.

The Sequence at Specific Positions in the Early Transcribed Region Sets the Rate of Transcript Synthesis by RNA Polymerase II in Vitro

To further understand the mechanism of promoter escape by RNA polymerase II, we have systematically investigated the effect of core promoter sequence on the rate of transcript synthesis in vitro. Chimeric and mutant promoters were made by swapping sequences between the human interleukin-2 promoter and the adenovirus major late promoter, which exhibit different rates of transcript synthesis. Kinetic studies at these promoters revealed that sequences downstream of the start sites set the rate of transcript synthesis. Specifically, the sequences at +2 and +7/+8 are critical for determining the rate; when either +2 is a C (nontemplate strand) or +7/+8 is a TT (nontemplate strand), transcript synthesis is slow. At +7/+8, the thermodynamic stability of the RNA:DNA hybrid controls the overall rate of transcript synthesis. Our data support a model in which the rate-limiting step during transcript synthesis by RNA polymerase II in vitro occurs at the point in the reaction at which early ternary complexes transform into elongation complexes.

Cytoplasmic-to-nuclear volume ratio affects AP-1 complex formation as an indicator of cell cycle responsiveness

Cytoplasmic volume undergoes a series of changes during mitosis in eukaryotes; in turn, signaling events such as osmotic stress can regulate the cytoplasmic volume in cells. In some organisms, increase in cytoplasmic-to-nuclear volume ratio was seen to affect the growth potential in cells, however, the mechanistics of such a regulation, if at all present, was unclear. In a computational model, we have constructed a growth factor-induced signaling pathway leading to AP-1 heterodimer formation through transcriptional regulation, and analyzed the effects of increasing the cytoplasmic-to-nuclear ratio on c-jun transcription and AP-1 complex. We have observed that larger cytoplasmic volumes caused both an increase in the final AP-1 product and a delay in the time of AP-1 accumulation.

TFIIH operates through an expanded proximal promoter to fine-tune c-myc expression

A continuous stream of activating and repressing signals is processed by the transcription complex paused at the promoter of the c-myc proto-oncogene. The general transcription factor IIH (TFIIH) is held at promoters prior to promoter escape and so is well situated to channel the input of activators and repressors to modulate c-myc expression. We have compared cells expressing only a mutated p89 (xeroderma pigmentosum complementation group B [XPB]), the largest TFIIH subunit, with the same cells functionally complemented with the wild-type protein (XPB/wt-p89). Here, we show structural, compositional, and functional differences in transcription complexes between XPB and XPB/wt-89 cells at the native c-myc promoter. Remarkably, although the mean levels of c-Myc are only modestly elevated in XPB compared to those in XPB/wt-p89 cells, the range of expression and the cell-to-cell variation of c-Myc are markedly increased. Our modeling indicates that the data can be explained if TFIIH integrates inputs from multiple signals, regulating transcription at multiple kinetically equivalent steps between initiation and promoter escape. This helps to suppress the intrinsic noise of transcription and to ensure the steady transcriptional output of c-myc necessary for cellular homeostasis.

Effect of sesquiterpene lactones on the expression of the activation marker CD69 and of IL-2 in T-lymphocytes in whole blood

We used flow cytometry to investigate the inhibitory effect of sesquiterpene lactones (SLs) on T-cell activation measured by the expression of its early marker CD69, and on interleukin (IL)-2, a mediator of activation, in whole blood. SLs are biologically active compounds found especially in plants from the Asteraceae family. Overnight treatment of blood with these substances led to the inhibition of CD69 and IL-2 expression. Interestingly, bifunctional SLs showed a weaker activity than monofunctional substances, which is in contradiction with the data obtained so far, using other biological test systems. Additionally, SLs did not completely inhibit CD69 or IL-2 expression. We also determined their toxicity and observed only a low effect. Up to now, studies on cytotoxicity have only been performed using cultured cell lines. From these results it may be supposed that these natural compounds preferentially show toxic effects towards transformed cell lines. Altogether, the results demonstrated that SLs effectively inhibit the activation of the T-lymphocyte response in whole blood and proved the utility of a whole blood system in studying their biological effects.

Promoter escape by RNA polymerase II

Transcription of protein-coding genes is one of the most fundamental processes that underlies all life and is a primary mechanism of biological regulation. In eukaryotic cells, transcription depends on the formation of a complex at the promoter region of the gene that minimally includes RNA polymerase II and several auxiliary proteins known as the general transcription factors. Transcription initiation follows at the promoter site given the availability of nucleoside triphosphates and ATP. Soon after the polymerase begins the synthesis of the nascent mRNA chain, it enters a critical stage, referred to as promoter escape, that is characterized by physical and functional instability of the transcription complex. These include formation of abortive transcripts, strong dependence on ATP cofactor, the general transcription factor TFIIH and downstream template. These criteria are no longer in effect when the nascent RNA reaches a length of 14-15 nucleotides. Towards the end of promoter escape, disruption or adjustment of protein-protein and protein-DNA interactions, including the release of some of the general transcription factors from the early transcription complex is to be expected, allowing the transition to the elongation stage of transcription. In this review, we examine the experimental evidence that defines promoter escape as a distinct stage in transcription, and point out areas where critical information is missing.