The Hormonal Control of Gene Transcription

Enterohepatic transport of bile salts and genetics of cholestasis

The inducible regulation of heat shock gene transcription is mediated by a family of heat shock factors (HSF) that respond to diverse forms of physiological and environmental stress including elevated temperature, amino acid analogs, heavy metals, oxidative stress, anti-inflammatory drugs, arachidonic acid, and a number of pathophysiological disease states. The vertebrate genome encodes a family of HSFs which are expressed ubiquitously, yet the DNA binding properties of each factor are negatively regulated and activated in response to specific conditions. This chapter will discuss the regulation of the HSF multi-gene family and the role of these transcriptional activators in the inducible expression of genes encoding heat shock proteins and molecular chaperones.

Pathways of Egr-1-Mediated Gene Transcription in Vascular Biology

Regulation of gene expression is one of the fundamental mechanisms by which cells utilize the information in their DNA to obtain diverse characteristics, such as ability of differentiated cells to play specific roles and ability to respond to extracellular stresses including ionizing radiation (IR). The research on transcriptional regulation of genes after exposure to IR has a long history tracing back to early studies in late 1980’s. In those studies, expression of individual genes was separately measured by a classical hybridization method. Recently, however, functional genomics approaches, such as microarray profiling, enable us to simultaneously monitor the expression of thousands of genes, and are now recognized as a firmly established methodology in radiation biosciences. The porpose of investigation of transcriptional gene regulation by IR is primarily to gain an insight into how the human bodies respond to IR and eventually how radiation hazards develop. IR-induced hematopoietic death is an example where proapoptotic gene expression is enhanced in radiosensitive hematopoietic stem cells after exposure to high doses of IR, which causes untolerable loss of peripheral blood cells, ultimately resulting in the individual death. Secondary, the purpose of the reserach on transcriptional gene regulation is to search for biomarkers which indicate the quantitative IR-exposure records. Such biomarkers may help us estimate the exposed dose of public peolpe in the emergency cases. For these purposes, studies have been extensively carried out by lots of researchers, and plenty of insights were obtained. In this review article, some of these studies, including those carried out in our laboratory, will be overviewed with an emphasis on the important roles of a tumor supressor p53 in transcriptional regulation after IR exposure and organ-dependence of transcriptional regulation in vivo. Methodology for the research on transcriptional regulation is also briefly touched. And the future perspectives of the research on transcriptional responses to IR will be discussed.

Introduction: Dishevelled (DVL) is a crucial component of Wnt-signaling and is vital for other physiological processes. There are three DVL paralogs, yet the paralog-specific functions and their regulation remain poorly understood. One of the goals of our study is to define how DVL1 mediates Wnt-signaling specificity and how it regulates the transcription of genes that impact tumor-intrinsic modulation of immune cell recruitment. While several studies suggest that DVL proteins could serve as critical mediators of malignancy for breast cancer and other cancer types, the mechanism by which DVL contributes to breast tumor progression and tumor immunology remain unanswered. This study utilizes data from our recent DVL ChIP-seq and RNA-seq analyses, publicly available data, genomic analyses, and other bioinformatics tools to investigate novel mechanisms of how DVL coordinates downstream signaling. Our study seeks to define the elusive function of nuclear DVL with respect to epigenetic and transcriptional regulation in models of triple-negative breast cancer. Methods: DVL ChIP-sequenced reads were aligned against GRCh38.p14, and peaks visualized using an integrative genomic viewer. RNA-seq FASTQ files were trimmed and aligned to GRCh38.p14; read counts were analyzed with edgeR and resulting differentially expressed genes with R and Cytoscape. To determine possible DVL binding partners, transcription factor and protein-protein interaction database mining and subsequent co-immunoprecipitation were performed. Results: Although much remains unknown regarding DVL function and regulation, the discovery of its translocation to the nucleus, binding to novel genomic loci, and regulation of novel gene expression raised new functionality. Our analysis shows DVL binding to core-promoter elements in essential immunological regulatory genes such as STAT1, IFN-y, HLA (-A, B, C, Ds, E, F), and interleukins. Data mining and co-immunoprecipitation analysis have identified several possible nuclear DVL binding partners, including candidate transcription factors that partner with DVL genes to regulate immune cell responses in the tumor microenvironment. DVL KO and WT transcriptional regulation analysis also identified several differentially expressed immunological genes. Summary: We have not only identified DVL binding to the promoter of genes involved in tumorigenesis and immune function but also identified possible DVL binding partners that aid in the regulation of these genes. These findings and future in silico and in vivo approaches will further define a novel DVL regulatory role of tumor and immune signaling in triple-negative breast cancer. Citation Format: Dalia Martinez-Marin, Jenna C van Wunnik, Monica Sharma, Kevin Pruitt. Role of DVL in transcription and epigenetic regulation of immunoregulatory genes in triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr B03.

In spite of prolonged and intensive treatment with combined antiretroviral therapy (cART), which efficiently suppresses plasma viremia, the integrated provirus of HIV-1 persists in resting memory CD4+ T cells as latent infection. Treatment with cART does not substantially reduce the burden of latent infection. Once cART is ceased, HIV-1 replication recrudesces from these reservoirs in the overwhelming majority of patients. There is increasing evidence supporting a role for noncoding RNAs (ncRNA), including microRNAs (miRNAs), antisense (as)RNAs, and short interfering (si)RNA in the regulation of HIV-1 transcription. This appears to be mediated by interaction with the HIV-1 promoter region. Viral miRNAs have the potential to act as positive or negative regulators of HIV transcription. Moreover, inhibition of virally encoded long-asRNA can induce positive transcriptional regulation, while antisense strands of siRNA targeting the NF-κB region suppress viral transcription. An in-depth understanding of the interaction between ncRNAs and the HIV-1 U3 promoter region may lead to new approaches for the control of HIV reservoirs. This review focuses on promoter associated ncRNAs, with particular emphasis on their role in determining whether HIV-1 establishes active or latent infection.

The testis and the adrenal are (transcriptionally) the same

Kinesins are motor proteins that transport their cargos along microtubules in an ATP-dependent manner. The testis-specific kinesin KIF17b was shown to directly regulate cAMP-response element modulator (CREM)-dependent transcription by determining the subcellular localization of the activator of CREM in testis (ACT), the testis-specific coactivator of CREM in postmeiotic male germ cells. CREM is a crucial transcriptional regulator of many important genes required for spermatid maturation, as demonstrated by the complete block of sperm development at the first steps of spermiogenesis in crem-null mice. To better understand the complex regulation of postmeiotic germ cell differentiation, we further characterized the ACT-KIF17b interaction, the function of KIF17b, and the signaling pathways governing its action. In this study, we demonstrated that the abilities of KIF17b to shuttle between the nuclear and the cytoplasmic compartments and to transport ACT are neither dependent on its motor domain nor on microtubules, thus revealing a novel microtubule-independent function for kinesins. We also showed that the cyclic AMP-dependent protein kinase A mediates the phosphorylation of KIF17b, and this modification is important for its subcellular localization. These results indicate that cyclic AMP signaling controls CREM-mediated transcription in male germ cells through modification of KIF17b function.

Most of studies on transcriptional regulation mainly focus on upstream regions of genes. More and more recent researches indicate that introns may have important biological functions in transcription regulation of genes. The characterization of words in DNA sequences can be facilitated by the sequences’ functions. Using U-score and Z-score statistic, respectively, we extracted some over-represented words in intron 1s of ribosomal protein genes. A majority of them are accordance with known transcriptional factor binding sites and are potential regulatory elements. And, the detected over-represented words are more likely to form wider potential sequences and are denser in intron 1s of RP genes. We speculate the properties of these words may be associated with the transcriptional regulation of RP genes.

Die Aufklärung der Mechanismen zur Kontrolle der Genexpression ist eines der wichtigsten Probleme der modernen Molekularbiologie. Detaillierte experimentelle Untersuchungen sind enorm aufwändig aufgrund der komplexen und kombinatorischen Wechselbeziehungen der beteiligten Moleküle. Infolgedessen sind bioinformatische Methoden unverzichtbar. Diese Dissertation stellt drei Methoden vor, die die Vorhersage der regulatorischen Elementen der Gentranskription verbessern. Der erste Ansatz findet Bindungsstellen, die von den Transkriptionsfaktoren erkannt werden. Dieser sucht statistisch überrepräsentierte kurze Motive in einer Menge von Promotersequenzen und wird erfolgreich auf das Genom der Bäckerhefe angewandt. Die Analyse der Genregulation in höheren Eukaryoten benötigt jedoch fortgeschrittenere Techniken. In verschiedenen Datenbanken liegen Hunderte von Profilen vor, die von den Transkriptionsfaktoren erkannt werden. Die Ähnlichkeit zwischen ihnen resultiert in mehrfachen Vorhersagen einer einzigen Bindestelle, was im nachhinein korrigiert werden muss. Es wird eine Methode vorgestellt, die eine Möglichkeit zur Reduktion der Anzahl von Profilen bietet, indem sie die Ähnlichkeiten zwischen ihnen identifiziert. Die komplexe Natur der Wechselbeziehung zwischen den Transkriptionsfaktoren macht jedoch die Vorhersage von Bindestellen schwierig. Auch mit einer Verringerung der zu suchenden Profile sind die Resultate der Vorhersagen noch immer stark fehlerbehafted. Die Zuhilfenahme der unabhängigen Informationsressourcen reduziert die Häufigkeit der Falschprognosen. Die dritte beschriebene Methode schlägt einen neuen Ansatz vor, die die Gen-Anotation mit der Regulierung von multiplen Transkriptionsfaktoren und den von ihnen erkannten Bindestellen assoziiert. Der Nutzen dieser Methode wird anhand von verschiedenen wohlbekannten Sätzen von Transkriptionsfaktoren demonstriert.

The role of transcriptional regulation in steroid hormone biosynthesis

The solute carrier family 11 member 1 (SLC11A1) gene is strictly regulated and exclusively expressed in myeloid lineage cells. However, little is known about the transcriptional regulation of the SLC11A1 gene during myeloid development. In this study, we used HL-60 cells as a model to investigate the regulatory elements/factors involved in the transactivation of the SLC11A1 gene during phorbol 12-myristate 13-acetate (PMA)-induced macrophage differentiation of HL-60 cells. Promoter deletion analysis showed that a 7-base AP-1-like element (TGACTCT) was critical for the responsiveness of the SLC11A1 promoter to PMA. Stimulation by PMA induced the binding of ATF-3 and the recruitment of two components of the SWI/SNF complex, BRG1 and β-actin, to this element in an ATF-3-dependent manner. RNAi-mediated depletion of ATF-3 or BRG1 markedly decreased SLC11A1 gene expression and its promoter activity induced by PMA. Luciferase reporter experiments demonstrated that ATF-3 cooperated with BRG1 and β-actin to activate the SLC11A1 promoter. Furthermore, we showed that PMA can induce the proximal (GT/AC)(n) repeat sequence to convert to the Z-DNA structure in the SLC11A1 gene promoter, and depletion of BRG1 resulted in a significant decrease of Z-DNA formation. Our results demonstrated that recruitment of the SWI/SNF complex initiated Z-DNA formation and subsequently helped to transactivate the SLC11A1 gene.

Recently, we have described a novel gene, DD3, which is one of the most prostate cancer-specific genes described to date (Bussemakers, M. J. G., van Bokhoven, A., Verhaegh, G. W., Smit, F. P., Karthaus, H. F. M., Schalken, J. A., Debruyne, F. M. J., Ru, N., and Isaacs, W. B. (1999) Cancer Res. 59, 5975-5979). The prostate cancer-specific expression of DD3 indicates that the DD3 gene promoter is a promising tool for the treatment of prostate cancer. To identify the promoter elements that are responsible for the prostate cancer-specific expression of DD3, we have isolated and characterized the DD3 promoter. Sequence analysis of the DD3 5'-flanking region was performed and several promoter-human growth hormone reporter constructs were prepared, which were transiently transfected in the DD3-positive cell line LNCaP and several DD3-negative cell lines. Using a 500-base pair DD3 promoter construct, we could detect promoter activity in LNCaP cells, which was not affected by increasing the size of the constructs. Truncated constructs, however, showed an increased transcriptional activity, suggesting the presence of a silencer that negatively regulates the expression of DD3. DNase-I footprint analysis, using nuclear extracts from LNCaP cells, revealed the presence of three DNase-I-protected areas within the DD3 proximal promoter. We show that the high mobility group I(Y) protein binds to one of the DNase-I-protected areas and recruits another, yet unidentified, protein to the DD3 promoter in LNCaP cells.

Distribution of Transcription Factor Binding Sites in the Yeast Genome Suggests Abundance of Coordinately Regulated Genes

I. INTRODUCTION In all eukaryotes, transcriptional regulation of heat shock genes in response to elevated ambient temperatures is mediated by a common, positive, cis -acting sequence, the heat shock element (HSE), that is present in multiple copies upstream of the transcriptional start site. Originally defined as a 14-nucleotide sequence CT-GAA--TTC-AG (Pelham 1982), the HSE has recently been revised by further analysis to two or three modules consisting of alternating GAA or TTC blocks, arranged in alternating orientations and at 2-nucleotide intervals (Amin et al. 1988; Xiao and Lis 1988; see Lis et al., this volume). In this chapter, we focus on our current understanding of the transcriptional activator protein that stimulates the synthesis of heat shock mRNA through interaction with the HSE. Transcription factors that regulate some heat shock genes through cis elements that are unrelated to the HSE are not covered in this discussion. Initial evidence for a factor that interacts with the HSE came from studies of protein/DNA interactions in Drosophila cell nuclei, in which a factor, heat shock activator protein, was found to bind specifically to the HSE only upon heat shock stimulation (Wu 1984a,b); parallel studies using DNA-binding and in vitro transcription assays also identified a heat shock transcription factor that bound specifically to the HSE (Parker and Topol 1984). At the 1987 Cold Spring Harbor Meeting entitled “The Role of Heat Shock and Stress Response in Biology and Human Disease,” HSE-binding factors were given a general designation: heat shock factor (HSF). In the following discussion,...