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Identifier 000460518
Title Establishment of a multi-omic strategy for the identification of enhancer-gene regulatory networks in model organisms
Alternative Title Εδραίωση πολυ-ωμικών μεθοδολογιών για τον προσδιορισμό ρυθμιστικών δικτύων ενισχυτών-γονιδίων στόχων σε οργανισμούς-μοντέλα
Author Μίτλεττον, Μυρτώ Φ.
Thesis advisor Lavigne, Matthieu
Reviewer Παυλόπουλος, Αναστάσιος
Δελιδάκης, Χρήστος
Abstract Ever since the emergence of Next Generation Sequencing techniques, -omics and multiomics strategies have been offering amazing insights in structural and functional annotation of genomes and have boosted the development of both research and therapeutic approaches. The first goal of this project was the construction and implementation of a pipeline for the analysis of ATAC-seq (chromatin accessibility) and RNA-seq (gene expression) data, enabling genome-wide enhancer identification and prediction of putative enhancer–gene links. The above pipeline was first established to analyze data derived from wild-type mice (Mus musculus) and mice with a gene knocked-out. Once established and tested on the mouse dataset, the pipeline was used for the analysis of a developmental time-course dataset derived from the crustacean model organisms Parhyale hawaiensis. Parhyale has been put forward as an attractive experimental model to study tissue and organ morphogenesis during normal development and regeneration. I analyzed already produced mRNA-seq and Omni-ATAC-seq datasets, acquired at different stages of Parhyale embryogenesis: S13, S17 and S19. My analyses identified Differentially Expressed Genes and Differentially Accessible Regions between these experimental conditions and generated hypotheses about the composition of enhancer-gene regulatory networks. I then selected three Parhyale genes for detailed analysis by quantitative RT-PCR and immunofluorescence: gooseberry (gsb), homothorax (hth) and lola-like (lolal), which were shown to have correlating expression and accessibility characteristics and implicated in developmental processes like segmentation, appendage formation and Hox gene regulation, respectively. The established pipeline provides great amounts of data available for future research in mouse and Parhyale, and can be easily adjusted for data analysis of other model organisms and types of experiments.
Language English
Subject Atac-sequancing analysis
Atac-sequancing ανάλυση
Correlation analysis
Mouse
Mus musculus
Ngs analysis
Ngs pipeline
Parhyale hawaiensis
Rna-sequencing analysis
Rna-sequencing ανάλυση
Αλληλουχίσης νέας γενιάς
Ανάλυση δεδομένων
Παρυαλός
Ποντίκι
Issue date 2023-11-24
Collection   School/Department--School of Sciences and Engineering--Department of Biology--Post-graduate theses
  Type of Work--Post-graduate theses
Permanent Link https://elocus.lib.uoc.gr//dlib/9/2/4/metadata-dlib-1700655868-951544-12956.tkl Bookmark and Share
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