Nucleosome positioning dynamics in evolution and disease

Nucleosome positioning is involved in a variety of cellular processes, and it provides a likely substrate for species evolution and may play roles in human disease. However, many fundamental aspects of nucleosome positioning remain controversial, such as the relative importance of underlying sequence features, genomic neighbourhood and trans-acting factors. In this thesis, I have focused on analyses of the divergence and conservation of nucleosome positioning, associated substitution spectra, and the interplay between them. I have investigated the extent to which nucleosome positioning patterns change following the duplication of a DNA sequence and its insertion into a new genomic region within the same species, by assessing the relative nucleosome positioning between paralogous regions in both the human (using in vitro and in vivo datasets) and yeast (in vivo) genomes. I observed that the positioning of paralogous nucleosomes is generally well conserved and detected a strong rotational preference where nucleosome positioning has diverged. I have also found, in all datasets, that DNA sequence features appear to be more important than local chromosomal environments in nucleosome positioning evolution, while controlling for trans-acting factors that can potentially confound inter-species comparisons. I have also examined the relationships between chromatin structure and DNA sequence variation, with a particular focus on the spectra of (germline and somatic) substitutions seen in human diseases. Both somatic and germline substitutions are found to be enriched at sequences coinciding with nucleosome cores. In addition, transitions appear to be enriched in germline relative to somatic substitutions at nucleosome core regions. This difference in transition to transversion ratio is also seen at transcription start sites (TSSs) genome wide. However, the contrasts seen between somatic and germline mutational spectra do not appear to be attributable to alterations in nucleosome positioning between cell types. Examination of multiple human nucleosome positioning datasets shows conserved positioning across TSSs and strongly conserved global phasing between 4 cancer cell lines and 7 non-cancer cell lines. This suggests that the particular mutational profiles seen for somatic and germline cells occur upon a common landscape of conserved chromatin structure. I extended my studies of mutational spectra by analysing genome sequencing data from various tissues in a cohort of individuals to identify human somatic mutations. This allowed an assessment of the relationship between age and mutation accumulation and a search for inherited genetic variants linked to high somatic mutation rates. A list of candidate germline variants that potentially predispose to increased somatic mutation rates was the outcome. Together these analyses contribute to an integrated view of genome evolution, encompassing the divergence of DNA sequence and chromatin structure, and explorations of how they may interact in human disease

The interaction between aluminium toxicity and drought stress in common bean (Phaseolus vulgaris L.) : physiological and molecular aspects

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Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening

<p>Abstract</p> <p>Background</p> <p>Grapes (<it>Vitis vinifera </it>L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variation. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses.</p> <p>Results</p> <p>Ripening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through <it>véraison </it>and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen^®genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5877 unigenes indicates the activation of common pathways between years despite the irregular development of Trincadeira grapes. These unigenes were assigned to the functional categories of "metabolism", "development", "cellular process", "diverse/miscellanenous functions", "regulation overview", "response to stimulus, stress", "signaling", "transport overview", "xenoprotein, transposable element" and "unknown". Quantitative RT-PCR validated microarrays results being carried out for eight selected genes and five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38). Metabolic profiling using ¹H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as secondary metabolism. These results were integrated with transcriptional profiling obtained using genome array to provide new information regarding the network of events leading to grape ripening.</p> <p>Conclusions</p> <p>Altogether the data obtained provides the most extensive survey obtained so far for gene expression and metabolites accumulated during grape ripening. Moreover, it highlighted information obtained in a poorly known variety exhibiting particular characteristics that may be cultivar specific or dependent upon climatic conditions. Several genes were identified that had not been previously reported in the context of grape ripening namely genes involved in carbohydrate and amino acid metabolisms as well as in growth regulators; metabolism, epigenetic factors and signaling pathways. Some of these genes were annotated as receptors, transcription factors, and kinases and constitute good candidates for functional analysis in order to establish a model for ripening control of a non-climacteric fruit.</p

Targeting Nrf2 in Inflammation and Cancer

The transcription factor Nrf2 protects against cellular stress by inducing cytoprotective proteins. Activation of Nrf2 protects against inflammation and oxidative damage in disease models in vitro and in vivo. Nrf2 activation may be a good therapeutic strategy in these diseases. Some dietary components activate Nrf2, which may be partially responsible for their beneficial effects in preventing disease. In this study a novel organosulfur compound from garlic, diallyl pentasulfide (DAPS), was investigated. DAPS strongly activated the Nrf2 pathway. Furthermore, it was a much more powerful activator of heme oxygenase-1 than any diallyl sulfides reported to date. Nrf2 is regulated by Keap1, which targets it for degradation. Disruption of the Nrf2/Keap1 interaction results in Nrf2 activation. In this study, a novel cell-penetrating peptide, based on the Keap1-binding site of Nrf2, disrupted the Nrf2/Keap1 interaction, and activated the Nrf2 pathway. Furthermore, it demonstrated anti-inflammatory activity, significantly inhibiting LPS-induced TNF expression in THP-1 monocytes, suggesting that the interaction is a valid therapeutic target in inflammation. In cancer, Nrf2 plays a dual role. Activation of Nrf2 protects cells from carcinogens. However, once a tumour has developed, Nrf2 can be hijacked by cancer cells to induce chemoresistance. This study examined the role of Nrf2 in malignant melanoma cells. Nrf2 was found to be overexpressed in 11 human melanoma cell lines in comparison with melanocytes. Chemoresistance to dacarbazine, doxorubicin and cisplatin correlated with Nrf2 expression, and Nrf2 siRNA increased the susceptibility of M202 and SK-MEL-5 cells to cisplatin, suggesting that Nrf2 plays a role in chemoresistance in melanoma. In conclusion, this study has identified novel activators of Nrf2, including a dietary compound and a cell penetrating peptide which inhibits inflammation in vitro. In addition, Nrf2 inhibition sensitises melanoma cells to chemotherapy. These results suggest that targeting Nrf2 is a viable strategy in both inflammation and cancer