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Identifier

000454825

Title

Chromatin accessibility and differential gene expression data analysis of immune response in Gilthead seabream (Sparus aurata)

Alternative Title

Ανάλυση δεδομένων προσβασιμότητας χρωματίνης και διαφορικής γονιδιακής έκφρασης κατά την ανοσολογική απόκριση στην τσιπούρα (Sparus aurata)

Author

Παπαδοπούλου, Ανδρομάχη

Thesis advisor

Μανουσάκη, Τερέζα

Reviewer

Νικολάου, Χριστόφορος
Ηλιόπουλος, Ιωάννης

Abstract

The gilthead seabream is a widely consumed species in the Mediterranean and due to its extensive aquaculture, the pressure on the improvement of production has increased. One fundamental limiting factor of aquaculture production is the incidence of bacterial and viral infections. Deeper understanding of the underlying mechanisms of the immune response will help to prevent and treat these health problems. To this point, there have not been many studies on genome wide profiling of the gene expression changes in response to specific pathogens on fish. As part of the AquaFAANG project, this work focuses on the characterization of the transcriptomic and chromatin accessibility landscape of the immune response of gilthead seabream following Vibrio and PIC infections in-vitro and in-vivo, by using ATAC and RNA sequencing. The bioinformatic analysis revealed not only the overall expression patterns implicated in the immune response, but also virus-specific (nfkbiaa, nod2, atf3, sting1, traf3, rsad2, tlr7, tnfrsf1a, irf7, traf6, tlr3) and bacteria-specific (pglyrp5, pglyrp6) up-regulated genes in-vitro and in-vivo. On top of the expression profiles, the association of differentially accessible peaks with differentially expressed genes allowed us to assemble a core immune related gene network. This comparative analysis offers new insight for identifying key processes that are activated as part of the immune response against infection in gilthead seabream.

Language

English

Subject

ATAC-SEQ

Bioinformatics

Βιοπληροφορική

Issue date

2023-04-05

Collection

School/Department--School of Medicine--Department of Medicine--Post-graduate theses

Type of Work--Post-graduate theses

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