Thesis advisor: Anthony T. Annunziato / The histone acetyltransferase Hat1 is an enzyme that specifically acetylates newly synthesized histone H4 at positions K5 and K12 (or their homologous positions) in all eukaryotes. In Schizosaccharomyces pombe, the deletion of hat1 presents a mutant phenotype. The telomeres in a hat1-del strain become permissive for transcription, as analyzed by a telomeric ura4 marker gene. In this study, we evaluate the efficacy of high copy suppression of this hat1 deletion. Due to high-frequency recombination events in the telomere, it became necessary to create a hat1-rad52 double deletion strain that also contains a telomeric ura4 reporter. High copy suppressor screens for recovery of telomeric silencing yielded several promising transformants. Multiple rounds of testing were performed to assess the recovery of transcriptional repression at the telomere. It was found that despite the anti-recombination effect of deleting rad52, the ura4 reporter was still lost from the telomere through recombination. Additional observation of the hat1-del rad52-del ura4-tel strain revealed a significant synthetic slow-growth phenotype. The double mutant displays a greatly decreased growth rate compared to hat1-del, as well as increased cellular length. Further study showed unique phenotypes on various media, and gene expression studies showed unique patterns of regulation in this double mutant when compared to both a wild- type and its single mutant counterparts (hat1-del, rad52-del). In summary, the telomeric ura4 marker in a hat1-del strain of S. pombe is not stable and is lost by recombination at a high frequency. This has led to the discovery of a double mutant (hat1-del rad52-del) that displays a severe synthetically sick phenotype. / Thesis (MS) — Boston College, 2014. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Plant viruses can cause many plant diseases, which result in substantial damage to crop production. To overcome viral infections, plants evolved RNA silencing which can recognise viral RNAs during their replications and slice them into small RNA (sRNA) using antiviral nucleases called DICER or Dicer-like (DCL). The resulting virus-derived small interfering RNA (vsiRNA, 21-24 nucleotides) then guides effector nucleases, namely ARGONAUTE (AGO), to cleave viral RNAs in the cytoplasm in a nucleotide-specific manner. However, the activity of vsiRNA is not restricted to the control of viral RNA accumulation. Virus-derived sRNAs can regulate host gene expression if host mRNAs share sequence complementarity with vsiRNAs. Interestingly, vsiRNAs are also able to target and methylate homologous DNA sequences in the nucleus indicating that vsiRNAs have potential to regulate endogenous genes at transcriptional level by modifying the epigenetic status of gene promoter sequences. This mechanism is referred to as transcriptional gene silencing (TGS). Thus, RNA silencing opens up new strategies to stably and heritably alter gene expression in plants. However, the mechanisms and efficacy of plant virus-induced TGS are largely unknown. The aim of my PhD was to investigate the molecular and environmental factors that are involved in virus-induced epigenetic modifications in the infected plants and in their progeny. First, I examined the required sequence complementary between sRNAs and their nuclear target sequence. I demonstrated for the first time that nuclear-imported vsiRNAs can induce RNA-directed DNA methylation (RdDM) and subsequently heritable virus-induced transcriptional gene silencing (ViTGS) even when they do not share 100% nucleotide sequence complementarity with the target DNA. This finding reveals a more dynamic interaction between viral RNAs and the host epigenome than previously thought. Secondly, I explored how environmental stimuli such as light and temperature can affect the efficacy of ViTGS. I found that ViTGS is greatly inhibited at high temperature. Using RNA-seq, I established that inefficient ViTGS at high temperature is due to the limited production of secondary sRNAs that may limit the initiation, amplification and spreading of virus-induced DNA methylation to neighbouring cells and down generations. Lastly, I studied the link between the viral suppressors of RNA silencing (VSRs): viral proteins that can interfere with plant RNA silencing and ViTGS. I established that VSRs of certain viruses can impair TGS in infected tissues, suggesting that viruses may alter the epigenome and consequently plant gene expression in the infected plants and their progeny. Collectively, my work reveals how viruses can re-program the epigenome of infected plants, and deepens our knowledge of how we can harness pathogens to modify the epigenome for plant breeding.

Due to medical advances in burn care, the survival rate of individuals with serious burns has significantly increased. This has lead to a great need to focus on psychological aspects of burn injury recovery, particularly how people adapt to their changed bodies. The literature indicates that burn size and severity is not directly associated with the degree of distress and that for women, dissatisfaction with their bodies increases in the year after injury. In this study, women’s experiences of their bodies were investigated by asking them about pain, social relationships, mental health, and appearance. In-depth interviews were conducted with female burn survivors in the first year after injury and the transcripts were analyzed using a narrative-discursive analytic methodology. On the surface, the women told narratives which emphasized how well they were doing, however, further analysis revealed subordinate narratives which indicated body dissatisfaction and difficulties with adjustment. In order to suppress narratives of distress, the women engaged in “self-silencing,” of which three forms are outlined. The self-silencing functioned to help the women resist the cultural devaluing associated with “disfigurement” and more personally, to maintain close relationships. As self-silencing has been linked to depression and anxiety, encouraging women to discuss their difficulties may prove to be pertinent in psychological adjustment following burn injury.

Due to medical advances in burn care, the survival rate of individuals with serious burns has significantly increased. This has lead to a great need to focus on psychological aspects of burn injury recovery, particularly how people adapt to their changed bodies. The literature indicates that burn size and severity is not directly associated with the degree of distress and that for women, dissatisfaction with their bodies increases in the year after injury. In this study, women’s experiences of their bodies were investigated by asking them about pain, social relationships, mental health, and appearance. In-depth interviews were conducted with female burn survivors in the first year after injury and the transcripts were analyzed using a narrative-discursive analytic methodology. On the surface, the women told narratives which emphasized how well they were doing, however, further analysis revealed subordinate narratives which indicated body dissatisfaction and difficulties with adjustment. In order to suppress narratives of distress, the women engaged in “self-silencing,” of which three forms are outlined. The self-silencing functioned to help the women resist the cultural devaluing associated with “disfigurement” and more personally, to maintain close relationships. As self-silencing has been linked to depression and anxiety, encouraging women to discuss their difficulties may prove to be pertinent in psychological adjustment following burn injury.

Thesis (Ph.D.)--George Mason University, 2008. / Vita: p. 175. Thesis director: Ancha Baranova. Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biosciences. Title from PDF t.p. (viewed Jan. 8, 2009). Includes bibliographical references (p. 156-174). Also issued in print.

ARGONAUTE proteins (AGOs) are generally accepted as key components of the post transcriptional gene silencing mechanism, also involved in plant antiviral defense. Except for reports on the antiviral roles of AGO1, AGO2 and AGO7 in Arabidopsis, the exact roles played by the individual AGOs in other plant species are largely unknown. This research focused on the identification and characterization of AGOs involved in antiviral RNAi response to various viruses in N. benthamiana. Based on the temporal and spatial distribution of AGO transcripts in 3 and 8-week old plant root, stem and leaf tissues, expressions of NbAGO mRNAs were found to vary with age and tissue specificity. Plant endogenous AGO mRNAs were knocked down through virus induced gene silencing techniques using the Tobacco rattle virus vector system and posteriorly challenged with a GFP-chimeric virus construct deficient of a silencing suppressor. Unlike in control non-silenced plants, the Tomato bushy stunt virus construct deficient of its P19 silencing suppressor was consistently seen to exhibit a strong fluorescence on N. benthamiana plants silenced for NbAGOs 2 and X. Similar results were also obtained upon silencing of NbAGO2 using hairpin vector techniques. Comparable observations were also made when Tobacco mosaic virus GFP constructs were agroinfiltrated on NbAGO2 silenced plants further hinting the antiviral defense roles played by these AGOs. Agroinfiltration of Foxtailmosaic virus, Sunnhemp mosaic virus, and Turnip crinkle virus GFP chimeric constructs on NbAGO2 silenced N. benthamiana plants, however did not result in accumulation of GFP indicating the AGO antiviral defense specificity to TBSV and TMV. The results also hinted at a role for AGO7. Collectively my findings suggest that the expression of AGOs in N. benthamiana is tissue and age dependent, and that unlike in the model plant Arabidopsis where the main antiviral AGO is thought to be AtAGO1; in N. benthamiana, NbAGOs 2 and X seem to be involved in an antiviral defense role against TBSV and TMV with other AGOs perhaps contributing.

published_or_final_version / abstract / Microbiology / Master / Master of Philosophy

published_or_final_version / abstract / Biochemistry / Doctoral / Doctor of Philosophy

No description available.

Chez Arabidopsis thaliana, le silencing transcriptionnel est associé notamment aux modifications post-traductionnelles des queues des histones et à la méthylation des cytosines en contexte CG, CHG et CHH (où H peut être indifféremment T, A ou C). Plusieurs voies indépendantes conduisent à la méthylation de l’ADN en tout contexte via les méthyltransférases. A contrario, ROS1, une ADN déméthylase, « élague » les profils de méthylation et prévient ainsi d’une hyperméthylation du génome. Or, de façon intéressante, plusieurs mutants impliqués dans les voies de méthylation de l’ADN voient l’expression du gène ROS1 diminuer, ce qui trahit l’existence d’une boucle de rétrocontrôle négative entre les voies de méthylation et de déméthylation de l’ADN. Nous avons donc réalisé un crible génétique afin d’identifier un régulateur de l’expression de ROS1. Pour cela, nous avons utilisé une lignée pROS1:GUS constituée du gène rapporteur de la glucuronidase sous contrôle du promoteur de ROS1. Dans le fond mutant nrpd1a-4, le gène de ROS1 et de la glucuronidase sont sous-exprimés. Le crible consiste alors à identifier un mutant qui relâche l’expression de la glucuronidase et de ROS1 dans le fond mutant nrpd1a-4. Six mutants présentent une expression de la glucuronidase plus forte que le témoin pROS1:GUS dans le fond nrpd1a-4. Cependant, contrairement à ce qui était attendu, l’expression de ROS1 endogène est plus basse encore que chez pROS1:GUS dans le fond nrpd1a-4.Face à ses résultats, nous avons alors réorienté la thèse vers l’étude d’une voie de contournement du silencing des éléments répétés. En effet, lorsque l’on applique un stress thermique de 37°C durant 24h, l’on observe un relâchement du silencing de ces derniers. Toutefois, aucune modification épigénétique connue ne semble être impliquée. Pour étudier ce phénomène, nous disposons d’une lignée L5 qui, dans des conditions normales de culture, voit son transgène soumis aux mécanismes de silencing. Parce que la construction L5 comprend plusieurs répétitions de la glucuronidase sous contrôle du promoteur 35S, elle est alors assimilée à n’importe quel autre élément répété et, à ce titre, se retrouve être également exprimée après stress thermique. L’équipe a alors réalisé un crible sur cette lignée et a mis en évidence 3-1S, un mutant qui est déficient dans le relâchement du silencing à 37°C. Dans un premier temps, nous avons mis en évidence que le phénotype de 3-1S est dû à une mutation de RH35, une hélicase ARN à boîte DEAD. D’autre part, nos résultats montrent que le gène RH35 est exprimé plus fortement à 37°C et sa protéine présente, en outre, une relocalisation dans ces conditions de stress. RH35 serait, en fait, impliquée de manière plus globale dans le métabolisme des ARN en réponse au stress thermique et jouerait également un rôle dans la réponse au stress thermique et salin. / In Arabidopsis thaliana, transcriptional silencing is associated with histone tail post-translational modifications and cytosine modifications in CG, CHG and CHH contexts (where H can be indifferently T, A or C). Numerous independent pathways lead to DNA methylation in all contexts through méthyltransférases. Conversely, the DNA demethylase ROS1 “prunes” methylation profiles and prevents genome hypermethylation. Interestingly, several mutants which are involved in DNA methylation pathways present a decrease in ROS1 gene expression, what reveals the existence of a negative feedback loop between DNA methylation and demethylation pathways. A genetic screening was carried out in order to find a ROS1 regulator. To do this, pROS1:GUS line, which carries the glucuronidase reporter gene under ROS1 promoter, was used. In the nrpd1a-4 mutant, ROS1 and glucuronidase genes are underexpressed. The screen consisted to find a mutant which release glucuronidase and ROS1 gene expression in nrpd1a-4 mutant background. Six mutants presented a higher expression of the glucuronidase than the pROS1:GUS control in nrpd1a-4 background. However, unlike what it was expected, endogene ROS1 expression is even lower than what we have for pROS1:GUS in nrpd1a-4 background.In view of these results, the thesis was redirected toward the study of the silencing circumvention pathway of the repeated elements. Indeed, when heat stress at 37°C during 24h is applied, a release of silencing is observed for repeated elements. Nevertheless, no known epigenetic modifications seem to be involved. To study this phenomenon, we used a L5 line. Its transgene is silenced in standard conditions. Because L5 construct is composed by several glucuronidase repetitions under 35S promoter, it is considered as any other repeated elements and, for this reason, it is also expressed after heat stress. The team performed a genetic screen on this line and found 3-1S, a mutant which is deficient in the release of silencing at 37°C. On the one hand, we demonstrated that 3-1S phenotype is due to a mutation in RH35 DEAD box RNA helicase. On the other hand, our results revealed that RH35 gene is expressed at 37°C and its protein is relocated in heat stress conditions. In fact, RH35 would be involved more globally in RNA metabolism and would play a role in heat and salt stress.