Date of Award

2024

Degree Type

Dissertation

Degree Name

Doctor of Philosophy in Biological and Environmental Sciences

Specialization

Cell and Molecular Biology

Department

Cell & Molecular Biology

First Advisor

Niall Howlett

Abstract

Fanconi Anemia (FA) is a rare genetic disease characterized by congenital abnormalities, bone marrow failure, and a predisposition to cancer. FA is caused by a mutation in one of 23 genes, the protein products of which function in a pathway to repair DNA and maintain genome stability. While an important role for the FA proteins in the repair of DNA interstrand crosslinks (ICLs) has been established in vitro, there is still much to be learned about the function of the pathway, and the endogenous sources of ICLs in FA patients. In this work we study FANCD2, a key protein in the FA pathway, using various sequencing approaches, to gain insights on its function in maintaining genome stability. In Manuscript I, we discover a novel link between retinoic acid metabolism and FA. We discover mis regulation of retinoic acid metabolism genes in an FA-D2 cell model through RNA-sequencing and show retinaldehyde induced genotoxicity in FA-D2 (FANCD2-/-) cells.

In Manuscript II, we report on FANCD2’s role in the maintenance of genome stability. We show that FANCD2 genome binding is nonrandom and enriched at transcription start sites. We also show that FANCD2 binds to large neural genes under conditions of replication stress. Finally, we report a relationship between FANCD2 genome binding, and regions of mitotic DNA synthesis, and copy number variation.

In Manuscript III, we report on the chromatin landscape of FA. We discover an altered chromatin landscape between FA-D2 (FANCD2-/-) and FANCD2-complemented cells, including differential accessibility of hallmark cellular pathways. We also uncovered differential accessibility of large genes between FA-D2 (FANCD2-/-) and FANCD2-complemented cells. Finally, we report on a correlation between high gene expression and accessibility in FANCD2-complemented cells.

In conclusion, we discover a novel link between retinoic acid signaling and FA, we report on FANCD2 recruitment to large neural genes that are prone to copy number variation, and we characterize the chromatin landscape of FA-D2 (FANCD2-/-) and FANCD2-complemented cells. Altogether, this work reveals novel pathways and mechanisms that are relevant to the pathophysiology of FA.

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