Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus... Show moreViruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the synthesis of viral enzymes), replication, transcription and encapsidation into progeny virions. The multifunctional nature of these viral RNA genomes requires the tight control of all these processes for which they are equipped with RNA sequence motifs and higher order RNA structures. At 25-32 kilobases, nidoviruses possess the largest known RNA genomes. One characteristic of nidoviruses is that in infected cells they produce a nested set of subgenomic (sg) mRNAs. The sg mRNAs of two nidovirus families, arteri- and coronaviruses, consist of two RNA stretches that are noncontiguous in the genome. It was demonstrated that primary and higher order RNA structures play a crucial role during the synthesis of these special sg mRNAs. The obtained knowledge of arterivirus RNA synthesis, formed the basis for an virus inhibitor study in which regulatory RNA sequences were targeted in an attempt to block virus replication in cell culture using phosphorodiamidate morpholino oligomers (P-PMOs). Show less
What we collectively call “stress” is how we experience our body’s reaction to a stressor. This response is aimed to deal with the current stressor and to prepare for recurrences in the future. The... Show moreWhat we collectively call “stress” is how we experience our body’s reaction to a stressor. This response is aimed to deal with the current stressor and to prepare for recurrences in the future. The stress response is for an important part dependent on glucocorticoid hormones. By and large, the acute response to glucocorticoids is beneficial, but chronic exposure often becomes maladaptive. To improve prevention and treatment of disorders we can develop due to stress, it is important to better understand the effects and working mechanisms of glucocorticoids. While we already possess extensive knowledge regarding glucocorticoids and glucocorticoid receptor signaling, we introduced and studied five “aspects of context”, which we felt address important current misconceptions or gaps of knowledge. Corticosterone was at the center of all the studies we performed, yet the eventual outcome of glucocorticoid receptor activation differed extensively in all experiments. Thus, the context in which corticosterone exerts its effects matters, and it is to researcher to be aware of this when designing new studies and interpreting available data. Whilst our research merely addressed some specific processes, the lessons learned from these experiments can be applied much broader to the biology of glucocorticoid signaling and other nuclear family members. Show less
Corticosteroid hormones act in the brain to support adaptation to stress via binding to mineralocorticoid and glucocorticoid receptors (MR and GR). These receptors act in large measure as... Show moreCorticosteroid hormones act in the brain to support adaptation to stress via binding to mineralocorticoid and glucocorticoid receptors (MR and GR). These receptors act in large measure as transcription factors. Corticosteroid effects can be highly divergent, depending on the receptor type, but also on brain region, cell type, and physiological context. These differences ultimately depend on differential interactions of MR and GR with other proteins, which determine ligand binding, nuclear translocation, and transcriptional activities. In this review, we discuss established and potential mechanisms that confer receptor and cell type-specific effects of the MR and GR-mediated transcriptional effects in the brain. Show less
Nucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional... Show moreNucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional chromosome re-modelling. This dissertation provides the first evidence to support this hypothesis. Using ensemble RT-qPCR and 3C-qPCR, in addition to in vivo and in vitro single molecule fluorescence microscopy techniques, the interplay between the expression of the H-NS-regulated, osmosensitive proVWX operon of Escherichia coli and structural re-modelling of the operon is shown. The formation of a loop anchored between the P2 promoter of proVWX and the terminus of the operon represses its expression. Destabilization of the loop activates transcription. The model presented in this thesis provides clues for how H-NS and H-NS-like proteins may regulate the expression of other operons and genes within their regulons. Show less
This thesis spans several years of work dedicated to understanding fish genomes. In the first chapter it describes the genome of the first fish for which the entire genome was sequenced through a... Show moreThis thesis spans several years of work dedicated to understanding fish genomes. In the first chapter it describes the genome of the first fish for which the entire genome was sequenced through a large-scale international project, Fugu rubripes. the pufferfish. In particular, it highlights how this fish has a genome that contains as many genes as the human genome, although it is ten times smaller. It also shows that the majority of genes that are found in the human genome can be found in this fish genome as well. In the second chapter we compared fish genomes to the human genome to find regions that have been preserved during evolution and which are therefore likely to have a function, even though they are not genes. We showed that indeed they are functional, and they help to regulate other genes. Knowing all the genes in the genome we could then interrogate how they are expressed, i.e. if they are switched __on__ or __off__ and in particular in chapter 4 we looked at how a specific gene is in charge of gradually switching off genes that are inherited from the mother in a newborn fish embryo. Finally in the last chapter since genome sequencing is now becoming much cheaper and simpler to achieve we set out to map the genome of the common carp and we discuss the best approaches and strategies to obtain a good genome sequence for this species. The common carp is a candidate model system for high-troughput screening. Show less
Grainyhead like 2 (GRHL2) is an essential transcription factor for development and function of epithelial tissues. It has dual roles in cancer by supporting tumor growth while suppressing... Show moreGrainyhead like 2 (GRHL2) is an essential transcription factor for development and function of epithelial tissues. It has dual roles in cancer by supporting tumor growth while suppressing epithelial to mesenchymal transitions (EMT). GRHL2 cooperates with androgen and estrogen receptors (ER) to regulate gene expression. We explore genome wide GRHL2 binding sites conserved in three ER?/GRHL2 positive luminal breast cancer cell lines by ChIP-Seq. Interaction with the ER?/FOXA1/GATA3 complex is observed, however, only for a minor fraction of conserved GRHL2 peaks. We determine genome wide transcriptional dynamics in response to loss of GRHL2 by nascent RNA Bru-seq using an MCF7 conditional knockout model. Integration of ChIP- and Bru-seq pinpoints candidate direct GRHL2 target genes in luminal breast cancer. Multiple connections between GRHL2 and proliferation are uncovered, including transcriptional activation of ETS and E2F transcription factors. Among EMT-related genes, direct regulation of CLDN4 is corroborated but several targets identified in other cells (including CDH1 and ZEB1) are ruled out by both ChIP- and Bru-seq as being directly controlled by GRHL2 in luminal breast cancer cells. Gene clusters correlating positively (including known GRHL2 targets such as ErbB3, CLDN4/7) or negatively (including TGFB1 and TGFBR2) with GRHL2 in the MCF7 knockout model, display similar correlation with GRHL2 in ER positive as well as ER negative breast cancer patients. Altogether, this study uncovers gene sets regulated directly or indirectly by GRHL2 in luminal breast cancer, identifies novel GRHL2-regulated genes, and points to distinct GRHL2 regulation of EMT in luminal breast cancer cells. Show less
The cellular response to transcription-blocking DNA lesions involves the stalling of elongating RNA Polymerase II (RNAPIIo) at the lesion as well as a global shutdown of transcription. The stalling... Show moreThe cellular response to transcription-blocking DNA lesions involves the stalling of elongating RNA Polymerase II (RNAPIIo) at the lesion as well as a global shutdown of transcription. The stalling of RNAPIIo at such lesions initiates the transcription-coupled nucleotide excision repair pathway (TCR) to efficiently remove the damage and restore transcription. The TCR proteins, CSB, CSA, and UVSSA, are essential for the repair of transcription-blocking DNA lesions, but how the interplay between these proteins targets the core repair machinery, including the TFIIH complex, to lesion stalled RNAPIIo remains largely unknown.Here, we demonstrate a sequential and highly cooperative assembly of TCR proteins and unveil the mechanism for TFIIH recruitment to DNA damage-stalled RNAPIIo. Importantly, we identified the previously uncharacterized ELOF1 gene as a core TCR factor with an additional role in preventing DNA damage during DNA replication. Show less
More than 45 years of research on the effects of glucocorticoids on brain function has yielded many insights, but also left a number of longstanding questions. One conundrum has been how activation... Show moreMore than 45 years of research on the effects of glucocorticoids on brain function has yielded many insights, but also left a number of longstanding questions. One conundrum has been how activation of the structurally comparable mineralocorticoid receptor (MR) and glucocorticoid receptor (GR) can lead to very different, or even opposite effects. It also remained unclear how the consequence of activation of a single receptor, GR, can differ from cell to cell and from situation to situation. In this thesis we have investigated two aspects of transcriptional regulation in response to glucocorticoids: the cause of MR/GR specificity, and the role of crosstalk with other transcription factors. Within the hippocampus, we found NeuroD factors to drive the specificity in corticosteroid receptor DNA binding and subsequent gene regulation, i.e. by stimulating MR signaling. We identified Jun dimerization protein 2 (Jdp2) as a stress-responsive MR-specific target gene. In a stress hormone relevant memory task, GR was suggested to act context-dependently and several novel GR target genes were detected. Further elucidation of distinct MR/GR downstream pathways will enable us to better understand the stress physiology and more specifically target aspects of glucocorticoid signaling for treatment of stress-related disorders. Show less
This thesis describes the investigation of the transcriptional regulation of the gene for anticoagulant plasma Protein S, PROS1. Protein S is a cofactor for Protein C in the Protein C anticoagulant... Show moreThis thesis describes the investigation of the transcriptional regulation of the gene for anticoagulant plasma Protein S, PROS1. Protein S is a cofactor for Protein C in the Protein C anticoagulant pathway. The coagulation cascade is negatively regulated by this pathway through inactivation of activated clotting factors V and VIII. Protein S deficiency is associated with an increased risk for the development of deep venous thrombotic disease and the deficiency can either be hereditary or acquired. The presented research was mainly aimed at resolving several basic scientific issues regarding the regulation of transcription of PROS1. In Chapter 2 we identified 3 transcription start sites through which transcription is mainly driven. In chapters 3 and 4 we investigated which transcription factors are involved in PROS1 transcription. We found an interaction of several transcription factors with the Protein S gene promoter and showed that constitutive transcriptional activity is mainly directed by transcription factor Sp1. Chapter 5 describes the regulation of Protein S levels by inflammatory mediator interleukin 6. The effect of interleukin 6 on Protein S levels was shown to be mediated though a direct interaction of transcription factor STAT3 with the Protein S gene promoter. In Chapter 6 an alternative PROS1 transcript is described. The protein that is generated from this transcript in vitro was shown not to be excreted from the cell but instead retained in the cell. Finally, our findings are discussed in Chapter 7. Show less
Plants produce a variety of secondary metabolites. In Catharanthus roseus, several have pharmaceutical applications, including the monomeric alkaloids serpentine and ajmalicine, which are used as a... Show morePlants produce a variety of secondary metabolites. In Catharanthus roseus, several have pharmaceutical applications, including the monomeric alkaloids serpentine and ajmalicine, which are used as a tranquillizer and to reduce hypertension, respectively, and the dimeric alkaloids vincristine and vinblastine, which are potent antitumour drugs. Jasmonic acid (JA) is a key defense hormone, which controls the expression of several alkaloid biosynthesis genes in Catharanthus. The JA-responsive expression is controlled by the AP2-domain transcription factors ORCA2 and ORCA3. The results in this thesis demonstrate that JA-responsive ORCA expression is controlled by an up-stream positive regulator, whose activities are affected by a family of repressors. Understanding the regulation mechanism may help to generate a very valuable tool for engineering the production of valuable secondary metabolites. Show less
