A template-based graph transformation system for the PROV data model

As data provenance becomes a significant metadata in validating the origin of information and asserting its quality, it is crucial to hide the sensitive information of provenance data to enable trustworthiness prior to sharing provenance in open environments such as the Web. In this paper, a graph rewriting system is constructed from the PROV data model to hide restricted provenance information while preserving the integrity and connectivity of the provenance graph. The system is formally established as a template-based framework and formalised using category theory concepts, such as functors, diagrams, and natural transformation

What Algebraic Graph Transformations Can Do For Model Transformations

Model transformations are key activities in model-driven development (MDD). A number of model transformation approaches have emerged for different purposes and with different backgrounds. This paper focusses on the use of algebraic graph transformation concepts to specify and verify model transformations in MDD

Systematic Dissection of Roles for Chromatin Regulators in Dynamics of Transcriptional Response to Stress in Yeast: A Dissertation

The following work demonstrates that chromatin regulators play far more pronounced roles in dynamic gene expression than they do in steady-state. Histone modifications have been associated with transcription activity. However, previous analyses of gene expression in mutants affecting histone modifications show limited alteration. I systematically dissected the effects of 83 histone mutants and 119 gene deletion mutants on gene induction/repression in response to diamide stress in yeast. Importantly, I observed far more changes in gene induction/repression than changes in steady-state gene expression. The extensive dynamic gene expression profile of histone mutants and gene deletion mutants also allowed me to identify specific interactions between histone modifications and chromatin modifiers. Furthermore, by combining these functional results with genome-wide mapping of several histone modifications in the same time course, I was able to investigate the correspondence between histone modification occurrence and function. One such observation was the role of Set1-dependent H3K4 methylation in the repression of ribosomal protein genes (RPGs) during multiple stresses. I found that proper repression of RPGs in stress required the presence, but not the specific sequence, of an intron, an element which is almost unique to this gene class in Saccharomyces cerevisiae. This repression may be related to Set1’s role in antisense RNA-mediated gene silencing. Finally, I found a potential role for Set1 in producing or maintaining uncapped mRNAs in cells through a mechanism that does not involved nuclear exoribonucleases. Thus, deletion of Set1 in xrn1Δ suppresses the accumulation of uncapped transcripts observed in xrn1Δ. These findings reveal that Set1, along with other chromatin regulators, plays important roles in dynamic gene expression through diverse mechanisms and thus provides a coherent means of responding to environmental cues

Analysis of Expressed Sequence Tags Mapping to the Critical Region of the 5q- Syndrome

The 5q- syndrome is a myelodysplastic syndrome characterised by a macrocytic anaemia, hypolobulated megakaryocytes, a low risk of transformation to AML, and a 5q- chromosome as the sole karyotypic abnormality. The approximate 5Mb critical region of gene loss of the 5q- syndrome has been defined in two patients with the 5q- syndrome at 5q31-q33, flanked by the genes for FGF1 and IL12ß. The frequent loss of genetic material from the long arm of chromosome 5 in association with a malignancy has led to the hypothesis that, by analogy with other malignancies characterised by genetic loss, the 5q- syndrome is caused by loss of function of a gene with tumour suppressor activity. A transcript map of the 5q- syndrome critical region was generated with the aim of identifying the putative tumour suppressor gene associated with this disease. The expressed sequence tag (EST) database, db(EST) was used to isolate novel coding sequences mapping to the critical region of gene loss. Ten novel coding sequences (C5orf4, AF010242, AF156165, Cdy-17a06, Bda-87b11 195312, 4885953 / 143772,120101,195971, and 199067) were localised to the YAC contig spanning the critical region at 5g31-q33. The ten cDNA clones were sequenced, and overlapping clones were identified and sequenced in order to generate complete or partial coding sequences. This included the cloning of novel gene, C5orf4, and the identification of the human synaptopodin and dynactin p62 genes. In addition, the human homologues of the Drosophila melanogaster RMSA-1 and Saccharomyces cerevisiae CDC60 genes, and two known human genes (PP2A and HAH1) were localised to the critical region. Expression in human peripheral blood leukocytes and CD34+ progenitor cells was investigated for each known and novel gene. Genomic localisation, expression patterns and predicted function would suggest these known and novel genes represent putative tumour suppressor genes. Mutation studies were carried out on six known, and two novel candidate genes mapping to the narrowed 1.5Mb critical region of gene loss at 5g31.3-q32. No mutations were found in the coding regions/exons of these genes, suggesting they are not involved in the pathogenesis of the 5q- syndrome

The sporulation-specific small regulatory RNAs of Bacillus subtilis

Constantly changing environments in nature have led to bacteria evolving regulatory strategies that result in differential gene expression. A novel and understudied aspect of these networks are regulatory RNAs. The Gram-positive model organism Bacillus subtilis not only modulates gene expression to survive a variety of stresses, but also can form endospores to ensure its survival. Sporulation is an essential survival mechanism for many species, allowing them to enter a state of dormancy with resistance to various harsh conditions. This, in turn, ensures survival of not only the population, but also the species. The process of sporulation requires the controlled expression of approximately a quarter of the genes encoded by B. subtilis. Previous large-scale studies have identified that many transcripts do not encode proteins, but exhibited expression profiles similar to genes already known to be part of the sporulation network. Many of these transcripts were selected to likely function as small regulatory RNAs (sRNAs). This study has shown that many putative sRNAs are active during sporulation, three of which show specific phenotypes that alter germination capabilities in the presence of specific germinants. Cells lacking the necessary components to reverse this process are at a strong disadvantage. Detection of favorable growth conditions is key, but how is this conveyed during metabolic inactivity? Initial selection of putative sRNAs was done by in silico characterization. Prediction of transcriptional control and regulatory regions combined with tiling array profiling was used to select putative sRNAs for confirmation in vivo. Transcriptional fusion constructs were generated to confirm compartmental specific expression during sporulation. Spore specific sRNAs were further characterized with phenotypic studies, which suggested a role in endospore formation. This study explored some of the global analysis methods to identify sRNA targets. Whilst no targets for the four chosen sRNAs could be identified, this study produced the most comprehensive data set of proteins to be identified from a B. subtilis endospore

IST Austria Thesis

Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer

Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways

Deep sequencing of mRNAs (RNA-Seq) is now the preferred method for transcriptome-wide quantification of gene expression. Yet many mRNA isoforms, such as those eliminated by nonsense-mediated decay (NMD), are inherently unstable. Thus a significant drawback of steady-state RNA-Seq is that it provides marginal information on the flux through alternative splicing pathways. Measurement of such flux necessitates capture of newly made species prior to mRNA decay. One means to capture nascent mRNAs is affinity purifying either the exon junction complex (EJC) or activated spliceosomes. Late-stage spliceosomes deposit the EJC upstream of exon-exon junctions, where it remains associated until the first round of translation. As most mRNA decay pathways are translation-dependent, these EJC- or spliceosome-associated, pre-translational mRNAs should provide an accurate record of the initial population of alternate mRNA isoforms. Previous work has analyzed the protein composition and structure of pre- translational mRNPs in detail. While in the Moore lab, my project has focused on exploring the diversity of mRNA isoforms contained within these complexes. As expected, known NMD isoforms are more highly represented in pre-translational mRNPs than in RNA-Seq libraries. To investigate whether pre-translational mRNPs contain novel mRNA isoforms, we created a bioinformatics pipeline that identified thousands of previously unannotated splicing events. Though many can be attributed to “splicing noise”, others are evolutionarily-conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis