3′ repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1.

Transcription factors activated by exogenous or endogenous stimuli alter gene expression with major effects on chromatin accessibility and the epigenome. This thesis investigates that impact of environmental chemical and hormonal exposure on liver chromatin accessibility in a mouse liver model. Exposure to the constitutive androstane receptor (CAR)-specific agonist ligand 1,4-bis-[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP) induces localized changes in chromatin accessibility at several thousand DNase hypersensitive sites (DHS). Activating histone marks, associated with enhancers and promoters, were induced by TCPOBOP and were highly enriched at opening DHS. Opening DHS were highly enriched for CAR binding sites and nuclear receptor direct repeat-4 motifs. These DHS were also enriched for the CAR heterodimeric partner RXRA, binding by CEBPA and CEBPB, and motifs for other liver-specific factors. Thus, TCPOBOP alters the enhancer landscape through changes in histone marks and by mechanisms linked to induced CAR binding. In other studies, the impact of pituitary growth hormone (GH) secretion patterns on chromatin accessibility changes associated with sex-biased liver gene expression was examined. In adult male liver, the transcription factor STAT5 is directly activated by each successive plasma GH pulse. In female liver, STAT5 is persistently activated by the near-continuous stimulation by plasma GH. A majority of the ~4,000 GH-regulated, sex-biased DHS have chromatin marks characteristic of enhancers and were enriched for proximity to sex-biased gene promoters. Chromatin accessibility is thus a key feature of sex-differential gene expression. Two major classes of male-biased DHS were identified: dynamic male-biased DHS, almost all bound by STAT5, which undergo repeated cycles of chromatin opening and closing induced by each GH pulse; and static male-biased DHS, whose accessibility is unaffected GH/STAT5 pulses and whose sex bias results from these chromatin sites being more closed in female liver. Sites with STAT5 binding showed greater chromatin opening, many of which also contain the STAT5 motif. Finally, the effect of a single GH pulse on hypophysectomized male mouse liver was investigated to identify DHS responsive to the male, pulsatile-GH, secretion pattern. These studies demonstrate that widespread epigenetic changes associated with target gene expression are induced by xenobiotics and hormones regulating liver gene expression. / 2022-01-31T00:00:00Z

Sepsis is defined as a life-threatening organ dysfunction that results in systemic activation of coagulation and inflammation in response to microbial infection. Neutrophil extracellular traps (NETs) have shown to be an important interface between innate immunity and coagulation in sepsis. The major structural components of NETs are nucleosomes (DNA-histone complexes). Although nucleosomes do not modulate coagulation, there are conditions where DNA and histones dissociate from each other in the circulation (e.g. in the presence of heparan sulfate or therapeutic heparin binding histones, or DNase digestion of DNA). In vitro, purified DNA was reported to activate coagulation, but this procoagulant activity has been questioned due to isolation methods that yield DNA that is contaminated with other procoagulant molecules. On the other hand, histones have been shown to not only activate coagulation but are cytotoxic to endothelial cells. However, their contribution to the pathogenesis of sepsis has yet to be determined in an in vivo model. Understanding the contribution of DNA, histones, and nucleosomes to the pathogenesis of sepsis may allow us to develop novel therapies that may prove targeting multiple components of NETs (i.e. DNA and histones) may be beneficial. Consequently, in this thesis, we (1) identified methods of DNA purification that produce DNA that is free of contamination and confirmed the procoagulant properties of the isolated DNA, (2) determined the harmful effects of DNA, histones, and nucleosomes cytotoxicity, coagulation, and inflammation in vitro and in vivo, (3) and then we explored the possibility of targeting both DNA and histones using a combination approach of DNase I and heparin in a mouse model of sepsis. Since heparin is administered to patients as a thromboprophylaxis and DNase I is a potential therapy in sepsis, it is important to understand any potential drug-drug interactions. / Thesis / Doctor of Philosophy (PhD) / Sepsis is a type of blood poisoning that occurs when the body has an over reactive response to an infection. This can lead to tissue damage, organ failure, and death. Sepsis is recognized as a global health priority. The death rate from sepsis is high between 15% to 30%, suggesting that an improved understanding of how sepsis leads to death may develop into new therapies. Recently, it was discovered that high levels of free-floating DNA and histones in the blood can predict death in sepsis. The DNA and histones are likely released by white blood cells in response to trying to fight off the infection. In test tubes, free-floating DNA can trigger clotting of blood. DNA often exists in blood together with histones. In test tubes, histones can kill blood vessels and make blood thicker. However, no one has confirmed that DNA and/or histones are harmful to mammals and contributes to death in sepsis. Some new studies show that getting rid of DNA with injections of DNase I minimally increases survival in mice. Other studies show that removing histones with a treatment called heparin shows a small increase in survival in mice. Heparin is also a blood thinner and decreases inflammation. No one knows if these drugs used together can improve sepsis survival. Because both drugs on their own show some survival improvement in sepsis, perhaps using them together will cure sepsis. This thesis has three objectives: (1) to confirm the clotting properties of free-floating DNA, (2) to find out if DNA and/or histones contributes to death in sepsis, and (3) if using a combination of DNase I and heparin can cure sepsis in a mouse model. Finding new therapies for sepsis can save millions of people's lives and decrease the financial burden on society and healthcare systems.

Neutrophil extracellular traps (NETs) are a link between infection and coagulation in sepsis. The major structural component of NETs is nucleosomes, consisting of DNA and histones. NETs not only act as a scaffold to trap platelets, but NET components also promote coagulation and impair fibrinolysis. Thus, removal of extracellular DNA by DNases may be a potential therapeutic strategy for sepsis. Since heparin is used for thromboprophylaxis in sepsis and may also be a potential anti-sepsis therapy, we investigated the mechanisms by which various forms of heparins modulate DNase function. There are two types of DNases in vivo: DNase I (produced by exocrine and endocrine glands) and DNase1L3 (secreted by immune cells). DNase I cleaves free DNA, whereas DNase1L3 preferentially cleaves DNA in complex with proteins such as histones. In this study, we investigated how DNase I and DNase1L3 activities are modulated by the following heparins: unfractionated heparin (UFH), enoxaparin (a low-molecular-weight heparin), Vasoflux (a low-molecular-weight, non-anticoagulant heparin), and fondaparinux (the pentasaccharide unit). Using agarose gel experiments, we showed that UFH, enoxaparin, and Vasoflux enhance the ability of DNase I to digest DNA-histone complexes (presumably by displacing DNA from histones), whereas fondaparinux does not. These findings are consistent with the KD values of the binding of heparin variants to histones, with fondaparinux having >1000-fold lower affinity for histones compared to the other heparins. Taken together, our data suggests that the ability of heparin to enhance DNase I-mediated digestion of DNA-histone complexes is size-dependent and independent of the pentasaccharide region of heparin. With respect to DNase1L3, we observed that it is able to digest histone-bound DNA, and that all heparins, except fondaparinux, inhibited DNase1L3-mediated digestion of histone-bound DNA. Next, we visualized the degradation of NETs by fluorescence microscopy. DNase I (± heparin variants) completely degraded NETs, presumably by digesting extracellular chromatin at histone-free linker regions, thereby releasing nucleosome units. DNase1L3 also degraded NETs, but not as effectively as DNase I, and was inhibited by all heparins except fondaparinux. Finally, we showed that DNase I levels are decreased and DNase1L3 levels are elevated in septic patients. Taken together, our findings demonstrate that heparin modulates the function of DNases, and that endogenous DNase levels are altered in sepsis pathophysiology. / Thesis / Master of Science (MSc) / Sepsis, a life-threatening condition due to hyperactivation of the immune system in response to infection, results in widespread inflammation and blood clotting. During sepsis, immune cells release sticky strands of DNA that block blood vessels and damage organs. Two different enzymes in the blood (DNase I and DNase1L3) can digest these DNA strands, and may represent a new class of anti-sepsis drugs. Our goal was to determine how heparins, commonly used blood thinners, alter the function of these enzymes. We found that (a) larger-sized heparins improved the activity of DNase I towards DNA-histone complexes and do not require any specific portion of heparin, (b) DNase I is more efficient than DNase1L3 in digesting DNA strands released from immune cells, and (c) levels of DNase I and DNase1L3 are altered in septic patients. Taken together, our studies provide new insights into how these enzymes function.

Enhancers regulate gene expression through epigenetic mechanisms influenced by internal and external stimuli. In mouse liver, growth hormone and environmental chemical exposures activate enhancers regulating gene expression in part through changes in chromatin accessibility. Identifying functional enhancers in the complex environment of mouse liver is challenging. This thesis presents HDI-STARR-seq, a massively parallel STARR-seq reporter assay that combines hydrodynamic injection (HDI)-driven plasmid delivery to mouse liver cells in vivo with expression from the liver-specific Albumin promoter to assay functional changes in enhancer-driven transcription induced by sex-dependent hormonal stimulation and xenobiotic exposure. HDI-STARR-seq employs a minimal albumin promoter, shows minimal innate immune response and apparently facilitates plasmid chromatinization recapitulating endogenous liver chromatin states. The assay is robustly reproducible in a small reporter library (~100 regions) and can be scalable for genome-wide analysis using 25,000-50,000 synthetic DNA fragments or enzyme-released mouse liver genomic fragments. Single nucleus-based 10x Genomics Multiome analysis identified accessible mouse liver chromatin regions genome-wide, their linked target genes in hepatocytes, and their differential accessibility between sexes and following exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand. Using HDI-STARR-seq, functional enhancer activity was determined for 1,789 accessible chromatin regions across biological conditions, identifying many sex-biased, GH-regulated enhancers undergoing chromatin changes. The regulated enhancers were associated with enrichment for H3K4me1 and H3K27ac histone marks, showed regulated activities that matched activating histone marks and contained Hnf4a and other enriched motifs in male-biased, GH-repressed enhancer sets. Further, the impact of TCPOBOP exposure for 1 day or 2 weeks on HDI-STARR-seq activity was evaluated in mice of both sexes at 1,834 accessible chromatin regions. Induced H3K27ac and static H3K4me1 were enriched at TCPOBOP-responsive enhancers, as were DR4 motifs bound by CAR/RXR heterodimers. Motifs bound by Tcf, involved in cell proliferation, were enriched in HDI-STARR-seq active enhancers only after 2-week TCPOBOP exposure, indicating activation of a late responding signaling pathway. This research gives novel insights into the relationship between functional enhancer activity in mouse liver and hormonal and xenobiotic regulated epigenetic landscapes, and establishes the utility of HDI-STARR-seq for discovery of biologically relevant enhancer sequences in vivo. / 2026-09-18T00:00:00Z

Les patients mucoviscidosiques sont prédisposés à une colonisation chronique de l’arbre bronchique par P. aeruginosa. Ce pathogène opportuniste se caractérise par sa capacité à adhérer à une surface et à y former un biofilm protecteur, hautement tolérant aux agents antimicrobiens. En routine, les antibiogrammes sont effectués sur des cultures bactériennes planctoniques. L’efficacité des antibiothérapies ainsi sélectionnées est donc peu probante pour l’éradication des biofilms bactériens. La réalisation d’Antibiofilmogrammes® sur des isolats cliniques mucoviscidosiques (nouvel outil évaluant la sensibilité des bactéries sessiles aux antibiotiques) a permis de mettre en évidence des phénomènes d’inhibition et d’induction de la formation du biofilm. Plus précisément, les aminosides sont capables de retarder l’adhérence bactérienne. À l’inverse, la famille des β-lactamines présente la capacité de stimuler l’adhésion précoce des micro-organismes. Ces différents effets de l’antibiothérapie générale sur le comportement microbien se vérifient par l’intermédiaire de techniques conventionnelles in vitro (Cristal Violet, traitement enzymatique à la DNase I) et cellulaires (modèle de co-culture statique cellules eucaryotes/bactéries). La pertinence clinique de l’Antibiofilmogramme® se confirme donc par sa capacité à détecter l’initiation précoce de l’adhésion bactérienne, à sélectionner les molécules l’inhibant et à écarter celles pouvant l’induire. Associée aux antibiogrammes traditionnels, son application peu permettre d’affiner les stratégies thérapeutiques pour le traitement des infections pulmonaires chroniques développées au cours de la mucoviscidose. / Cystic fibrosis (CF) patients are predisposed to chronic colonisation of the upper airways by P. aeruginosa. This opportunist pathogen is characterized by its ability to adhere to a surface and to form a protective biofilm, which is highly tolerant to antimicrobials. In routine, antibiograms are realised on planktonic bacterial cultures. The efficacy of the corresponding antimicrobial therapies appears low for the eradication of bacterial biofilms. The realisation of Antibiofilmograms® on CF clinical isolates (a new tool investigating the susceptibility of sessile bacteria to antibiotics) highlighted phenomena of biofilm formation inhibition and induction. More precisely, aminoglycosides are able to delay the bacterial adherence. Conversely, the β-lactam family shows the ability to stimulate the early adhesion of microorganisms. These different effects of antimicrobials on the bacterial behaviour are confirmed with more conventional in vitro methods (Crystal Violet, enzymatic treatment with DNase I) and a cell model (static co-culture of eukaryotic cells and bacteria). The clinical relevance of the Antibiofilmogram® is reinforced by its ability to detect the initiation of the early bacterial adhesion, to select inhibitor molecules and to avoid the inducer ones. Associated to traditional antibiograms, its application should be pertinent to optimise the CF therapies for the treatment of chronic lung infections.

Cis-regulatorische Elemente wie Promotoren und Enhancer, die die Regulation der Transkription von Genen steuern, befinden sich in Regionen des dekondensierten Chromatins. DNase-seq und ATAC-seq sind weit verbreitete Verfahren, um solche offenen Chromatinregionen genomweit zu untersuchen. Die einzel-Nukleotid-Auflösung von DNase-seq wurde des Weiteren genutzt, um Transkriptionsfaktor-Bindungsstellen (TFBS) in regulatorischen Regionen durch TF-Footprinting zu bestimmen. Kürzlich durchgeführte Studien haben jedoch gezeigt, dass DNase I einen Sequenzbias aufweist, welcher nachteilige Auswirkungen auf die Footprinting-Effizienz hat. Auch wurden das Footprinting und die Auswirkungen des Sequenzbias auf ATAC-seq noch nicht umfassend untersucht. In dieser Arbeit nehme ich einen systematischen Vergleich der beiden Methoden vor und zeige, dass die beiden Methoden unterschiedliche Sequenzbiases haben und korrigiere diese protokollspezifischen Biases beim Footprinting. Der Einfluss von Bias-Korrekturen der Footprinting Ergebnisse ist für DNase-seq größer als für ATAC-seq, und Footprinting mit DNase-seq führt zu besseren Ergebnissen in unserer Datensätze. Trotz dieser Unterschiede zeige ich, dass die Integration replizierter Experimente die Ableitung von qualitativ hochwertigen Footprints ermöglicht, wobei die beiden Techniken weitgehend übereinstimmen. Diese Techniken werden ferner eingesetzt, um die cis-regulatorischen Elemente zu charakterisieren, die die Embryogenese der Fruchtfliege Drosophila melanogaster bestimmen. Durch die Verwendung von Embryonen die sich im richtigen Entwicklungsstadium befinden, sowie gewebespezifischer Kernsortierung mit offenem Chromatin-Profiling können zeitlich und gewebespezifisch aufgelöste vermeintliche cis-regulatorische Elemente definiert werden. Zusammengenommen demonstrieren diese Analysen die Fähigkeit der offenen Chromatin-Profilierung und der Computeranalyse zur Aufklärung der Mechanismen der Genregulation. / Cis-regulatory elements such as promoters and enhancers, that govern transcriptional gene regulation, reside in regions of open chromatin. DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions through TF footprinting. However, recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. Furthermore, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. In this thesis, I undertake a systematic comparison of the two methods and demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. The impact of bias correction on footprinting performance is greater for DNase-seq than for ATAC-seq, and footprinting with DNase-seq leads to better performance in our datasets. Despite these differences, I show that integrating replicate experiments allows the inference of high-quality footprints, with substantial agreement between the two techniques. These techniques are further employed to characterize the cis-regulatory elements governing the embryogenesis of a complex organism, the fruit fly Drosophila melanogaster. Combining tight staging of embryos and tissue-specific nuclear sorting with open chromatin profiling, enables the definition of temporally and tissue-specifically resolved putative cis-regulatory elements. Taken together, these analyses demonstrate the power of open chromatin profiling and computational analysis in elucidating the mechanisms of transcriptional gene regulation.

Variation at regulatory elements, identified through hypersensitivity to digestion by Deoxyribonuclease I (DNase I), is believed to contribute to variation in complex traits, but the extent and consequences of this variation are poorly characterized. To investigate the relationship between sequence variation, and the functional consequences of variation in chromatin accessibility, genome-wide DNase I hypersensitive sites (DHS) of terminally differentiated erythroblasts were studied in eight inbred strains of mice studied (A/J, AKR/J, BALBc/J, C3H/HeJ, C57BL/6J, CBA/J, DBA/2J, and LP/J). These strains were selected because of the availability of their genome sequence and quantitative trait loci (QTL) data. After confirming that next generation sequencing could identify DNase I hypersensitive sites with high sensitivity and specificity, and that differential peaks could be found, an automated peak calling pipeline was developed and optimized. 36,693 DHS peaks were identified covering 9.1 Mb (0.29%) of mouse genome. There was no indication of within strain variation. Between strains reproducible variation was observed at approximately 5% of DNase hypersensitive sites (1,397 DHSs). Variable DHSs were more likely to be enhancers than promoters and less likely to occur at conserved regions of the genome. Only 36% of such variable DHSs contain a sequence variant predictive of site variation and 12% contain at least one variant that disrupts transcription factor binding sites. The majority (86%) of variable DHSs differ in size/shape and the remaining 14% demonstrate discrete variation in single peak or cluster of peaks. Sequence variants within variable DHS are more likely to be associated with complex traits than those in non-variant DHS, and variants associated with complex traits preferentially occur in enhancer-like elements. Changes at a small proportion (7%) of discretely variable DHS are associated with changes in nearby transcriptional activity. Our results show that whilst DNA sequence variation is not the major determinant of variation in open chromatin, where such variants exist they are likely to be causal for complex traits.

The goal of the Encyclopedia of DNA Elements (ENCODE) project has been to characterize all the functional elements of the human genome. These elements include expressed transcripts and genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, or hypersensitive to DNase I cleavage, etc. Chromatin Immunoprecipitation (ChIP-seq) is an experimental technique for detecting TF binding in living cells, and the genomic regions bound by TFs are called ChIP-seq peaks. ENCODE has performed and compiled results from tens of thousands of experiments, including ChIP-seq, DNase, RNA-seq and Hi-C. These efforts have culminated in two web-based resources from our lab—Factorbook and SCREEN—for the exploration of epigenomic data for both human and mouse. Factorbook is a peak-centric resource presenting data such as motif enrichment and histone modification profiles for transcription factor binding sites computed from ENCODE ChIP-seq data. SCREEN provides an encyclopedia of ~2 million regulatory elements, including promoters and enhancers, identified using ENCODE ChIP-seq and DNase data, with an extensive UI for searching and visualization. While we have successfully utilized the thousands of available ENCODE ChIP-seq experiments to build the Encyclopedia and visualizers, we have also struggled with the practical and theoretical inability to assay every possible experiment on every possible biosample under every conceivable biological scenario. We have used machine learning techniques to predict TF binding sites and enhancers location, and demonstrate machine learning is critical to help decipher functional regions of the genome.

Pathogenesis of enterotoxigenic Escherichia coli (ETEC) and Shigella flexneri relies predominantly on members of the AraC/XylS family of transcriptional regulators, Rns (or its homolog, CfaD) and MxiE, respectively. Rns/CfaD regulate the expression of pili, which allow the bacteria to attach to the intestinal epithelium. Better understanding of the role Rns plays in virulence was attained by expanding our knowledge of the Rns regulon, revealing that it functions as an activator of cexE, a previously uncharacterized gene. By in vitro DNase I footprinting two Rns-binding sites were identified upstream of cexEp, both of which are required for full activation of cexE. The amino terminus of CexE also contains a secretory signal peptide that is removed during translocation to the periplasm. Though the function of CexE remains unknown, these studies suggest that CexE is a novel ETEC virulence factor since it is regulated by Rns/CfaD. In Shigella flexneri, the expression of a subset of virulence genes (including, ipaH9.8 and ospE2) is dependent upon the activator MxiE and a cytoplasmic chaperone IpgC. To define the molecular mechanism of transcriptional activation by this chaperone-activator pair, an in vitro pull down assay was performed revealing that MxiE specifically interacts with IpgC in a complex. Additionally, IpgC recognizes three polypeptide regions in MxiE: within MxiE(1-46), MxiE(46-110) and MxiE(196-216). Furthermore, it seems that MxiE and IpgC regulate transcription of ipaH9.8 and ospE2 promoters differently. In the bacterium, the formation of the MxiE-IpgC complex is initially prevented because IpgC is sequestered in individual complexes with effector proteins, IpaB and IpaC. Upon contact with an eukaryotic host cell the effector proteins are secreted, thereby freeing IpgC to form a complex with MxiE and activate the expression of virulence genes. This new characterization of the role of Rns and MxiE in virulence gene regulation in ETEC and S. flexneri, respectively will give new insights into the pathogenesis of the regulators.