Genomic environments scale the activities of diverse core promoters

A classical model of gene regulation is that enhancers provide specificity whereas core promoters provide a modular site for the assembly of the basal transcriptional machinery. However, examples of core promoter specificity have led to an alternate hypothesis in which specificity is achieved by core promoters with different sequence motifs that respond differently to genomic environments containing different enhancers and chromatin landscapes. To distinguish between these models, we measured the activities of hundreds of diverse core promoters in four different genomic locations and, in a complementary experiment, six different core promoters at thousands of locations across the genome. Although genomic locations had large effects on expression, the intrinsic activities of different classes of promoters were preserved across genomic locations, suggesting that core promoters are modular regulatory elements whose activities are independently scaled up or down by different genomic locations. This scaling of promoter activities is nonlinear and depends on the genomic location and the strength of the core promoter. Our results support the classical model of regulation in which diverse core promoter motifs set the intrinsic strengths of core promoters, which are then amplified or dampened by the activities of their genomic environments.

Emerging Principles in the Transcriptional Control by YAP and TAZ

Yes-associated protein (YAP) and TAZ are transcriptional cofactors that sit at the crossroad of several signaling pathways involved in cell growth and differentiation. As such, they play essential functions during embryonic development, regeneration, and, once deregulated, in cancer progression. In this review, we will revise the current literature and provide an overview of how YAP/TAZ control transcription. We will focus on data concerning the modulation of the basal transcriptional machinery, their ability to epigenetically remodel the enhancer–promoter landscape, and the mechanisms used to integrate transcriptional cues from multiple pathways. This reveals how YAP/TAZ activation in cancer cells leads to extensive transcriptional control that spans several hallmarks of cancer. The definition of the molecular mechanism of transcriptional control and the identification of the pathways regulated by YAP/TAZ may provide therapeutic opportunities for the effective treatment of YAP/TAZ-driven tumors.

Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms

Archaea represent a diverse phylogenetic group that includes free-living, extremophile, mesophile, symbiont, and opportunistic organisms. These prokaryotic organisms share a high significant similarity with the basal transcriptional machinery of Eukarya, and they share regulatory mechanisms with Bacteria, such as operonic organization and DNA-binding transcription factors (TFs). In this work, we identified the repertoire of TFs in 415 archaeal genomes and compared them with their counterparts in bacterial genomes. The comparisons of TFs, at a global level and per family, allowed us to identify similarities and differences between the repertoires of regulatory proteins of bacteria and archaea. For example, 11 of 62 families are more highly abundant in archaea than bacteria, and 13 families are abundant in bacteria but not in archaea and 38 families have similar abundances in the two groups. In addition, we found that archaeal TFs have a lower isoelectric point than bacterial proteins, i.e., they contain more acidic amino acids, and are smaller than bacterial TFs. Our findings suggest a divergence occurred for the regulatory proteins, even though they are common to archaea and bacteria. We consider that this analysis contributes to the comprehension of the structure and functionality of regulatory proteins of archaeal organisms.

Uncoupling of Chromatin Assembly from DNA Replication in Sciara Reveals a Domain of Postreplicative Immature Chromatin

DNA replication in dividing eukaryotic cells imposes a requirement for the faithful recreation on the newly synthesized chromatids of the nucleoprotein architecture of parent chromosomes. Practically nothing is known about the structure of postreplicative immature chromatin (a very short-lived entity of <30 min.). We report here the unexpected discovery that during DNA amplification of locus II/9A in salivary gland polytene chromosomes of the fungus fly Sciara coprophila, DNA replication fork passage is uncoupled from postreplicative chromatin assembly; this enables visualization and analysis of chromatin fibers disassembled by DNA replication. We used electron microscopy to visualize a wealth of low nucleosome density immature chromatin fibers in preparations of Sciara chromatin from amplification-stage tissue. Remarkably, as gauged by high sensitivity to micrococcal nuclease and an unusually short length of DNA associated with each histone octamer, we found that locus II/9A which undergoes amplification and is replicated once every 4-6 hrs. (but not the bulk genome or a replicatively quiescent DNA stretch) was maintained in such an ummature fiber for ca. 24 hrs. Following amplification, locus II/9A assumed conventional chromatin organization, indicating that the epigenetic mark targeting nascent DNA to the chromatin assembly machinery is stable for several hours. We propose that this very unusual prolonged maintenance of a segment of the genome in immature chromatin facilitates access by the basal transcriptional machinery to the amplified DNA, and thus is an evolutionary adaptation to the demand for high transcription from genes that reside in the amplified loci.

Novel function of transcription factor Uga3 as an activator of branched-chain amino acid permease BAP2 gene expression

Gene regulation in yeast occurs at the transcription level, i.e. the basal level of expression is very low and increased transcription requires gene-specific transcription factors allowing the recruitment of basal transcriptional machinery. Saccharomyces cerevisiae BAP2 gene encodes the permease responsible for most uptake of leucine, valine and isoleucine, amino acids that this yeast can use as nitrogen sources. Moreover, BAP2 expression is known to be induced by the presence of amino acids such as leucine. In this context, the results presented in this paper show that BAP2 is an inducible gene in the presence of nitrogen-non-preferred source proline but exhibits high constitutive non-inducible expression in nitrogen-preferred source ammonium. BAP2 expression is regulated by the SPS sensor system and transcription factors Leu3, Gcn4 and Dal81. This can be achieved or not through a direct binding to the promoter depending on the quality of the nitrogen source. We further demonstrate here that an interaction occurs in vivo between Uga3 ‒ the transcriptional activator responsible for γ-aminobutyric acid (GABA)-dependent induction of the GABA genes ‒ and the regulatory region of the BAP2 gene, which leads to an increase in BAP2 transcription.

Abstract 333: MED13-dependent Regulation of Cardiac Thyroid Hormone Signaling

Thyroid hormone (TH) is a key regulator of cardiac metabolism. While hypothyroidism is known to result in adverse cardiac effects, the molecular mechanisms that modulate TH signaling are not completely understood. Mediator is a multiprotein complex that coordinates signal dependent transcription factors with basal transcriptional machinery. Mediator complex protein, MED13, was previously demonstrated to repress numerous thyroid receptor (TR) response genes in the heart. Furthermore, we have previously demonstrated that mice overexpressing cardiac MED13 (MED13cTg) treated with propylthiouracil (PTU), an inhibitor of T3 biosynthesis, were resistant to PTU-dependent decreases in cardiac contractility. Here we demonstrate that MED13 expression is induced in the hearts of mice in response to a PTU diet. To elucidate the role of MED13 in transcriptional regulation of cardiac TH signaling, cardiac-specific Med13 knockout mice (MED13cKO) and control mice were placed on a PTU diet or normal chow diet for 4 weeks. An additional group of mice on PTU diet were treated acutely with thyroid hormone (T3). While heart weight to body weight ratios did not differ between genotypes, RNA sequencing was performed from hearts of these mice to understand the role of MED13 in TR-dependent transcription. Echocardiography was performed to assess cardiac function in these mice. In addition, histology was performed to evaluate cardiac structure and fibrosis. These studies demonstrate that MED13 is induced in response to hypothyroidism and further deciphers molecular mechanisms of MED13 regulation of TR-dependent transcription.

Abstract 317: Med12 is a Transcriptional Mediator of Cardiac Contractile Function

The Mediator complex serves as a central governor of gene transcription by linking the basal transcriptional machinery with DNA-bound transcription factors. The activity of the Mediator complex is modulated by a kinase submodule comprised of four proteins: MED12, MED13, CDK8, and Cyclin C. The kinase submodule components are ubiquitously expressed, however recent studies support the hypothesis that these proteins differentially regulate gene expression in a tissue-specific manner. We previously demonstrated that MED13 acts in the heart to modulate systemic energy homeostasis through signaling to extracardiac tissues, but the role of the other kinase components in the heart has not yet been investigated. MED12 regulates development in a variety of cell types, and MED12 null mice are embryonically lethal. To investigate the cardiac functions of MED12, we generated mice with conditional cardiac-specific deletion of MED12. MED12 mutant mice displayed postnatal cardiomyopathy seven days after birth with a continual decline in cardiac function with age. RNAseq experiments identified specific dysregulation of genes involved in calcium homeostasis and contractility in the ventricles as early as postnatal day one. Defects in calcium handling were detected in cardiomyocytes isolated just after birth, suggesting that perturbed calcium transients lead to altered cardiac contractility and dysfunction. The consequences of cardiac deletion of MED12 and MED13 are clearly distinct, underscoring the unique functions of these Mediator components. These findings highlight the importance of the kinase submodule of the mediator complex in the control of cardiac function and reveal highly specific and distinct transcriptional actions of MED12 and MED13.