Heterochromatin assembly in fission yeast (Schizosaccharomyces pombe) requires conserved components that mediate RNA interference (RNAi) directed methylation of histone H3 on lysine 9 (H3K9). Fission yeast heterochromatin is mainly found at centromeres, telomeres, and the mating-type locus. At centromeres, transcripts from repetitive elements are processed to siRNAs and RNAi promotes chromatin modification by recruiting the Clr4 methyltransferase. RNAi is not required to maintain silent chromatin at the mating-type locus. This RNAi-directed form of centromeric heterochromatin provides an ideal system for in vivo screening to allow the identification of compounds that inhibit the activity of proteins involved in RNA silencing, chromatin modification and heterochromatin assembly in fission yeast and may inhibit conserved proteins in other organisms. A dominant selectable marker gene system at fission yeast centromeres that reports loss of heterochromatin integrity by increased resistance to G418 in 96-well plate format liquid cultures was developed. The resulting strain was used to screen a nontargeted chemically diverse compound library in vivo to identify compounds that disrupt the integrity of RNAi-directed heterochromatin. Two compounds, Emi1 and Emi14, were identified and found to cause a significant decrease in the level of H3K9 methylation on the outer repeats at fission yeast centromeres. Growth in the presence of Emi1 or Emi14 also caused a reduction in H3K9 methylation levels at the mating-type locus, suggesting that they do not act through RNAi. Consistent with this, Emi1 and Emi14 did not cause a decrease in centromeric siRNA levels. Analyses therefore suggest that Emi1 and Emi14 do not disrupt RNAi but that they inhibit downstream events in chromatin modification and heterochromatin assembly. Cells lacking RNAi due to loss of Dicer (dcr1Δ) or cells lacking the histone deacetylase (HDAC) Sir2 (sir2Δ) retain significant but lower levels of H3K9 methylation on the centromeric outer repeats. When dcr1Δ or sir2Δ cells were grown in the presence of Emi1 or Emi14 a further reduction in H3K9 methylation levels was observed on the outer repeats. This mimics the effect of combining clr3Δ with dcr1Δ or sir2Δ and suggests that Emi1 and Emi14 may interfere with SHREC function. SHREC is a chromatin remodelling complex that includes the HDAC Clr3 and the chromatin remodeler Mit1 and is known to contribute to heterochromatin integrity. Expression profiling performed on Emi1 and Emi14 treated cells confirmed the previous results. The changes in gene expression following Emi1 and Emi14 treatment were compared to known mutants defective in heterochromatin integrity. The profile of expression changes following Emi14 treatment was found to correlate with alterations in the expression pattern observed in cells with SHREC components deleted. No correlation with mutants lacking other HDACs or RNAi components was detected. Emi1 had a weaker correlation with defective SHREC function and thus may also partially inhibit the SHREC complex. Murine erythroleukemia (MEL) cells harbouring a silenced eGFP reporter transgene were used to assess whether Emi1 and Emi14 also affect silencing in mammalian cells. Emi1 was found to disrupt silencing at the eGFP reporter and this correlated with a decrease in H3K9 methylation. Structurally related analogues of Emi1 and Emi14 were selected and tested in the fission yeast assay. Interpretation of the obtained structure-activity relationships allowed identification of the chemical moieties key to Emi1 and Emi14 activity. Overall, an approach was developed to identify two novel small molecule inhibitors of a well-characterized chromatin modification pathway. The SHREC complex was identified as the putative target of these two compounds and structurally related active analogues were identified for them. Importantly, one of the compounds was also active in mammalian cells, highlighting the usefulness of this approach in identifying compounds that affect higher organisms.

The encysted embryos (cysts) of the crustacean Artemia franciscana have several molecular mechanisms to enable anhydrobiosis – life without water. This study examines the function of group 1 Late Embryogenesis Abundant (LEA) proteins, hydrophilic unstructured proteins which accumulate in the stress-tolerant cysts of A. franciscana. Group 1 LEA proteins were knocked down in cysts using RNA interference. Cysts without group 1 LEA proteins exhibited low survival following desiccation and/or freezing, suggesting a role for these proteins in tolerance of low water conditions. In contrast, cysts with or without group 1 LEA proteins responded similarly to hydrogen peroxide exposure , indicating little to no function in reducing damage due to oxidative stress. This is the first in vivo functional study of group 1 LEA proteins in an animal, and may have applied significance in aquaculture, where Artemia is an important feed source, and in the cryopreservation of cells for therapeutic applications.

RNA interference (RNAi) is a conserved pathway that plays key roles in heterochromatin formation, gene regulation and genome surveillance across a wide range of eukaryotes. One of the most utilised model organisms for studying the RNAi pathway is the fission yeast Schizosaccharomyces pombe. However, this species is somewhat atypical, in that it has not retained the ancestral role for RNAi in the silencing of mobile genetic elements. In contrast, the related fission yeast S. japonicus has a large and diverse retrotransposon complement that appears to give rise to abundant siRNAs. For this reason, we believe that S. japonicus may be a more suitable model for studying the role of RNAi in silencing mobile genetic elements, a function that is conserved in many higher eukaryotes. Functional analysis of the S. japonicus RNAi pathway proved more challenging than expected, as it was generally not possible to recover strains bearing deletions of core RNAi components (Ago1/Clr4/Rdp1/Arb1/Arb2). This suggests that a functional RNAi pathway may be required for viability in S. japonicus, unlike in S. pombe. However, disruption mutants were isolated for the sole Dicer ribonuclease Dcr1, at very low frequency. Analysis of these mutants revealed that disruption of Dcr1 impaired the generation of retrotransposon derived siRNAs, and caused de-repression of retroelement transcript accumulation and mobilisation in an element dependent manner. Surprisingly however, Dcr1 appeared dispensable for the maintenance of H3K9me2 at transposons, suggesting that, in contrast to S. pombe, silencing may occur principally at the post-transcriptional level. It is also possible that the isolated Dcr1 mutants represent rare survivors that are viable due to the presence of suppressor mutations elsewhere in the genome. I utilised my genome wide RNA sequencing data to help improve the annotation of the S. japonicus genome, with a specific focus on the retrotransposon complement. From this, I identified 12 new families of LTR retrotransposon, which increased the annotated retrotransposon complement by around 40% in S. japonicus. Finally, I characterised the integrative preference of the S. japonicus retrotransposon Tj1, and found that it shares characteristics associated with the S. cerevisiae retrotransposons Ty1 and Ty3, mostly integrating upstream of RNA PolIII transcribed tRNA genes. The findings of this work highlight some potentially key differences in the way the RNAi pathway functions across the fission yeast clade, both in terms of its importance for viability and its mode of action. The work undertaken here also contributes to the establishment of S. japonicus as a model for the study of RNA interference and genome regulation.

Psoroptic mange, caused by the Astigmatid mite Psoroptes ovis, is an ectoparasitic disease of significant economic importance to agriculture on a global scale and poses a serious welfare concern. With the current chemotherapeutic controls considered unsustainable, there is pressing need for novel control strategies. RNA interference has been proposed as a potential high throughput approach for the identification of novel therapeutic targets with high specificity, speed and at a relatively low cost compared to the existing methods. The presence of the components of the RNA interference (RNAi) pathway in P. ovis was first confirmed through in silico analyses of the P. ovis transcriptome and, following development of a non-invasive immersion method of double stranded RNA (dsRNA) delivery, gene silencing by RNAi was demonstrated in P. ovis. Statistically-significant reduction of transcript level was measured for the three genes targeted: P. ovis mite group 2 allergen (Pso o 2), P. ovis mu class glutathione S-transferase (PoGST-mu1) and P. ovis beta tubulin (Poβtub). This is the first demonstration of gene silencing by RNAi in P. ovis and provides a key mechanism for mining transcriptomic and genomic datasets in the future for novel targets of intervention against P. ovis. The first assessment of gene silencing was also performed in two related Astigmatid mites of high medical importance; the European house dust mite Dermatophagoides pteronyssinus and the scabies mite Sarcoptes scabiei. A statistically-significant reduction in expression of a D. pteronyssinus mu class glutathione S-transferase (DpGST-mu1) transcript was observed. No significant reduction in expression of a S. scabiei mu class glutathione S-transferase (SsGST-mu1) transcript was observed. Additionally, microRNAs (miRNAs) from the related miRNA pathway were identified in a P. ovis small RNA sample and were sequenced and annotated.

High mobility group box 1 (HMGB-1) protein is a non-histone chromosomal protein. As a DNA binding protein, HMGB-1 is involved in the maintenance of nucleosome structure, regulation of gene transcription and it is active in DNA recombination and repair. It has been known that HMGB-1 is a late mediator of endotoxemia and sepsis. HMGB-1 is released from activated macrophages, induces the release of other proinflammatory mediators, and mediates cell death when overexpressed. We speculated that the course of sepsis maybe different without the involvement of HMGB-1. The aims of this study are to investigate the role of HMGB-1 in mediating sepsis and to observe the effects by using RNAi to affect the production of HMGB-1. Lipopolysaccharide (LPS) was used to simulate sepsis in culture as well as stimulate the release of HMGB-1 from RAW 264.7 cells. Levels of HMGB-1 in the culture medium were subsequently measured by Western blot. Other proinflammatory cytokines (TNF-£\, IL-6 and TGF-£]) were measured by ELISA. HMGB-1 could not be detected in the culture medium in the absence of LPS stimuli, but after 0.5 £gg/ml LPS treatment HMGB-1 release could be detected. HMGB-1 the amount of released from LPS activated RAW 264.7 cells was in a time- and dose-dependent manner. The present study demonstrated that RNAi in the treatment of LPS-stimulated RAW264.7 cells resulted in the blockade of HMGB-1 and decreased LPS-induced inflammatory response. The results demonstrated that HMGB-1 plays a pivotal role in macrophage inflammatory responses by modulating the production of inflammatory mediators.

No description available.

We have explored correlations between the measured efficiency of the RNAi process and several computed signatures that characterize equilibrium secondary structure of the participating mRNA, siRNA, and their complexes. A previously published data set of 609 experimental points was used for the analysis. While virtually no correlation with the computed structural signatures are observed for individual data points, several clear trends emerge when the data is averaged over 10 bins of N ~ 60 data points per bin. The strongest trend is a positive linear (r² = 0.87) correlation between ln(remaining mRNA) and ΔG_ms, the combined free energy cost of unraveling the siRNA and creating the break in the mRNA secondary structure at the complementary target strand region. At the same time, the free energy change ΔG_total of the entire process mRNA + siRNA → (mRNA – siRNA)_complex is not correlated with RNAi efficiency, even after averaging. These general findings appear to be robust to details of the computational protocols. The correlation between computed ΔG_ms and experimentally observed RNAi efficiency can be used to enhance the ability of a machine learning algorithm based on a support vector machine (SVM) to predict effective siRNA sequences for a given target mRNA. Specifically, we observe modest, 3 to 7%, but consistent improvement in the positive predictive value (PPV) when the SVM training set is pre- or post-filtered according to a ΔG_ms threshold. / Master of Science

Mutationen im Protein LRRK2 wurden im Zusammenhang mit klinischen Symptomen beschrieben, die dem Idiopathischen Parkinsonsyndrom (IPS) nahezu gleichen. So findet sich neben vielen anderen Mutationen die häufigste pathogene Mutation für das IPS im LRRK2-Gen. Die Aufklärung der molekularbiologischen Mechanismen, die zur Pathologie der spezifischen Neurodegeneration in der Substantia nigra Pars Compacta (SNpc) und somit zur Idiopathischen Parkinsonssyndrom führen, ist mit der Hoffnung auf kausale und kurative Therapieansätze verbunden. In dieser medizinischen Doktorarbeit soll daher versucht werden, die biologische Funktion des LRRK2 in einem dopaminergen Mauszellmodell näher zu beschreiben. Hierfür soll die genetische Aktivität des LRRK2 in mesenzephalen, sogenannten MN9D-Zellen reduziert werden, indem der Mechanismus der RNA-Interferenz in vitro durch Transfektion von siRNA angestoßen wird. Durch die Reduktion der LRRK2-Aktivität sollen Veränderungen in den MN9D-Zellen induziert und diese objektiviert werden. Die Darstellung der Beobachtungen konzentriert sich auf die transkriptionelle Expression von Genen des Zellzyklus sowie der neuralen und dopaminergen Differenzierung (Tyrosinhydroxylase, Nestin und β-Tubulin) durch PCR. Die Proliferation der Zellen vor und nach den RNA-Interferenzexperimenten soll global durch MTT- und BrdU-Test gemessen werden.

No description available.

The transcription factor Krüppel homolog 1 (Kr-h1) is crucial in multiple reproductive processes of Aedes aegypti mosquitoes, including previtellogenesis, vitellogenesis, and oogenesis. This study explores the interaction between Kr-h1 and its potential associated proteins (KAPs), with a specific focus on the dimerization partner (DP-1), and how this interaction regulates gene expression pathways critical for mosquito reproduction. Utilizing RNA interference (RNAi), the research identifies DP-1 as a significant regulator of follicle growth post-eclosion (PE), highlighting its vital role in the mosquito reproductive regulatory pathway. The experimental approach included RNAi-mediated knockdown of DP-1, accompanied by evaluations using quantitative PCR (qPCR), Western blotting (WB), co-immunoprecipitation (Co-IP), follicle length measurement, and egg counting to assess the role of DP-1 in reproductive functions. For the first time, the inhibition of DP-1 expression was found to significantly impede A. aegypti follicular development. The elucidation of the mechanistic roles of Kr-h1 and DP-1 provides valuable insights that could lead to innovative strategies for mosquito population control and effective disease vector management. / Master of Science in Life Sciences / Mosquitoes can spread serious insect-borne diseases such as dengue, Zika, and malaria, etc. These diseases can infect hundreds of millions of individual and cause around a million of death annually. This study focuses on a specific mosquito species, Aedes aegypti, which is a major carrier of these diseases. To manage their populations and reduce the spread of these diseases, scientists are constantly seeking new methods to control their reproduction. Chemical insecticides are one of the most efficient and widely used strategies. However, these insecticides face significant challenges, including the development of resistance in mosquito populations and the potential damage to non-target species to affect the ecosystem. To address this issue, the development of new insecticides is crucial. We can identify new targets to pave the way to research novel effective insecticides. Inside mosquitoes, there are various proteins that help control their ability to reproduce. One of these proteins is called Krüppel homolog 1 (Kr-h1). Kr-h1 plays a crucial role in the development and reproductive processes of mosquitoes. Our research looked at how Kr-h1 interacts with other types of protein to control mosquito reproduction. Through various experiments, including gene expression analysis and protein studies, we found that DP-1 is essential for the proper development of mosquito eggs. This insight helps us understand more about the biological processes and hormonal pathways during mosquito reproduction, therefore provide greater opportunity to develop insecticides to reduce their populations and the spread of the diseases they carry.