TY - JOUR. T1 - Adenovirus E1A protein activates transcription of the E1A gene subsequent to transcription complex formation. AU - Schaack, J.. AU - Logan, J.. AU - Vakalopoulou, E.. AU - Shenk, T.. PY - 1991. Y1 - 1991. N2 - The mechanism of transcriptional activation of the adenovirus E1A and E3 genes by E1A protein during infection was examined by using transcription-competition assays. Infection of HeLa cells with one virus led to inhibition of mRNA accumulation from a superinfecting virus. Synthesis of the E1A 289R protein by the first virus to infect reduced inhibition of transcription of the superinfecting virus, indicating that the E1A 289R protein was limiting for E1A-activated transcription. Infection with an E1A- virus, followed 6 h later by superinfection with a wild-type virus, led to preferential transcriptional activation of the E1A gene of the first virus, suggesting that a host transcription component(s) stably associated with the E1A promoter in the absence of E1A protein and ...
Has anyone ever worked with tagetitoxin, a selective transcription inhibitor of chloroplast with arabidopsis? I would like to know who sells tagetitoxin, and at which concentrations it is recommendable to work with on Arabidopsis. I would appriciate very much any info on this subject. Diana ,http://bgumail.bgu.ac.il/agent/[email protected], leicaj at bgumail.bgu.ac.il ...
The wheat bZip transcription factor TaABF1 mediates both abscisic acid (ABA)-induced and ABA-suppressed gene expression. As levels of TaABF1 protein do not change in response to ABA, and TaABF1 is in a phosphorylated state in vivo, we investigated whether TaABF1 could be regulated at the post-translational level. In bombarded aleurone cells, a TaABF1 protein carrying phosphomimetic mutations (serine to aspartate) at four sites (S36D, S37D, S113D, S115D) was three to five times more potent than wild-type TaABF1 in activating HVA1, an ABA-responsive gene. The phosphomimetic mutations also increased the ability of TaABF1 to downregulate the ABA-suppressed gene Amy32b. These findings strongly suggest that phosphorylation at these sites increases the transcriptional regulatory activity of TaABF1. In contrast to the activation observed by the quadruple serine to aspartate mutation, a single S113D mutation completely eliminated the ability of TaABF1 to upregulate HVA1 or downregulate Amy32b. Thus ...
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factor, to a specific DNA sequence referred to as a promoter to form an RNA polymerase-promoter closed complex. In the closed complex the promoter DNA is still fully double-stranded.[5]. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter open complex. In the open complex the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the transcription bubble.[5]. RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[5]. In bacteria, RNA ...
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factor, to a specific DNA sequence referred to as a promoter to form an RNA polymerase-promoter closed complex. In the closed complex the promoter DNA is still fully double-stranded.[5]. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter open complex. In the open complex the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the transcription bubble.[5]. RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[5]. In bacteria, RNA ...
Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. Also unlike DNA replication where DNA is synthesized, transcription does not involve an RNA primer to initiate RNA synthesis.Transcription can be reduced to the following steps, each moving like a wave along the DNA.One or more sigma factors initiate transcription of a gene by enabling binding of RNA polymerase to promoter DNA.RNA ...
Embryonic differentiation depends upon tissue-specific gene expression programs, created by temporally and spatially regulated transcription. Production of specific mRNAs can be stimulated or repressed via regulation of transcription initiation. Transcript production can also be controlled through a rate-limiting step of transcription elongation (Lis, 1998). For example, heat shock response genes, such as hsp70, are constitutively occupied by a RNA polymerase II (Pol II) complex that is paused proximal to the promoter after transcription initiation (Rougvie and Lis, 1988; Rasmussen and Lis, 1993). Transcription elongation is inhibited until heat shock stimulation occurs, at which time the paused Pol II becomes hyperphosphorylated and transcript synthesis proceeds. Several factors have been implicated in the stimulation or repression of transcription elongation (Conaway et al., 2000; Winston, 2001; Yamaguchi et al., 2001; Zorio and Bentley, 2001), but their precise regulatory roles during ...
In cells productively infected with adenovirus type 5, transcription is not terminated between the E1a gene and the adjacent downstream E1b gene. Insertion of the mouse beta(maj)-globin transcription termination sequence (GGT) into the E1a coding region dramatically reduces early, but not late, E1b expression (E. Falck-Pedersen, J. Logan, T. Shenk, and J. E. Darnell, Jr., Cell 40:897-905, 1985). In the study described herein, we showed that base substitution mutations in the globin DNA that specifically relieved transcription termination also restored early E1b promoter activity in cis, establishing that maximal early E1b expression requires readthrough transcription originating from the adjacent upstream gene. To identify potential targets of readthrough activation, a series of recombinant viruses with double mutations was constructed. Each double-mutant virus strain had the transcription termination sequences in the first exon of E1a and a deletion within the transcription control region of ...
Focused transcription typically initiates within the Inr, and the A nucleotide in the Inr consensus is usually designed as the + 1 position, whether or not transcription actually initiates at that particular nucleotide. This convention is useful because other core promoter motifs, such as the MTE and DPE, function with the Inr in a manner that exhibits a strict spacing dependence with the Inr consensus sequence (and hence, the A + 1 nucleotide) rather than the actual transcription start site (Burke and Kadonaga, 1997, Kutach and Kadonaga, 2000 and Lim et al., 2004).[2]. NC2 (negative cofactor 2; also known as Dr1-Drap1) [...] was identified as repressor of TATA-dependent transcription [...].[2]. Several core promoter elements have been previously identified in eukaryotes, but those cannot account for transcription from most RNA polymerase II-transcribed genes.[1]. ...
The major antiinflammatory effects of glucocorticoids appear to be due largely to interaction between the activated glucocorticoid receptor and transcription factors, notably nuclear factor-kappaB (NF-kappaB) and activator protein-1, that mediate the expression of inflammatory genes. NF-kappaB switc …
Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene
A retroviral vector-rescue system in which co-packaging of the two co-expressed vectors is required for transduction of one of the vectors has been established previously. By using this rescue system, two distinct packaging-cell populations have been generated. One cell population expressed retroviral RNA from co-localized transcription sites, resulting in local and overlapping accumulation of both RNA transcripts. In the other cell population, the two transcription cassettes were introduced separately, leading to distinct transcription sites of the two RNAs and no significant co-localization of the RNAs. Titre measurements from the two distinct cell populations showed large differences in rescue titre, which is an indirect measure of co-packaging efficiency. Thus, the cell populations with overlapping RNA accumulation gave rise to 15-80-fold-higher rescue titres than cell populations with non-overlapping RNA accumulation. These data show that the spatial position of proviral transcription sites affects
Transcription elongation elements in the NusG family members are ubiquitous from bacterias to human beings and play diverse assignments in the legislation of gene appearance. than facilitates transcript elongation by its cognate RNAP. Alternatively much like the regulators Tth NusG evidently binds close to the upstream end from the transcription bubble competes with σA Cdh13 and mementos forwards translocation by RNAP. Our data claim that the system of NusG recruitment to RNAP is normally universally conserved despite the fact that the regulatory final results among its homologs can happen distinct. Launch The transcription elongation aspect NusG continues to be identified in based on its requirement of phage λ N-dependent gene appearance and thus called N utilization product G (1). Following studies showed that (Eco) NusG impacts Rho-dependent termination (2) transcriptional arrest by HK022 Nun proteins (3) RNA string elongation (4) and translation (5) and can be an essential component from ...
Detects differential transcription between pairs of samples or between groups of replicates. FDM is based on a statistical method for performing a permutation test on ACT-Graphs that does not depend on annotations or an underlying transcripts inference. The application first align RNA-seq reads to a reference genome and determines the regions of differential RNA transcript expression between pairs of splice graphs for finally assess the significance of differential transcription.
Acute myeloid leukemia (AML) is characterized by impaired myeloid lineage differentiation, uncontrolled proliferation, and inhibition of proapoptotic pathways. In spite of a relatively homogeneous clinical disease presentation, risk of long-term survival in AML varies from 20% to 80% depending on molecular disease characteristics. In recognition of the molecular heterogeneity of AML, the European Leukemia Net (ELN) and WHO classification systems now incorporate cytogenetics and increasing numbers of gene mutations into AML prognostication. Several of the genomic AML subsets are characterized by unique transcription factor alterations that are highlighted in this review. There are many mechanisms of transcriptional deregulation in leukemia. We broadly classify transcription factors based on mechanisms of transcriptional deregulation including direct involvement of transcription factors in recurrent translocations, loss-of-function mutations, and intracellular relocalization. Transcription ...
Dehydroepiandrosterone (DHEA) is a peroxisome proliferating agent when administered in pharmacological dosages, but it has not been shown to function through the peroxisome proliferator-activated receptor in cell-based assays. Because members of the thyroid hormone/vitamins A and D nuclear receptor subfamily, including PPAR, are known to modulate each others function in gene expression by heterodimerization, we sought to establish whether DHEA and thyroid hormone interact to regulate several of the hepatic and renal enzymes associated with peroxisome proliferation, i.e., peroxisomal beta-oxidation and microsomal NADPH:cytochrome P450 oxidoreductase and the cytochromes P450 4A. In rats administered exogenous T3 to attain a hyperthyroid state, induction of the three isozymes of CYP4A (4A1, 4A2, and 4A3) by DHEA was suppressed , 60-80% at the mRNA level, with induction of CYP4A2 mRNA being completely inhibited. Nuclear run-on transcription assays indicated that this inhibitory effect was regulated ...
It recently has been established that adenine-containing cofactors, including nicotinamide adenine dinucleotide (NAD+), reduced nicotinamide adenine dinucleotide (NADH), and 3-desphospho-coenzyme A (dpCoA), can serve as non-canonical initiating nucleotides (NCINs) for transcription initiation by bacterial and eukaryotic cellular RNA polymerases (RNAPs) and that the efficiency of the reaction is determined by promoter sequence (Bird et al., 2016). Here we describe a protocol to quantify the relative efficiencies of transcription initiation using an NCIN vs. transcription initiation using a nucleoside triphosphate (NTP) for a given promoter sequence.
Recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. Can both act as an activator or a repressor depending on the context. Mediates MBD1-dependent transcriptional repression, probably by recruiting complexes containing histone methyltransferase activity. May belong to a complex that represses transcription and couples DNA methylation and histone H3 Lys-9 trimethylation (H3K9me3) (By similarity).
Transcriptome Sequencing analyses provide information to detect novel transcribed regions, splice events and additional promoters and exons. Transcript annotation studies also help to analyze the impact of transcriptional complexity on current models of key signaling pathways. Next Generation Sequencing can also provide information on aberrant transcription events, like pseudogenes, fusion genes, and genome rearrangements. However, the greatest advantage is to decipher quantitative gene expression profile.. ...
Here, I investigate the question of identifying and annotating promoters, one of the most important regulatory signals in the genome, which mark the points where transcription is initiated, and regulate the transcription of genes. I present a new computational method, EponineTSS, which can predict transcription start sites in bulk genomic sequence data with excellent sensitivity and specificity. Unlike the existing methods, it gives an indication of the actual location of the transcription start site. Comparisons with available experimental data suggest that the positional accuracy of these predictions is very good. Results form this method are included as part of the Ensembl human genome annotation. Having located transcription start sites for genes, I also discuss the use of results from comparative genomics the estimate the extent of the fundamental promoter region upstream of the start site. I show that the extent of promoters is very variable, and that promoter size is correlated with the ...
Transcription has the capacity to mechanically modify DNA topology, DNA structure and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dy …
1. History of molecular biology. Nucleic acids and proteins (Structure and function of DNA, RNA and proteins; interaction of proteins with DNA) 2. Genome structure and genetic information (Structure of bacterial and eukaryotic genome, genome evolution, genetic code, transcription unit) 3. Genome replication, DNA repair and recombination (Replication of bacterial and eukaryotic genome, molecular basis of mutagenesis, DNA recombination and repair mechanisms) 4. Genome transcription (Transcription of bacterial and eukaryotic genome, post-transcriptional processing of RNA, mechanisms of RNA splicing) 5. Genome translation (Translation of bacterial and eukaryotic mRNA, the ribosome structure, post-translational processing) 6. Regulation of gene expression (Control of bacterial and eukaryotic genome expression, induction and repression, operon, transcription factors, posttranscriptional regulatory mechanisms) 7. Molecular mechanisms of signalling (Molecules involved in signalling pathways, receiving ...
Renaud Dumas. Significance: In most biological processes, genes have to be activated and/or repressed. In plants, the TOPLESS protein is essential for gene repression through its action as a corepressor bridging transcription factor with chromatin remodeling complexes. Here we combine biochemical and structural studies to describe the structure of TOPLESS, how it tetramerizes, and how it interacts with its protein partners. We show that both the tetramerization interface and the binding site for protein partners have been conserved since algae, highlighting the ancestrality of TOPLESS function. Comparison of this plant protein with one of its animal counterparts also shows how corepressors can use a common domain differently to achieve similar properties, illustrating the tinkering of evolution in transcriptional repression.. Abstract: Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as ...
Precise patterns of gene expression during development are regulated predominantly at the level of transcription. In transcription-driven gene regulation, transcriptional activators bind to enhancer elements and orchestrate the colocalization of proteins at the gene promoter to activate transcription. The transcriptional status of a particular gene in a cell or developing tissue is therefore determined primarily by the precise combination of transcription factors that can bind to the enhancer sequence in that specific cell.. There are, however, well-known exceptions to transcription-driven gene regulation. Most notably, in newly fertilized embryos of chicken, fish, frog, flies and worms, early cell divisions and fate specification are primarily controlled by proteins and RNAs deposited into the egg by the mother (Newport and Kirschner, 1982; Edgar and Schubiger, 1986; Powell-Coffman et al., 1996). Even in mammals, maternally contributed factors play an essential role early in preimplantation ...
One of the simplest ways to model GFP transcription is to use an ODE:. $\frac{d [GFP_{mRNA}]}{dt} = a - b{\cdot}[GFP_{mRNA}]$. where $a$ is GFP transcription rate and $b$ is GFP mRNA degradation rate (both constants). Normally, we assume $a,,b$.. Suppose we wish to account for plasmid concentration with the value of transcription rate $a$ - e.g. with higher plasmid concentration, the ratio $a/b$ should increase as the mRNA saturation levels are expected to be reached faster. In other words, suppose we transfect 2 individual constructs depicted above, 10 ng of one and 30 ng of the other - how should this difference in concentration impact the rate constants values, assuming the constructs are otherwise identical?. Assuming this, approximately how does gene transcription rate $a$ change as a function of the amount of transfected plasmid containing the above construct? Ideally, Id be interested in knowing this for HEK 293 cells, but any other decent estimation is acceptable. One simple option is ...
The recently determined three-dimensional (3D) structure of a bacterial class II transcription complex helps to reveal how it binds to specific DNA sequences, thus driving transcription of downstream genes. This X-ray-based structural analysis provides the first atomic structure for such an intact class II transcription activation complex, according to Richard H. Ebright at Rutgers University in Piscataway, N.J. He and his colleagues reported their findings on 10 June 2016 in Science (doi:10.1126/science.aaf4417).
Once transcription is initiated at the transcription start site (TSS), Pol II pauses at the site just downstream of TSS and requires elongation factors to allow it to proceed. Switching of the RNA Pol II complex from the initiation to the elongation complexes is important for functional transcription, which is mediated by P-TEFb kinase phosphorylating Ser2 position in CTD (Fig. 3A) (Jonkers and Lis, 2015). As assumed, most of the mRNA processing complexes are assembled during the elongation step of transcription (Perales and Bentley, 2009) So chromatin-associated and pol II-interacting mRNA processing proteins are likely to function in regulating transcription elongation (Allemand et al., 2008).. A direct role for SR proteins in transcriptional regulation has been shown for SRSF2. In contrast to shuttling SR proteins (such as SRSF1, SRSF3, and SRSF7), SRSF2 is a non-shuttling protein located in the nucleus. Interestingly, SRSF2 associates with DNA only, but not with cytoplasmic mRNA, suggesting ...
It has been shown that the overall transcription of ribosomal RNA genes can be stimulated by many signals (41); however, increased transcription is not due to an increased number of actively transcribed rDNA units but instead is due to changes in the rate of transcription, especially of elongation (42, 43). B-WICH is an ATP-dependent chromatin remodeling complex containing SNF2h, a human ISWI ATPase, and it was shown to associate with Pol I facilitating its transcription (30). The SIRT7 interaction with components of the B-WICH complex supports a hypothesis where SIRT7 regulates the rate of elongation of Pol I through the ATP-dependent remodeling activities of B-WICH.. SIRT7 knockdown is known to inhibit rDNA transcription (9, 10), and our results show for the first time that SIRT7 knockdown also leads to a reduction in the large subunit of Pol I at the protein level but not at the mRNA level. A question to be addressed in future studies is whether this regulation of Pol I protein level occurs ...
Cyclin-dependent kinase 7 (CDK7) is an important constituent of the cellular transcriptional machinery, where it phosphorylates the C-terminal domain (CTD) of RNAP polymerase II (RNAPII). Because many tumor types are critically dependent on transcription for maintenance of their oncogenic state, pharmacological modulation of CDK7 kinase activity is considered as an approach to treat cancer. Multiple series of CDK7 inhibitors were identified by iterative medicinal chemistry efforts and SAR based approach. Early compounds were optimized towards attaining good physicochemical properties, high potency, good selectivity and desirable pharmacokinetic profile to achieve anti-tumor activity. We have identified compounds from two distinct chemical series that are highly potent in inhibiting CDK7 in biochemical assays. These inhibitors demonstrate time-dependent inhibition of CDK7 indicating covalent nature of binding. The compounds showed potent anti-proliferative activity in cell lines derived from ...
Transcription. Molecular model of DNA (deoxyribonucleic acid, upper right) transcription. During transcription, a complementary messenger ribonucleic acid (mRNA) strand (bottom left) is synthesised. The enzyme RNA polymerase (not shown) recognises a start sign on the DNA strand and moves along the strand building the mRNA. mRNA is the intermediary between DNA and its protein product. - Stock Image C015/4455
Gene regulation at transcriptional and post-transcriptional levels has been the central focus of my research program. While transcription initiation begins the process of gene expression, the post-transcriptional steps of RNA splicing, cleavage polyadenylation, transport and stability all contribute to the type and final levels of protein that will be produced. In addition, these steps are coupled to each other, which can contribute to overall regulation. My lab has been studying several different model systems that allow us to address aspects of gene regulation including immunoglobulin gene expression during B lymphocyte development and, in collaboration with the lab of Brett Spear, liver development and disease. In liver, we have identified Zhx2 as a regulator of genes involved in lipid metabolism and genes that are misregulated during liver cancer.. ...
Transcription and translation are fundamental molecular mechanisms of gene activity regulation with profound implications for human health. The ligand-dependent transcriptional regulation by nuclear receptors bound to DNA response elements involves the transient assembly of large co-regulator complexes. These trigger chromatin remodeling and facilitate the assembly of the general transcription machinery on the promoter of the target gene. Gene expression is also regulated at the level of protein synthesis, for example, by protein factors that bind to the ribosome during the translation initiation, elongation and termination phase. The initiation phase is strongly regulated by factors and also by the mRNA itself and well-characterized reaction intermediates of the initiating ribosomal nano-machinery are potential targets for antibiotics. Both transcription and translation complexes represent large, transient macromolecular assemblies that we investigate by using an integrative structural biology ...
In vitro analysis of transcription and the factors that play a role in transcription require preparation of an extract that faithfully reproduces in vivo transcription
Mice lacking the lymphocyte-specific transcription factor Bob1 (also called OBF-1 or OCA-B) fail to generate germinal centers and a robust Ig response. We show that peripheral B cells in Bob1−/− mice bear characteristics of chronically activated or anergic-like B cells and identify the immunosuppressive microRNA-146a, together with other microRNAs, as novel transcriptional targets of Bob1. The inability to restrict B cell signaling could contribute to the immunodeficient phenotype of these mice and is consistent with an important role for Bob1 in suppressing B cell activation in vivo. ...
Solving structures of complexes is inherently more difficult than solving those for individual proteins. As a result, significantly fewer structures of protein complexes than individual proteins have been determined experimentally [1]. In recent years, homology modeling [2, 3] proved to be successful when the target protein has a similar sequence to proteins with known structures. However, the lack of a sufficiently large database of reference complexes makes the method unsuitable for structural modeling of protein complexes. A conceptually simple and straightforwardly applicable approach for modeling structures of bio-molecular complexes is highly desirable. When proposing new protein complexes, the models developed should be checked against the following attributes: stereo-chemically sound, having sufficient interfacial Solvent Excluded Surface Areas [4] (SESAs) to provide adequate binding strengths, physically meaningful for transcription regulation and consistency with the known experimental ...
Although recent studies have revealed that the majority of human genes are subjected to regulation of alternative promoters (APs), the biological relevance of this phenomenon remains unclear. In order to understand biological significance of the presence of diverg .. [more]ent transcription initiation events in the respective cell types, it is indispensable to obtain bird-view of the transcriptome figures at every step of the gene expression; namely, i) how the genomic structure change to transcriptionally active form, ii) where the transcription initiation complex is recruited, iii) to what extent the transcription is activated, iv) what transcripts formed and sorted to what subcellular fractions. We have recently started multi-faceted use of the Illumina GA to answer these questions. Integrative analysis produced for respective aspects of the gene expression regulations revealed the comprehensive figures of the complex human gene transcriptome for the first time. [less] ...
387448814 - EP 0851912 A4 2000-01-05 - NOVEL FACTORS WHICH MODIFY GENE TRANSCRIPTION AND METHODS OF USE THEREFOR - [origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.[origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May play a role as a target recruitment subunit in E3 ubiquitin-protein ligase complexes and thus in ubiquitination and subsequent proteasomal degradation of target proteins.
Yeast RNA polymerase II initiation factor b copurifies with three polypeptides of 85, 73, and 50 kilodaltons and with a protein kinase that phosphorylates the carboxyl-terminal repeat domain (CTD) of the largest polymerase subunit. The gene that encodes the 73-kilodalton polypeptide, designated TFB1, was cloned and found to be essential for cell growth. The deduced protein sequence exhibits no similarity to those of protein kinases. However, the sequence is similar to that of the 62-kilodalton subunit of the HeLa transcription factor BFT2, suggesting that this factor is the human counterpart of yeast factor b. Immunoprecipitation experiments using antibodies to the TFB1 gene product demonstrate that the transcriptional and CTD kinase activities of factor b are closely associated with an oligomer of the three polypeptides. Photoaffinity labeling with 3-O-(4-benzoyl)benzoyl-ATP (adenosine triphosphate) identified an ATP-binding site in the 85-kilodalton polypeptide, suggesting that the ...
Didier Picard, January 2015 Current list of HBD fusion proteins_ Protein X a HBD b regulated as c Refs. transcription factor in Arabidopsis transcription factor Arabidopsis transcription factor in tobacco coactivator transcription factor 1 2 3 transcription factor transcription factor, differentiation factor transcription factor putative transcription factor in arabidposis transcription factor oncoprotein transcription factor transcription factor oncoprotein oncoprotein oncoprotein transcription factor oncoprotein, transcription factor 6 7 transcription factor transcription factor in yeast, tissue culture cells and zebra fish transcriptional repressor transcription factor transcription factor in yeast, in tissue culture cells, transgenic mice, Xenopus, Drosophila and plants transcription factor, promoter of proliferation transcription factor transcription factor 19 20, 21, i Transcription factors APETALA3 ATF6α Athb-1 GR ER e GR Bob1/OBF1 ER e CCAT (from calcium ER e 4 5 channel cav1.2) C/EBP ...
In vitro studies using highly purified calf thymus RNA polymerase II and a fragment spanning the first intron of H3.3 as template DNA have demonstrated the existence of a strong transcription termination site consisting of thymidine stretches. In this study, nuclear run-on experiments have been performed to assess the extent to which transcription elongation is blocked in vivo using DNA probes corresponding to region 5 and 3 of the in vitro termination sites. These studies suggest that H3.3 expression is stimulated following the inhibition of DNA synthesis through the elimination of the transcription elongation block. Interestingly, both the in vivo and in vitro experiments have revealed that the transcriptional block/termination sites are positioned immediately downstream of a 73 bp region that has been over 90% conserved between the chicken and human H3.3 genes. The extreme conservation of this intronic region suggests a possible role in maintaining cis-acting function. Electrophoretic ...
We have used nuclear run-on, RT-PCR, and transient-transfection analyses to characterize transcription initiation and termination of LmjF chr3. Our data suggest that, like chr1 (19), specific Pol II transcription starts upstream of the most-5′ gene of the two long polycistronic clusters. We have also identified a region where Pol III transcription starts for a tRNA gene located at the convergence of these two gene clusters. Termination of Pol II transcription on both DNA strands, as well as Pol III transcription of the tRNA, seems to occur within this region. Thus, we have now characterized the transcriptional organization of two entire chromosomes and have identified sequences involved in both Pol II and Pol III transcription initiation and termination.. Identification and characterization of the Pol II promoters that drive the expression of protein-coding genes in trypanosomatids has proven to be an elusive goal, complicated by factors such as relatively low transcriptional activity and ...
TY - JOUR. T1 - Phosphorylation of the carboxy-terminal repeat domain in RNA polymerase II by cyclin-dependent kinases is sufficient to inhibit transcription. AU - Gebara, Maha M.. AU - Sayre, Michael H.. AU - Corden, Jeffry L.. PY - 1997/3/1. Y1 - 1997/3/1. N2 - Cdc2 kinase triggers the entry of mammalian cells into mitosis, the only cell phase in which transcription is globally repressed. We show here that Cdc2 kinase phosphorylates components of the RNA polymerase II transcription machinery including the RNA polymerase II carboxy-terminal repeat domain (CTD). To test specifically the effect of CTD phosphorylation by Cdc2 kinase, we used a yeast in vitro transcription extract that is dependent on exogenous RNA polymerase II that contains a CTD. Phosphorylation was carried out using immobilized Cdc2 so that the kinase could be removed from the phosphorylated polymerase. ATPγS and Cdc2 kinase were used to produce an RNA polymerase 110 that was not detectably dephosphorylated in the ...
Transcriptional termination by RNA polymerase II at the 3 end of genes encoding poly(A)+ mRNAs is thought to require two distinct cis-active elements: a functional poly(A) signal and a downstream transcriptional pause site. An important requirement for efficient termination is to prevent transcriptional interference of downstream-located promoters. We have therefore investigated whether these two elements, individually or in combination, can prevent transcriptional interference of RNA polymerase II-activated promoters. For this purpose, we constructed an expression plasmid containing two tandem retroviral long terminal repeats (LTRs) derived from HIV-1. When transfected into HeLa cells, this construct resulted in transcriptional interference of the LTR promoters. Using this assay, we were able to show that a single poly(A) signal was able to protect an otherwise occluded promoter. This effect depended on the RNA-processing strength of the poly(A) signal. Furthermore, transcriptional pause sites
The DNA sequence that a transcription factor binds to is called a transcription factor binding site or response element. Chemically, transcription factors usually interact with their binding sites using a combination of hydrogen bonds and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor binding site may actually interact with the transcription factor. In addition some of these interactions may be weaker than others. Thus, transcription factors dont bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA binding protein (TBP) is: TATAAAA the TBP transcription factor can also bind similar sequences such as: TATATAT or TATATAA Because transcription factors can bind a set of related sequences and the sequences dont tend ...
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element.[55]. Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor-binding site may actually interact with the transcription factor. In addition, some of these interactions may be weaker than others. Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA-binding protein (TBP) is TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT or TATATAA. Because transcription factors can bind a set of related ...
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as transcription factories, but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes.
Transcription factors are key proteins in the regulation of gene transcription. An important step in this process is the opening of chromatin in order to make genomic regions available for transcription. Data on DNase I hypersensitivity has previously been used to label a subset of transcription factors as Pioneers, Settlers and Migrants to describe their potential role in this process. These labels represent an interesting hypothesis on gene regulation and possibly a useful approach for data analysis, and therefore we wanted to expand the set of labeled transcription factors to include as many known factors as possible. We have used a well-annotated dataset of 1175 transcription factors as input to supervised machine learning methods, using the subset with previously assigned labels as training set. We then used the final classifier to label the additional transcription factors according to their potential role as Pioneers, Settlers and Migrants. The full set of labeled transcription factors was used
Transition from the closed to the open promoter complex happens by separation of the DNA strands to form an unwound DNA region. Once the transcription bubble forms the template single strand DNA gets positioned in the active center of Pol II. RNA synthesis then can initiate from the transcription start site. The initially transcribing complex (ITC) is unstable and releases short RNAs during abortive initiation (not shown in the movie). When the RNA reaches a certain length, initiation factors are released, and a stable elongation complex (EC) is formed. Elongation complex contains a DNA-RNA hybrid of eight to nine base pairs. During transcription elongation, the EC repeatedly performs the nucleotide addition cycle (NAC) to attach a nucleotide to the growing messenger RNA (mRNA) chain by catalyzing DNA template-directed formation of an RNA phosphodiester bond. Errors do occur during RNA transcription and must be corrected to prevent synthesis of mutated, nonfunctional proteins that possibly ...
The various steps of mRNP biogenesis (transcription, processing and export) are interconnected. It has been shown that the transcription machinery plays a pivotal role in mRNP assembly, since several mRNA export factors are recruited during transcription and physically interact with components of the transcription machinery. Although the shuttling DEAD-box protein Dbp5p is concentrated on the cytoplasmic fibrils of the NPC, previous studies demonstrated that it interacts physically and genetically with factors involved in transcription initiation. We investigated the effect of mutations affecting various components of the transcription initiation apparatus on the phenotypes of mRNA export mutant strains. Our results show that growth and mRNA export defects of dbp5 and mex67 mutant strains can be suppressed by mutation of specific transcription initiation components, but suppression was not observed for mutants acting in the very first steps of the pre-initiation complex (PIC) formation. Our results
Author Summary The transcription of eukaryotic genes involves a highly ordered series of events, including the recruitment of RNA polymerase to promoters, the production of the RNA transcript, and termination. These events are coordinated with changes in chromatin structure that allow regulatory proteins and RNA polymerase to access the DNA template. The recruitment of RNA polymerase II to promoters is rate-limiting for the expression of most eukaryotic genes. However, RNA polymerase often pauses or stalls a short distance downstream of promoters, providing an additional step at which transcription can be regulated. In this study, we present evidence suggesting that a chromatin-remodeling factor, KIS-L, activates transcription by counteracting promoter-proximal pausing in Drosophila. KIS-L also counteracts histone H3 lysine 27 methylation-a covalent modification of chromatin involved in hereditable gene silencing. Our findings provide a plausible explanation for the developmental abnormalities
On specific signals, segments of DNA corresponding to one or more cistrons become de-repressed and ready to transcribe. Each such DNA transcription segment has a promoter region, initiation site, coding region and a terminator region. Transcription begins at the initiation site and ends at the terminator region. A promoter region has RNA polymerase recognition site and RNA polymerase binding site.. Chain opening occurs in the region occupied by TATAATG nucleotides (TATA box) in most procaryotes. Enzymes required for chain separation are unwindases, gyrases and single stranded binding proteins. Terminator region has either poly A base sequence or palindromic sequence (iden-tical base sequence running in opposite directions in the two DNA chains).. RNA polymerase (common in procaryotes and specific in eucaryotes) binds itself to the promoter region. The two strands of DNA uncoil progressively from the site of polymerase binding. One of the two strands of DNA (3-» 5′) functions as a template ...
Transcription factors directly control when, where, and the extent to which genes are expressed. Signal transduction pathways are responsible for either activating or inhibiting many of them. Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. Many transcription factors, such as nuclear receptors, reside in the cytoplasm and enter the nucleus upon activation (e.g., ligand binding). Posttranslational modifications and coregulating proteins provide additional layers of regulation. Transcription factors are involved in a wide variety of processes, such as development, stress responses, and immunity. Activation or inhibition of transcription factors is often dysregulated during oncogenesis. Transcription factors can also be dysregulated during developmental processes, promoting or inhibiting cellular differentiation. Analyzing the expression, regulation, activity, and sequence of transcription factor genes can help determine ...
Antibodies for proteins involved in negative regulation of transcription elongation from RNA polymerase I promoter pathways, according to their Panther/Gene Ontology Classification
Microscopy and Western blots data of Sharma et al., 2018 entitled ¨Arginine citrullination at the C-terminal domain controls RNA polymerase II transcription¨
Transcriptional repression is a general mechanism for regulating transcriptional initiation in organisms ranging from yeast to humans. Accurate initiation of transcription from eukaryotic protein-encoding genes requires the assembly of a large multiprotein complex consisting of RNA polymerase II and general transcription factors such as TFIIA, TFIIB, and TFIID. DR1 is a repressor that interacts with the TATA-binding protein (TBP) of TFIID and prevents the formation of an active transcription complex by precluding the entry of TFIIA and/or TFIIB into the preinitiation complex. The protein encoded by this gene is a corepressor of transcription that interacts with DR1 to enhance DR1-mediated repression. The interaction between this corepressor and DR1 is required for corepressor function and appears to stabilize the TBP-DR1-DNA complex. [provided by RefSeq, Jul 2008 ...
The Arabidopsis genome contains a large number of gene pairs that encode sense and antisense transcripts with overlapping 3′ regions, indicative for a potential role of natural antisense transcription in regulating sense gene expression or transcript processing. When we mapped poly(A) transcripts of three plant gene pairs with long overlapping antisense transcripts, we identified an unusual transcript composition for two of the three gene pairs. Both genes pairs encoded a class of long sense transcripts and a class of short sense transcripts that terminate within the same polyadenylation region as the antisense transcripts encoded by the opposite strand. We find that the presence of the short sense transcript was not dependent on the expression of an antisense transcript. This argues against the assumption that the common termination region for sense and antisense poly(A) transcripts is the result of antisense-specific regulation. We speculate that for some genes evolution may have especially ...
Aplha, transcription related growth factors and stimulating factors or repressing nuclear factors are complex subunits of proteins involved in cell differentiation. Complex subunit associated factors are involved in hybridoma growth, Eosinohils, eritroid proliferation and derived from promotor binding stimulating subunits on the DNA binding complex. NFKB 105 subunit for example is a polypetide gene enhancer of genes in B cells.The activation of transcription factor subunits is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerases. Transcription factors, unites and elongations can be RNA and DNA nucleic acids, base pairs of nucleotides . Converting from DNA to RNA is made by enzymatic reactions. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, anti-parallel RNA strand called a primary transcript. Transcriptions are key functions in signal transduction pathways. Signaling ...
PDOC51319} {PS51319; TFIIS_N} {BEGIN} *********************************** * TFIIS N-terminal domain profile * *********************************** Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N- terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophane residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [1,2]: - MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. - Elongin ...
Transcription is a crucial step in gene expression, orchestrated by RNA polymerase (RNAP), a molecular machine that transfers genetic information from DNA to RNA . Bacterial transcription provides a tractable model system which provides mechanistic insights on its more complex eukaryotic counterpart. Bacterial transcription is initiated after an RNAP holoenzyme (core RNAP bound to a σ initiation factor) melts the double-stranded DNA (dsDNA) around the transcription start to form a transcription bubble in the RNAP-promoter DNA open complex (RPo). Subsequently, RNAP performs cycles of RNA synthesis and dissociation (abortive initiation) and at a certain point, escapes from the promoter and enters elongation. RNAP has been studied extensively using genetic, biochemical and structural methods. Recent X-ray structures 3,4 vastly improved our understanding of transcription, leading to mechanistic proposals, and experiments that tested these proposals and further examined RNAP function. However, crystal
High-resolution transcription start site (TSS) mapping in D. melanogaster embryos and cell lines has revealed a rich and detailed landscape of both cis- and trans-regulatory elements and factors. However, TSS profiling has not been investigated in an orthogonal in vivo setting. Here, we present a comprehensive dataset that links TSS dynamics with nucleosome occupancy and gene expression in the wandering third instar larva, a developmental stage characterized by large-scale shifts in transcriptional programs in preparation for metamorphosis. The data recapitulate major regulatory classes of TSSs, based on peak width, promoter-proximal polymerase pausing, and cis-regulatory element density. We confirm the paucity of divergent transcription units in D. melanogaster, but also identify notable exceptions. Furthermore, we identify thousands of novel initiation events occurring at unannotated TSSs that can be classified into functional categories by their local density of histone modifications. Interestingly,
Cells are subjected to dramatic changes of gene expression upon environmental changes. Stresscauses a general down-regulation of gene expression together with the induction of a set of stress-responsivegenes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription uponosmostress in yeast. Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stressresponsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq ...
TY - JOUR. T1 - Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. AU - Yin, Y. Whitney. AU - Steitz, Thomas A.. PY - 2002/11/15. Y1 - 2002/11/15. N2 - To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase, which only makes short RNA fragments, to a stable elongation phase. We have determined at 2.1 angstrom resolution the crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a transcription bubble interacting with a 17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex. Formation of the exit tunnel explains the enhanced processivity of the ...
TY - JOUR. T1 - In vivo transcription analysis utilizing chromatin immunoprecipation reveals a role for trypanosome transcription factor PBP-1 in RNA polymerase III-dependent transcription. AU - Gilinger, Gwen. AU - Luo, Hua. AU - Bellofatto, Vivian. PY - 2004/1/1. Y1 - 2004/1/1. UR - http://www.scopus.com/inward/record.url?scp=1642431643&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=1642431643&partnerID=8YFLogxK. U2 - 10.1016/j.molbiopara.2003.10.020. DO - 10.1016/j.molbiopara.2003.10.020. M3 - Article. C2 - 14747156. AN - SCOPUS:1642431643. VL - 134. SP - 169. EP - 173. JO - Molecular and Biochemical Parasitology. JF - Molecular and Biochemical Parasitology. SN - 0166-6851. IS - 1. ER - ...
Injury-elicited differential transcriptional regulation of phospholipid growth factor receptors in the cornea.: The phospholipid growth factors (PLGFs), includi
There are three major forms of life on Earth, bacteria, archaea and eukaryotes (Figure 3). RNA polymerase in bacteria is less complex than RNA polymerase in eukaryotes. Some of the increased complexity of RNA polymerase in eukaryotes reflects differences between DNA in eukaryotes and DNA in bacteria. Two important differences are that eukaryotes organize their DNA into nucleosomes and have more complex mechanisms for regulation of gene transcription.[5] Nucleosomes are a complex of DNA and histone proteins (Figure 4). In order for transcription to occur, DNA must be released from being tightly coiled in nucleosomes. Bacteria do not have nucleosomes. Another complication of eukaryotic gene expression regulation is that gene sequences controlling transcription are often distant from the DNA site where transcription starts. The RNA polymerase of bacteria is relatively small with a core of five protein subunits and one additional protein that recognizes the start points for transcription[6]. In ...
A promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters can be about 100-1000 [nucleotides] long.[1]. A promoter is on the template strand for the gene and near the gene in numbers of nucleotides (nts) along the DNA template strand. Usually, the promoter lies within the string of nucleotides between genes. Some promoters are called constitutive as they are active in all circumstances in the cell, while others are regulated becoming active in response to specific stimuli. These specific stimuli for a gene find a receptive portion within that genes promoter. In the case of genes that are used to produce proteins, the RNA polymerase II holoenzyme that actually performs the transcription from the template strand needs to find chemical cues for attachment to the DNA and where to begin transcription. Preceding this are chemical cues for which DNA strand is the template strand and in what direction transcription is to be performed. A promoter contains cues for ...
Recent work suggests a role for multiple host factors in facilitating HIV-1 reverse transcription. Previously, we identified a cellular activity which increases the efficiency of HIV-1 reverse transcription in vitro. Here, we describe aspects of the activity which shed light on its function. The cellular factor did not affect synthesis of strong-stop DNA but did improve downstream DNA synthesis. The stimulatory activity was isolated by gel filtration in a single fraction of the exclusion volume. Velocity-gradient purified HIV-1, which was free of detectable RNase activity, showed poor reverse transcription efficiency but was strongly stimulated by partially purified cell proteins. Hence, the cell factor(s) did not inactivate an RNase activity that might degrade the viral genomic RNA and block completion of reverse transcription. Instead, the cell factor(s) enhanced first strand transfer and synthesis of late reverse transcription suggesting it stabilized the reverse transcription complex. The ...
Author(s): Bardales Mendieta, Jorge Adalberto | Advisor(s): Darzacq, Xavier | Abstract: Enhancers are DNA regulatory elements that play an important role in the preciseregulation of Pol II transcription initiation and, consequently, in the generation andmaintenance of patterns of gene expression. A defining characteristic of enhancers is theircapacity to regulate transcription from their target promoter, independent of the genomicdistance that separates them. Importantly, in order for enhancers to exert their regulatoryaction, they must first relocalize into close spatial proximity to their target promoter andform long-range interactions. Although these interactions have been demonstrated tooccur, the mechanisms that allow their specific and efficient formation remains largelyobscure. In this thesis, I focus on the development of tools and the expansion of ourunderstanding with regard to this important topic.In the first chapter, I begin by providing a perspective of transcription initiation asa hub of
Bacterial transcription regulation. Bacteria transcribe their genomes with the help of multi-subunit RNA polymerases (RNAPs), which comprise two large β and β subunits that form the active site, two regulatory α subunits and an ω subunit that supports RNAP assembly. The α2ββω core enzyme cooperates with transcription factors and responds to signals on DNA templates and nascent RNAs to achieve full functionality in vivo. For example, elongating RNAP frequently enters an elemental paused state, and pausing can be stabilized by an RNA hairpin invading the RNA exit tunnel or by RNAP backtracking. RNA synthesis is terminated intrinsically, when the elongation complex transcribes a stable RNA hairpin followed by a uridine-rich stretch, or with the aid of transcription termination factor ρ. Pausing and termination can be further modulated by elongation factors, such as N-utilization substances A and G. Some regulatory factors or RNAs can stably insulate RNAP from the destabilizing effects of ...
How does RNA polymerase II coordinate the synthesis of messenger RNA, resulting in proper cellular regulation and organismic development? The sessions will cover new findings in transcriptional initiation, elongation and termination and the role of RNA polymerase II, its C-terminal domain and the associated factors in this process. New findings on the roles of chromatin, their interacting proteins and post-translational modifications, their numerous transcriptional properties and their role in development also will be addressed. The plenary lecture will be presented by Ramin Shiekhattar, who will describe his work on the functions of long noncoding RNAs in transcriptional regulation, development and disease pathogenesis. This years meeting represents the 10th anniversary of this important and influential conference. ...
During RNA Polymerase II transcription, the C-terminal domain (CTD) of Rpb1 has been proposed to act as a scaffold to coordinate transcription initiation, elongation, termination, histone modification, and mRNA processing events. These events have been shown to correlate with distinct changes in the pattern of CTD phosphorylation across open reading frames. The major focus of our research is to study the role of the CTD phosphatase Rtr1 during the transcription cycle and to understand how alterations in the phosphorylation state of the CTD influence gene expression and mRNA processing.. ...
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation. ...
Free CAK and rCAK complexes show a stronger preference for the cdk2 substrate versus the ctd oligopeptide. CAK is thus most likely involved in regulation of the cell cycle through cdk phosphorylation (Morgan, 1995). Although free CAK is able to use the ctd oligopeptide as a substrate, it cannot phosphorylate the CTD of RNA pol II alone or when added to an in vitro transcription system lacking TFIIH. On the contrary, TFIIH which contains CAK, is able to phosphorylate the CTD of RNA pol II, in addition to TBP and TFIIEα, two polypeptides absolutely required for basal transcription of protein‐coding genes.. Free CAK and rCAK are not able to substitute for TFIIH in transcription. TFIIH lacking CAK complex allows RNA synthesis when added to an in vitro transcription system that contains all the components of the basal transcription machinery. However, when a CAK subcomplex (free CAK or rCAK) is added, the level of RNA synthesis is significantly increased. TFIIH may thus incorporate CAK to become ...
Discontinuous transcription has been described for different mammalian cell lines and numerous promoters. However, our knowledge of how the activity of individual promoters is adjusted by dynamic signaling inputs from transcription factors is limited. To address this question, we characterized the activity of selected target genes that are regulated by pulsatile accumulation of the tumor suppressor p53 in response to ionizing radiation. We performed time-resolved measurements of gene expression at the single-cell level by smFISH and used the resulting data to inform a mathematical model of promoter activity. We found that p53 target promoters are regulated by frequency modulation of stochastic bursting and can be grouped along three archetypes of gene expression. The occurrence of these archetypes cannot solely be explained by nuclear p53 abundance or promoter binding of total p53. Instead, we provide evidence that the time-varying acetylation state of p53s C-terminal lysine residues is ...
Transcription factors are frequently the chief determinants of the composition and stability of large transcription complexes. Transcriptional regulation is mediated through the interactions of transcription factors with specific binding sites. Transcription factors help to recruit RNA polymerases to active genes for the production of RNA transcripts. Detect Transcription factors using Mercks antibodies.
Transcription factors are frequently the chief determinants of the composition and stability of large transcription complexes. Transcriptional regulation is mediated through the interactions of transcription factors with specific binding sites. Transcription factors help to recruit RNA polymerases to active genes for the production of RNA transcripts. Detect Transcription factors using Mercks antibodies.
Cyclin-dependent kinase-associated protein 1 (Cks1) is involved in the control of the transcription of a subset of genes in addition to its role in controlling the cell cycle in the budding yeast Saccharomyces cerevisiae. By directly ligating Cks1 onto a GAL1 promoter-driven reporter, we demonstrated that Cks1 acts as a transcription activator. Using this method, we dissected the downstream events from Cks1 recruitment at the promoter. We showed that subsequent to promoter binding, Cdc28 binding is required to modulate the level of gene expression. The ubiquitin-binding domain of Cks1 is essential for implementing downstream transcription events, which appears to recruit the proteasome via ubiquitylated proteasome subunits. We propose that the selective ability of Cks1 to bind ubiquitin allows this small molecule the flexibility to bind large protein complexes with specificity and that this may represent a novel mechanism of regulating transcriptional activation.
The second session will delve into fundamental mechanisms in gene regulation. Joan Conaway (Stowers Institute for Medical Research) will focus on the Mediator complex, which bridges interactions between transcription activators and RNA polymerase II, helping to recruit polymerase to a genes promoter. New results from the Conaway lab reveal that Mediator also can enhance transcription elongation through stimulating the release of paused Pol II.. Dylan Taatjes (University of Colorado at Boulder) will provide additional insights into Mediator and its interactions with the transcription machinery. Structural analyses of Mediator in complex with various transcription activators shed light on how Mediator translates activator binding to Pol II and the general transcription factors to influence transcription. In addition to protein factors, RNA species are emerging as important regulators of gene expression. Ramin Shiekhettar (Wistar Institute) will present his recent findings on the roles of long ...