Nitrogen (N), an essential plant macronutrient, is among the most limiting factors of crop yield. To sustain modern agriculture, N is often amended in soil in the form of chemical N fertilizer, a major anthropogenic contributor to nutrient pollution that affects climate, biodiversity and human health. To achieve agricultural sustainability, a comprehensive understanding of the regulation of N response in plants is required, in order to engineer crops with higher N use efficiency. Recently, epigenetic mechanisms, such as histone modifications, have gained increasing importance as a new layer of regulation of biological processes. However, our understanding of how epigenetic processes regulate N uptake and assimilation is still in its infancy. To fill this knowledge gap, we first performed a meta-analysis that combined functional genomics and network inference approaches to identify a set of N-responsive epigenetic regulators and predict their effects in regulating epigenome and transcriptome during plant N response. Our analysis suggested that histone modifications could serve as a regulatory mechanism underlying the global transcriptomic reprogramming during plant N response. To test this hypothesis, I applied chromatin immunoprecipitation-sequencing (ChIP-Seq) to monitor the genome-wide changes of four histone marks (H3K27ac, H3K4me3, H3K36me3 and H3K27me3) in response to N supply in tomato plants, followed by RNA-Seq to profile the transcriptomic changes. To investigate the organ specificity of histone modifications, I assayed shoots and roots separately. My results suggest that up to two-thirds of differentially expressed genes (DEGs) are modified in at least one of the four histone marks, supporting an integral role of histone modification in regulating N response. I observed a synergistic modification of active histone marks (H3K27ac, H3K4me3 and H3K36me3) at gene loci functionally relevant to N uptake and assimilation. Surprisingly, I uncovered a non-canonical role of H3K27me3, which is conventionally associated with repressed genes, in modulating active gene expression. Interestingly, such regulatory role of H3K27me3 is specifically associated with highly expressed genes or low expressed genes, depending on the organ context. Overall, I revealed the multi-faceted role of histone marks in mediating the plant N response, which will guide breeding and engineering of better crops with higher N use efficiency

The rationale behind targeted molecular therapy in cancer, oncogene addiction, is that tumors rely on driver oncogenes to control their proliferation and survival. Therefore, an efficacious targeted therapy should induce a dual, detrimental response to the tumor. While there have been clinical success stories using targeted therapies, even tumors that are initially sensitive invariably develop resistance. In the case of triple negative breast cancer (TNBC), despite extensive evidence pointing to its driver oncogene status, inhibitors of the Epidermal Growth Factor Receptor (EGFR) are considered clinically inefficacious. Resistance to EGFR inhibition has been predominantly described as due to genetic alterations. Yet it remains unclear why patients exhibiting the same dysregulated status of a driver oncogene react to targeted therapy, as in the case of EGFR-mutant non-small cell lung cancer, while others do not at all (i.e., TNBC). Furthermore, not all of resistance can be described by genetic alterations to EGFR, to its pathway effectors, or to compensatory pathways. Emerging data reveals that drugs can induce resistance by rewiring epigenomic, transcriptional, and translational regulatory mechanisms. Unfortunately, a major limitation in designing efficacious treatments is our inability to predict whether cell types can rewire in response to drug exposure. Therefore, it is necessary to elucidate mechanisms of growth and survival in cells that have undergone rewiring. This study characterized intrinsic resistance to EGFR inhibition in TNBC. We found that EGFR inhibition induces rewiring, which results in a resistant growth state that bypasses the EGFR-MAPK pathway as a whole. Additionally, we found that a tRNA-modifying complex masks the oncogene addiction status of EGFR in TNBC by stabilizing the protein abundance of a pro-survival protein. Importantly, this happens solely in the context of EGFR inhibition. Taken together, this study highlights potential therapeutic strategies for TNBC and strategies that can be used to improve our understanding of targeted therapy resistance, especially intrinsic resistance.

<p>Lung cancer is the third most prevalent cancer in the world; however it is the leading cause of cancer related deaths worldwide. Non-small cell lung cancer (NSCLC) accounts for ~85% of the lung cancer cases. The current strategies to treat NSCLC patients with frequent causal genetic mutations is through targeted therapeutics. Approximately 10-35% of NSCLC patient tumors have activated mutations in the Epidermal Growth Factor Receptor (EGFR) resulting in uncontrolled cellular proliferation. The standard-of care for such patients is EGFR-Tyrosine Kinase Inhibitors (EGFR-TKIs), a class of targeted therapeutics that specifically inhibit EGFR activity. One such EGFR-TKI used in this study is erlotinib. Following erlotinib treatment, tumors rapidly regress at first; however, over 50% of patients develop erlotinib resistance within a year post treatment. Development of resistance remains to be the major challenge in treatment of NSCLC using EGFR-TKIs such as erlotinib. </p> <p>In approximately 60% of cases, acquired erlotinib resistance in patients is attributed to a secondary mutation in EGFR, whereas in about 20% of cases, activation of alternative signaling pathways is the reported mechanism. For the remaining 15-20% of <a>cases</a> the mechanism of resistance remains unknown. Therefore, it can be speculated that the common methods used to identify genetic mutations in tumors post erlotinib treatment, such as histologic analysis and genetic screening may fail to identify alterations in epigenetic mediators of erlotinib resistance, also including microRNAs (miRNAs). MiRNAs are short non-coding RNAs that post-transcriptionally negatively regulate their target transcripts. Hence, in this study two comprehensive screens were simultaneously conducted in erlotinib sensitive cells: 1) a genome-wide knock-out screen, conducted with the hypothesis that loss of function of certain genes drive erlotinib resistance, 2) a miRNA overexpression screen, conducted with the hypothesis that certain miRNAs drive the development of erlotinib resistance when overexpressed. The overreaching goal of the study was to identify novel drivers of erlotinib resistance such as microRNAs or other epigenetic factors in NSCLC.</p><p>The findings of this study led to the identification of a tumor suppressive protein and an epigenetic regulator, SUV420H2 (KMT5C) that has never been reported to be involved in erlotinib resistance. On the other hand, the miRNA overexpression screen identified five miRNAs that contribute to erlotinib resistance that were extensively analyzed using multiple bioinformatic tools. It was predicted that the miRNAs mediate erlotinib resistance via multiple pathways, owing to the ability of each miRNA to target multiple transcripts via partial complementarity. Importantly, a correlation between the two screens was identified clearly supporting the use of two simultaneous screens as a reliable technique to determine highly significant miRNA-target interactions. Overall, the findings from this study suggest that epigenetic factors, such as histone modifiers and miRNAs function as critical mediators of erlotinib resistance, possibly belonging to the 15-20% of NSCLC cases with unidentified mechanisms involved in erlotinib resistance.</p><p></p>

The following work demonstrates that paternal diet controls medically important metabolic phenotypes in offspring. We observe transmission of dietary information to the zygote via sperm, and this information evades reprogramming that typically occurs after fertilization. Cytosine methylation is implicated as a major contributor to meiotic epigenetic inheritance in several transgenerational phenomena. Our extensive characterization of the sperm methylome reveals that diet does not significantly affect methylation patterns. However, we find that extensive epivariability in the sperm epigenome makes important contributions to offspring variation. Importantly, coordinate cytosine methylation and copy number changes over the ribosomal DNA locus contributes to variation in offspring metabolism. Thus, rDNA variability acts independently of postadolescent paternal diet to influence offspring metabolism. Therefore, at least two mechanisms exist for epigenetically controlling offspring metabolism: stochastic epivariation and diet acting by an unknown mechanism to further modulate metabolism. This work argues that an offspring's phenotype can no longer be viewed solely as the result of genetic interactions with the developmental environment - the additional influences of paternal environment and inherited epigenetic variability must also be considered. These findings reveal novel contributions to metabolism that could revolutionize how we think about the risk factors for human health and disease.

<p dir="ltr">Skeletal muscle accounts for 40% of total body weight and the homeostasis of muscle tissue is critical in maintaining proper body function. Skeletal muscle develops during the embryonic stages from the muscle progenitor cells derived from the dermomyotome structure. The myogenic progenitor cells contribute to the primary myogenesis by forming the primary myotubes which are the founding structures that the secondary myogenesis continues to build on. A portion of the myogenic progenitor cells makes up the adult muscle stem cells residing in homeostatic muscle tissue. The adult muscle stem cells contribute substantially for the adult muscle regeneration. Due to the significance of the muscle tissue and the importance of muscle stem cells, dysregulation of the muscle homeostasis or the muscle stem cell homeostasis will result in severe pathological conditions such as myopathy.</p><p dir="ltr">Mitochondria are cellular organelles that are responsible for generating energy needed for cellular processes, especially for muscle tissue where muscle contraction requires the presence of ATP. On the other hand, mitochondria also serve as signaling molecules and provide macromolecules for the biosynthesis. FAM210A (Family With Sequence Similarity 210 Member A) protein was shown to impact the lean mass of human subjects yet a detailed study on the effect of FAM210A in skeletal muscle was not performed, nor has the molecular mechanisms through which FAM210A function been elucidated. Therefore, I take on the task to unveil the function of FAM210A in muscle development, muscle homeostasis and muscle stem cell behavior by using a combination of mouse models with different myogenic promoters to target <i>Fam210a</i> at different developmental stages.</p><p dir="ltr">In the first part of the thesis, I investigated the role of FAM210A in post differentiation myofibers. Using the <i>Myl1</i>^<em>Cre</em> driven deletion of <i>Fam210a</i>, I found that <i>Fam210a</i>^<em>MKO</em> had normal development before 3 weeks of age, but the growth was stagnant from 4 weeks on, and the mice did not survive past 8 weeks of age. I found that the assembly of the ribosomes in the <i>Fam210a</i>^<em>MKO</em> was defective, leading to impaired translation which attenuated the muscle atrophy phenotype. I identified through proteomics that the mitochondrial autophagy and proteostatic control pathways were significantly induced yet mitochondrial organization and energetic proteins were downregulated. Metabolomics analysis showed that the signaling metabolite acetyl-CoA was increased in the <i>Fam210a</i>^<em>MKO</em> which led to increased protein acetylation, specifically, we showed that the ribosomal proteins were hyperacetylated, and that the acetylation increase was elicited by the <i>Fam210a</i>-null mitochondria.</p><p dir="ltr">In the second part of the thesis, I investigated the function of FAM210A in muscle progenitor cells. In the <i>FamMKO</i> mice, I found that deletion of <i>Fam210a</i> from embryonic myogenic progenitor cells led to developmental arrest and postnatal death at day 6. In the <i>FamPKO</i> mice, I found that <i>Fam210a</i> is needed for adult muscle stem cell to contribute to regeneration. Loss of <i>Fam210a</i> leads to the regenerative defects when the muscle was exposed to injury cues. We further showed that <i>Fam210a</i> deletion in muscle stem cells resulted in disruption of the proteostatic control over muscle stem cell activation, thereby forbidding the translational increase necessary to facilitate activation and proliferation. Furthermore, I showed that <i>Fam210a</i> deletion leads to excessive OPA1 cleavage, which contributes to the regenerative failure of muscle stem cells as fusion is required for the mitochondrial network remodeling during regeneration. Therefore, <i>Fam210a</i> safeguards the mitochondrial network and proteostasis during regeneration.</p><p dir="ltr">In summary, my studies characterized the functional contribution of FAM210A during embryonic muscle development, muscle mass maintenance and adult muscle stem cell homeostasis. The regulation of FAM210A in these three processes impinge on the translational regulation. My studies further demonstrated the importance of mitochondrial regulated protein translation in skeletal muscle and muscle stem cells.</p>

<p dir="ltr">H3K27me3 is a transcriptional repressive epigenetic mark that plays vital roles in many biological processes in <i>Arabidopsis thaliana</i>. A number of biochemical and functional characterizations of PKL, an ATP-dependent CHD chromatin remodeler, suggest that PKL contributes to maintain the homeostasis of H3K27me3. To identify other factors that act with PKL together to contribute to the homeostasis of H3K27me3, we undertook an EMS-mutagenesis screen for <i>pkl</i>-associated phenotypes. This genetic screen suggests that PKL may contribute to maintaining the homeostasis of H3K27me3 in an H2A.Z associated or a Mediator associated pathway.</p><p dir="ltr">Here, we took advantage of a combined genetic and bioinformatic method to characterize the contribution of PKL in these two pathways as described above. Our analysis revealed a robust genetic interaction between <i>HTA9</i>, <i>HTA11</i>, and <i>PKL</i> in maintaining proper H2A.Z distribution and enrichment of H3K27me3. In addition, the characterization also sheds light on unexpected roles of PKL in promoting the homeostasis of H3K4me3 and acting with histone demethylases to promote removal of H3K27me3 in an H2A.Z dependent manner. Furthermore, our result also raised the possibility that the tail module of the Mediator complex also plays a critical role in the homeostasis of H3K27me3. While we were examining <i>PKL</i>-dependent chromatin features, we largely optimized the protocol for preparation ChIP-seq samples and libraries and implemented a gene-centric ChIP-seq bioinformatics pipeline for providing robust analysis.</p><p dir="ltr">Ultimately, the work presented in this thesis highlights several divergent pathways that PKL contributes to maintain chromatin homeostasis. By and large, the combined observation from this thesis advances our knowledge of how PKL interacts with other chromatin-associated machineries together to maintain proper epigenetic states and promote other more emergent DNA-templated processes, including replication and transcription.</p>

<p>  </p> <p>Fungal pathogens are an increasing threat to humans, plants, and animals worldwide. Death and disease caused by fungal pathogens results in the loss of over 1.5 million lives, 12 million tons of crops, and even entire species every year. <em>Candida </em>species are the leading cause of invasive fungal species lead by <em>Candida albicans, </em>and <em>Candida glabrata </em>in second. <em>Candida glabrata </em>intrinsically has a low susceptibility to azole treatment, and multidrug resistant isolates are becoming more common. Additionally, new emerging <em>Candida </em>species have been found, and most clinical isolates are resistant to one or more drugs. There is a critical need to better understand drug resistance and pathogenesis to generate new therapies. </p> <p>Drug resistance can be caused by several different genetic factors, but until recently epigenetic factors have been frequently overlooked. Epigenetic research has revolutionized the treatment and detection of many cancers. And now, early research has shown epigenetic mechanisms play a role in drug resistance and pathogenesis in fungal species. Limited resources exist to combat fungal infections and understanding the epigenetic mechanisms that contribute to drug resistance and pathogenicity will provide new drug targets for future treatment.</p> <p>Previous publications from the Briggs’ lab showed Set1-mediated histone H3K4 methylation was necessary for proper ergosterol homeostasis and Brefeldin A resistance. One of the three classes of antifungals, azoles, target the ergosterol pathway. The ergosterol connection resulted into this thesis project, investigating the role of Set1-mediated histone H3K4 methylation in drug resistance and pathogenicity in <em>Saccharomyces cerevisiae, Candida glabrata, Candida albicans, </em>and <em>Candida auris. </em>This research was the first to characterize the Set1 complex in <em>C. glabrata </em>and show it is the sole histone H3K4 methyltransferase in <em>C. glabrata </em>and <em>C. auris. </em>Additionally, it shows loss of <em>SET1 </em>in <em>C. glabrata </em>and <em>C. auris </em>reduces pathogenicity and alters drug efficacy. Interestingly, although the loss of <em>SET1</em> seems to cause a similar pathogenic defect in all three <em>Candida </em>species, the role Set1 plays in drug efficacy including which drug and severity varies amongst species and isolates. Altogether, this research project provides new possible drug targets for fungal treatment and knowledge added to the scientific community on the role of epigenetics in fungal pathogens. </p>

Einzelzell-Omics-Daten stehen derzeit im Fokus der Entwicklung computergestützter Methoden in der Molekularbiologie und Genetik. Einzelzellexperimenten lieferen dünnbesetzte, hochdimensionale Daten über zehntausende Gene oder hunderttausende regulatorische Regionen in zehntausenden Zellen. Diese Daten bieten den Forschenden die Möglichkeit, Gene und regulatorische Regionen zu identifizieren, welche die Bestimmung und Aufrechterhaltung der Zellidentität koordinieren. Die gängigste Strategie zur Identifizierung von Zellidentitätsmarkern besteht darin, die Zellen zu clustern und dann Merkmale zu finden, welche die Cluster unterscheiden, wobei davon ausgegangen wird, dass die Zellen innerhalb eines Clusters die gleiche Identität haben. Diese Annahme ist jedoch nicht immer zutreffend, insbesondere nicht für Entwicklungsdaten bei denen sich die Zellen in einem Kontinuum befinden und die Definition von Clustergrenzen biologisch gesehen potenziell willkürlich ist. Daher befasst sich diese Dissertation mit Clustering-unabhängigen Strategien zur Identifizierung von Markern aus Einzelzell-Omics-Daten. Der wichtigste Beitrag dieser Dissertation ist SEMITONES, eine auf linearer Regression basierende Methode zur Identifizierung von Markern. SEMITONES identifiziert (Gruppen von) Markern aus verschiedenen Arten von Einzelzell-Omics-Daten, identifiziert neue Marker und übertrifft bestehende Marker-Identifizierungsansätze. Außerdem ermöglicht die Identifizierung von regulatorischen Markerregionen durch SEMITONES neue Hypothesen über die Regulierung der Genexpression während dem Erwerb der Zellidentität. Schließlich beschreibt die Dissertation einen Ansatz zur Identifizierung neuer Markergene für sehr ähnliche, dennoch underschiedliche neurale Vorlauferzellen im zentralen Nervensystem von Drosphila melanogaster. Ingesamt zeigt die Dissertation, wie Cluster-unabhängige Ansätze zur Aufklärung bisher uncharakterisierter biologischer Phänome aus Einzelzell-Omics-Daten beitragen. / Single-cell omics approaches are the current frontier of computational method development in molecular biology and genetics. A single single-cell experiment provides sparse, high-dimensional data on tens of thousands of genes or hundreds of thousands of regulatory regions (i.e. features) in tens of thousands of cells (i.e. samples). This data provides researchers with an unprecedented opportunity to identify those genes and regulatory regions that determine and coordinate cell identity acquisition and maintenance. The most common strategy for identifying cell identity markers consists of clustering the cells and then identifying differential features between these clusters, assuming that cells within a cluster share the same identity. This assumption is, however, not guaranteed to hold, particularly for developmental data where cells lie along a continuum and inferring cluster boundaries becomes non-trivial and potentially biologically arbitrary. In response, this thesis presents clustering-independent strategies for marker feature identification from single-cell omics data. The primary contribution of this thesis is a linear regression-based method for marker feature identification from single-cell omics data called SEMITONES. SEMITONES can identify markers or marker sets from diverse single-cell omics data types, identifies novel markers, outperforms existing marker identification approaches. The thesis also describes how the identification of marker regulatory regions by SEMITONES enables the generation of novel hypotheses regarding gene regulation during cell identity acquisition. Lastly, the thesis describes the clustering-independent identification of novel marker genes for highly similar yet distinct neural progenitor cells in the Drosophila melanogaster central nervous system. Altogether, the thesis demonstrates how clustering-independent approaches aid the elucidation of yet uncharacterised biological patterns from single cell-omics data.

L'épigénome est défini par l’ensemble de l’information chromatinienne autre que celle fournie par la séquence ADN. Au sein d'une même espèce et pour un type cellulaire donné, chaque individu présente des caractéristiques particulières de l'épigénome. Les épi-polymorphismes, définis comme étant les différences inter-individus de marques chromatiniennes, sont encore partiellement caractérisés et peuvent être liés aux phénotypes de chacun. La première partie de mon travail a été d'identifier et d'interpréter chez S.cerevisiae l'impact des épi-polymorphismes de modification des queues d'histones. Pour y parvenir, j'ai cartographié les épigénomes de cinq modifications différentes (3 acétylations et 2 méthylations) chez trois souches de levures issues de différents isolats naturels. Par une méthode de ChIP-seq et le développement d'un outil informatique, j'ai comparé les épigénomes de ces souches à l'échelle de nucléosomes individuels. L'étude des propriétés génomiques des épi-polymorphismes m'a alors permis de découvrir certaines caractéristiques encore inconnues et décrites dans ce manuscrit.Par ailleurs, j'ai voulu aborder le lien entre épi-polymorphismes et réponse transcriptionnelle à l'environnement. Pour cela, j'ai construit un jeu de souches mutantes dérivées de souches naturelles, où certains épi-polymorphismes ne peuvent plus être maintenus. J'ai analysé par RNA-seq les transcriptomes de certaines de ces souches avant et après un changement environnemental. Malheureusement, l'analyse des résultats a révélé que la qualité des données ne permettent pas d'établir le lien recherché mais les outils mis en place sont désormais disponibles.J'ai enfin étudié la dynamique d'évolution d'un épigénome en présence ou en l'absence de pression de sélection. Pour cela, j'ai suivi une modification d'histone (l'acétylation de la lysine 14 de l'histone H3) chez la levure pendant 1.000 générations dans deux conditions d'évolution expérimentale différentes : l'une sélective, l'autre neutre. J'ai mis en évidence des différences remarquables et inattendues entre ces deux régimes évolutifs. Des études mécanistiques détaillées restent à faire pour caractériser la nature et les propriétés de ces différences. / Epigenome is defined as the entire chromatin information other than the DNA sequence. Within a given species and for a given cell type, each indivual has specific epigenomic characteristics. Epigenomic differences between individuals (refered to as 'epi-polymorphisms') remain poorly characterized, although cases were reported where they could be linked to phenotypic differences. In my thesis, I used the model organism S. cerevisiae to identify histone modification epi-polymorphisms and study their biological impact. I profiled the epigenome of five different histone modifications (3 acetylations and 2 methylations) in three natural yeast strains. By ChIP-seq methods and software developments, I compared these strains at single-nucleosome resolution and discovered novel characteristics of these epi-polymorphisms which are described in this manuscript.Furthermore, I constructed a research framework to investigate the link between epi-polimorphisms and response to environmental cues. For this, I built a set of mutant strains derived from natural strains but where some epi-polymorphisms can no longer be maintained. I analyzed by RNA-seq the transcriptomes of some of these mutant strains before and after an environmental shift. Unfortunately, the quality of this initial data produced was not sufficient to link epi-polymorphisms to differntial responses, but the strain resources remain available for further investigations. Finally, I studied the evolutionary dynamics of epi-polymorphisms in the presence or absence of selection pressure. To do so, I followed the evolution of H3K14ac for 1.000 generations under two conditions of yeast experimental evolution ( selective or neutral). Marked differences were observed between the two regimes, revealing unexpected consequences of the presence of selection. Further mechanistic studies will be needed to elucidate the full properties of these differences.

Prostate cancer is one of the most frequently diagnosed cancers and failure to manage localized disease contributes to the majority of deaths. Radiation therapy (RT) is a common treatment for localized prostate cancer and uses ionizing radiation (IR) to damage DNA. Although RT is potentially curative, tumors often recur and progress to terminal disease. The cellular response to RT is multidimensional. For example, cells respond to a single dose of IR by activating the DNA damage response (DDR) to repair the DNA. Targeting proteins involved in the DDR is an effective clinical strategy to sensitize cancer cells to RT. However, multiple radiation treatments, as in fractionated ionizing radiation (FIR), can promote neuroendocrine differentiation (NED). FIR-induced NED is an emerging resistance mechanism to RT and tumors that undergo NED are highly aggressive and remain incurable.<br><br> Currently, the only clinical approach that improves RT for prostate cancer treatment is androgen deprivation therapy (ADT). ADT blocks androgen receptor (AR) signaling which inhibits the repair of DNA damage. In 2017, my lab reported that targeting Protein arginine methyltransferase 5 (PRMT5) blocks AR protein expression. Therefore, targeting PRMT5 may also sensitize prostate cancer cells to RT via a novel mechanism of action.<br><br> This dissertation focuses on the role of PRMT5 in the cellular response to IR and the goal of my work is to validate PRMT5 as a therapeutic target to enhance RT for prostate cancer treatment. I demonstrate that PRMT5 has several roles in the cellular response to IR. Upon a single dose of IR, PRMT5 cooperates with pICln to function as a master epigenetic activator of DDR genes and efficiently repair IR-induced DNA damage. There is an assumption in the field that the methyltransferase activity and epigenetic function of PRMT5 is dependent on the cofactor MEP50. I demonstrate that PRMT5 can function independently of MEP50 and identify pICln as a novel epigenetic cofactor of PRMT5. During FIR, PRMT5, along with both cofactors MEP50 and pICln, are essential for initiation of NED, maintenance of NED, and cell survival. Targeting PRMT5 also sensitizes prostate cancer xenograft tumors in mice to RT, significantly reduces and delays tumor recurrence, and prolongs overall survival. Incredibly, while 100% of control mice died due to tumor burden, targeting PRMT5 effectively cured ~85% of mice from their xenograft tumor. Overall, this work provides strong evidence for PRMT5 as a therapeutic target and suggests that targeting PRMT5 during RT should be assessed clinically.<br>