Thèses (M.Sc.)--Université de Sherbrooke (Canada), 2000. / Titre de l'écran-titre (visionné le 20 juin 2006). Publié aussi en version papier.

Thesis (Ph. D.) -- California Institute of Technology, 2010. / Title from home page (viewed 04/05/10). Advisor and committee chair names found in the thesis' metadata record in the digital repository. Includes bibliographical references.

Thesis (Ph.D.) - University of Queensland, 2003. / Includes bibliography.

Thesis (Ph. D.)--State University of New York at Binghamton, Psychology Dept., 2005. / Includes bibliographical references.

No description available.

No description available.

The CCR4-NOT complex is a global regulator of gene expression which controls mRNA levels by removing the poly-(A) tail, a step known as deadenylation and one that constitutes the rate-limiting step in mRNA decay. The human complex is comprised of eight stably associated CNOT subunits where CNOT1 forms the scaffold onto which CNOT2-11 bind. Although much has been learnt about the CCR4-NOT complex, questions still remain. Thus, this study focused on a number of sub-complexes of CNOT subunits and associated proteins to determine the mode of interaction with a hope to explore the mechanism of deadenylation by the CCR4-NOT complex. Firstly, the complex of CNOT10:CNOT11, found only in higher eukaryotes, was reconstituted for the first time using recombinant proteins. Crystallisation trials, limited proteolysis and mass spectrometry were used to isolate novel interaction regions between CNOT10 and CNOT11 which may provide direction for future structural and functional studies. Secondly, the interaction between CNOT9 and TTP was characterised. TTP is a RNA-binding protein which targets inflammatory mRNAs for deadenylation by recruiting the CCR4-NOT complex. This study highlights novel interactions between TTP and both CNOT2 and CNOT9. Moreover, BioLayer interferometry (BLI), peptide arrays and site-directed mutagenesis identified that TTP interacts with CNOT9 in a tryptophan-mediated manner. These findings change the known interface between TTP and the CCR4-NOT complex. Lastly, the MultiBac system was used to reconstitute a number of human CNOT sub-complexes, one of which was shown to effectively degrade a poly-(A) substrate, demonstrating it is enzymatically active. This achievement provides a tool for the future study of the CCR4-NOT complex. In summary, this study highlights novel interactions and characterises previously unknown binding mechanisms between CCR4-NOT subunits which expands our current understanding of the complex.

>Magister Scientiae - MSc / A large volume of gene expression data exists in public repositories like the NCBI’s Gene Expression Omnibus (GEO) and the EBI’s ArrayExpress and a significant opportunity to re-use data in various combinations for novel in-silico analyses that would otherwise be too costly to perform or for which the equivalent sample numbers would be difficult to collects exists. For example, combining and re-analysing large numbers of data sets from the same cancer type would increase statistical power, while the effects of individual study-specific variability is weakened, which would result in more reliable gene expression signatures. Similarly, as the number of normal control samples associated with various cancer datasets are often limiting, datasets can be combined to establish a reliable baseline for accurate differential expression analysis. However, combining different microarray studies is hampered by the fact that different studies use different analysis techniques, microarray platforms and experimental protocols. We have developed and optimised a method which transforms gene expression measurements from continuous to discrete data points by grouping similarly expressed genes into quantiles on a per-sample basis. After cross mapping each probe on each chip to the gene it represents, thereby enabling us to integrate experiments based on genes they have in common across different platforms. We optimised the quantile discretization method on previously published prostate cancer datasets produced on two different array technologies and then applied it to a larger breast cancer dataset of 411 samples from 8 microarray platforms. Statistical analysis of the breast cancer datasets identified 1371 differentially expressed genes. Cluster, gene set enrichment and pathway analysis identified functional groups that were previously described in breast cancer and we also identified a novel module of genes encoding ribosomal proteins that have not been previously reported, but whose overall functions have been implicated in cancer development and progression. The former indicates that our integration method does not destroy the statistical signal in the original data, while the latter is strong evidence that the increased sample size increases the chances of finding novel gene expression signatures. Such signatures are also robust to inter-population variation, and show promise for translational applications like tumour grading, disease subtype classification, informing treatment selection and molecular prognostics.

Genes are typically expressed in equal amounts from both parentally inherited chromosomes. However, recent studies have demonstrated that genes can be preferentially transcribed from a locus. Non-random preferential expression of alleles can occur in a parent-of-origin pattern, known as imprinting, where epigenetic factors regulate their transcription. Alternatively, it can occur in a haplotype-specific pattern, where cis-acting polymorphisms in regulatory regions are thought to underlie the phenomenon. Both forms of unequal allelic expression have been associated with human disease. Consequently, it is important to identify genes subject to unequal allelic expression and characterize mechanisms that regulate differential transcription. This thesis presents the results of a screen for unequal allelic expression where approximately 50 murine transcripts homologous to genes on human chromosome 7 were analyzed. Human chromosome 7 was selected due to its association with several human disorders that show parent-of-origin effects. The screen identified non-imprinted preferential allelic expression in numerous transcripts and demonstrated that such patterns can occur in tissue specific patterns. Paraoxonase-1 (Pon1), a gene implicated in arthrosclerosis, was identified as having a dynamic pattern of allelic expression which varies throughout embryonic development. This finding represents the first report of a developmentally regulated pattern of allelic variance. Carboxypeptidase-A4 (Cpa4) was identified as having a tissue-specific imprinted pattern of expression, where the maternal allele was preferentially expressed in all embryonic tissues, with the exception of the brain. The Krüppel-like factor 14 gene (Klf14), a novel imprinted transcript, was found to have ubiquitous maternal expression in all human and murine tissues analyzed. A differentially methylated region, generally associated with imprinted transcripts, was not found in the gene’s CpG island, nor was a differential pattern of histone modifications identified. However, it was determined that maternal methylation regulates the transcript. The data in this thesis contribute to our understanding of the numerous patterns of allelic expression that exist in nature and the diverse mechanisms that regulate them. Ultimately, quantitative analyses of allelic expression patterns and the identification of their underlying genomic DNA sequences will become standard protocol in all biomedical studies.

Reproduction de : Thèse de doctorat : Sciences cognitives. Psychologie : Lyon 2 : 2004. Reproduction de : Thèse de doctorat : Sciences cognitives. Psychologie : Grenoble : 2004. / Titre provenant de l'écran-titre. Bibliogr.