Molecular Mechanisms of Nuclear Hormone Receptor Transcriptional Synergy and Autoinduction.

Thyroid hormone (TH) and glucocorticoids (GC) play critical roles in the development and function of the central nervous system (CNS) by binding to their cognate nuclear hormone receptors (NRs), which function as ligand-activated transcription factors. In my dissertation, I studied the TH and GC-mediated regulation of Krüppel like factor 9 (Klf9/Basic Transcription Element Binding Protein 1; Bteb1), a member of the Sp1/KLF family of zinc finger transcription factors that bind GC rich genomic sequences, and plays an important role in neuronal development and plasticity. In prior work Klf9 was found to be a direct TH receptor (TR) target gene. I showed that Klf9 is also directly targeted by the GC receptor (GR), and that TH and GCs cause synergistic induction of Klf9. This synergistic regulation is phylogenetically ancient, and was likely present in the earliest tetrapods and has been evolutionarily conserved from frogs to mammals. I identified a genomic region in the 5’ flanking region of the Klf9 gene (the ‘Klf9 synergy module’) that contains TR/GR binding sites and confers synergistic gene regulation by TH and GC. The synergistic effect of TH and GC on Klf9 can be explained by a TR-dependent increase in the recruitment of the GR and enhanced association of stalled RNA polymerase II at the Klf9 synergy module, and an interaction between the synergy module and the Klf9 promoter by chromosomal looping. I also conducted a genome-wide microarray analysis, the first study to identify transcriptional targets that are coordinately regulated by TH and GC in the brain. Lastly, I demonstrated a role for KLF9 as an accessory transcription factor to support TH-dependent expression of TRβ (autoinduction), a process that is necessary for the progression of amphibian metamorphosis, and normal mammalian brain development. Given the synergistic regulation of the Klf9 gene by TR and GR, and its role in TRβ autoinduction, my findings support that KLF9 is an important intermediate that functions to integrate TH and GC by enhancing the cell sensitivity to hormonal signals. Taken together, my thesis broadens our understanding of the molecular mechanisms of NR cooperativity and autoinduction, with important implications for animal development.PHDMolecular, Cellular, and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/93977/1/piab_1.pd

Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells.

The hippocampus is a well-known target of thyroid hormone (TH; e.g., 3,5,3'-triiodothyronine-T3) and glucocorticoid (GC; e.g., corticosterone-CORT) action. Despite evidence that TH and GC play critical roles in neural development and function, few studies have identified genes and patterns of gene regulation influenced by the interaction of these hormones at a genome-wide scale. In this study we investigated gene regulation by T3, CORT, and T3 + CORT in the mouse hippocampus-derived cell line HT-22. We treated cells with T3, CORT, or T3 + CORT for 4 hr before cell harvest and RNA isolation for microarray analysis. We identified 9 genes regulated by T3, 432 genes by CORT, and 412 genes by T3 + CORT. Among the 432 CORT-regulated genes, there were 203 genes that exhibited an altered CORT response in the presence of T3, suggesting that T3 plays a significant role in modulating CORT-regulated genes. We also found 80 genes synergistically induced, and 73 genes synergistically repressed by T3 + CORT treatment. We performed in silico analysis using publicly available mouse neuronal chromatin immunoprecipitation-sequencing datasets and identified a considerable number of synergistically regulated genes with TH receptor and GC receptor peaks mapping within 1 kb of chromatin marks indicative of hormone-responsive enhancer regions. Functional annotation clustering of synergistically regulated genes reveal the relevance of proteasomal-dependent degradation, neuroprotective effect of growth hormones, and neuroinflammatory responses as key pathways to how TH and GC may coordinately influence learning and memory. Taken together, our transcriptome data represents a promising exploratory dataset for further study of common molecular mechanisms behind synergistic TH and GC gene regulation, and identify specific genes and their role in processes mediated by cross-talk between the thyroid and stress axes in a mammalian hippocampal model system

Stressor and Glucocorticoid-Dependent Induction of the Immediate Early Gene Krü ppel-Like Factor 9: Implications for Neural Development and Plasticity

Krü ppel-like factor 9 (KLF9) is a thyroid hormone-induced, immediate early gene implicated in neural development in vertebrates. We analyzed stressor and glucocorticoid (GC)-dependent regulation of KLF9 expression in the brain of the frog Xenopus laevis, and investigated a possible role for KLF9 in neuronal differentiation. Exposure to shaking/confinement stressor increased plasma corticosterone (CORT) concentration, and KLF9 immunoreactivity in several brain regions, which included the medial amygdala and bed nucleus of the stria terminalis, anterior preoptic area (homologous to the mammalian paraventricular nucleus), and optic tectum (homologous to the mammalian superior colliculus). The stressor-induced KLF9 mRNA expression in the brain was blocked by pretreatment with the GC receptor antagonist RU486, or mimicked by injection of CORT. Treatment with CORT also caused a rapid and dose-dependent increase in KLF9 mRNA in X. laevis XTC-2 cells that was resistant to inhibition of protein synthesis. The action of CORT on KLF9 expression in XTC-2 cells was blocked by RU486, but not by the mineralocorticoid receptor antagonist spironolactone. To test for functional consequences of up-regulation of KLF9, we introduced a KLF9 expression plasmid into living tadpole brain by electroporation-mediated gene transfer. Forced expression of KLF9 in tadpole brain caused an increase in Golgi-stained cells, reflective of neuronal differentiation/maturation. Our results support that KLF9 is a direct, GC receptor target gene that is induced by stress, and functions as an intermediary in the actions of GCs on brain gene expression and neuronal structure. S tress can have profound and complex effects on brain function and morphology, and consequently on learning, memory, and behavior. The effects of stress can be facilitatory or inhibitory, the outcome dependent on the duration and type of stressor, and the behavioral context within which the stress is experienced. Chronic stress leads to neurodegeneration and impairment of learning and memory (1-3). By contrast, short-term stress may enhance neurotransmission, promote long-term potentiation (LTP), increase dendritic spine density in the hippocampus, and facilitate memory consolidation and reconsolidation (1-5). Stress hormone actions on the brain lead to changes in neuronal structure, but little is known about the transcriptional mechanisms that underlie cellular changes after exposure to a stressor (3). The primary vertebrate stress hormones, the glucocorticoids (GCs), are responsible for many effects of stress on the brain, and their actions are mediated by two nuclear receptors, the mineralocorticoid receptor (MR) and the GC receptor (GR) (6, 7). Receptors located in the plasma membrane transduce rapid, nongenomic actions of GCs on neural function (8 -10). The initial, facilitatory effects of GCs on neurotransmission and induction of LTP may be mediated by membrane GRs, whereas subsequent genomic actions, dependent on the nuclear GR, may reverse and normalize the enhanced excitability (2) and generate structural changes in neurons (3). This is considered to be an adaptive mechanism for limiting the stress response (i.e. through negative feedback) and facilitating information storage. Earlier, we showed that a member of the Sp/Krü ppel-like family of zinc-finger domain transcription factors (11, 12), the Krü ppellike factor 9 (KLF9) [also basic transcription element binding protein 1 (13)], plays a key role in thyroid hormone-dependent actions on neurite extension and branching (14 -18). Forced expression of KLF9 in Neuro-2a cells caused a dose-dependen

Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module.

Cooperative, synergistic gene regulation by nuclear hormone receptors can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid hormone (TH) and glucocorticoid (GC) synergy on the Krüppel-like factor 9 (Klf9) gene, which codes for a zinc finger transcription factor involved in development and homeostasis of diverse tissues. We identified regions of the Xenopus and mouse Klf9 genes 5-6 kb upstream of the transcription start sites that supported synergistic transactivation by TH plus GC. Within these regions, we found an orthologous sequence of approximately 180 bp that is highly conserved among tetrapods, but absent in other chordates, and possesses chromatin marks characteristic of an enhancer element. The Xenopus and mouse approximately 180-bp DNA element conferred synergistic transactivation by hormones in transient transfection assays, so we designate this the Klf9 synergy module (KSM). We identified binding sites within the mouse KSM for TH receptor, GC receptor, and nuclear factor κB. TH strongly increased recruitment of liganded GC receptor and serine 5 phosphorylated (initiating) RNA polymerase II to chromatin at the KSM, suggesting a mechanism for transcriptional synergy. The KSM is transcribed to generate long noncoding RNAs, which are also synergistically induced by combined hormone treatment, and the KSM interacts with the Klf9 promoter and a far upstream region through chromosomal looping. Our findings support that the KSM plays a central role in hormone regulation of vertebrate Klf9 genes, it evolved in the tetrapod lineage, and has been maintained by strong stabilizing selection. Mol Endocrinol 2015 Jun; 29(6):856-72