Développement et application d'un outil bio-informatique pour cartographier la machinerie de l'ARN polymérase I chez les mammifères

Authors: Sabourin-Félix, Marianne
Advisor: Moss, Tom
Abstract: Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a technique that allows to visualize interactions between DNA and proteins. However in practice, the resolution of this technique leaves much to be desired. During our studies of the ribosomal RNA genes (rDNA), we observed that one major factor limiting resolution results from the unequal recovery of sequence data across any given locus. This inequality is superimposed on the actual distribution of immunoprecipitated DNA sequences resulting in aberrant protein binding profiles. A software was developed to correct the unequal coverage of ChIP-seq data by normalizing to the input (Whole Cell Extract) with a deconvolution protocol. When applied on the rDNA, this approach has been especially useful in providing a detailed map of chromatin and transcription factor distribution across the gene. On the other hand, genome-wide localization of protein interaction sites for UBF, a transcription factor associated to rDNA, coupled with DNase-seq and microarray experiments shed light on the potential roles of UBF in non-ribosomal regions. In conclusion, we developed a tool allowing the normalization by deconvolution of high-throughput sequencing data that allows to increase the resolution of protein binding profiles on the rDNA. In addition we identified the potential roles of UBF at genome scale.
Document Type: Mémoire de maîtrise
Issue Date: 2018
Open Access Date: 24 May 2018
Permalink: http://hdl.handle.net/20.500.11794/29846
Grantor: Université Laval
Collection:Thèses et mémoires

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