The modified base, 5-methylcytosine (5mC) is enriched at repetitive DNA sequences including satellite repeats that surround chromosome centromeres. These centromeric and pericentromeric satellite repeats are important for stable chromosome structure and proper chromosome segregation. Loss of 5mC at pericentromeric repeats is common in cancer and senescence. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. 5mC loss at pericentromeric repeats is a molecular hallmark of the rare genetic disease Immunodeficiency, Centromere instability and Facial abnormalities (ICF) syndrome. To date, attempts to model specific loss of 5mC at pericentromeres in mouse through mutation of ICF associated genes have been unsuccessful. Here, I develop a zebrafish model for ICF syndrome by mutating the zebrafish ortholog of ZBTB24, a poorly characterized gene that is disrupted in ~30% of ICF patients. zbtb24 mutant zebrafish recapitulate key features of ICF syndrome including immunodeficiency, facial abnormalities, gastrointestinal defects, impaired growth and reduced lifespan. I also show that homozygous mutation of zbtb24 causes a progressive loss of 5mC at pericentromeric satellite repeats in zebrafish. This progressive loss of methylation allowed for elucidation of primary vs secondary consequences of hypomethylation at these sequences. Transcriptome analysis revealed that one of the earliest consequences of pericentromeric hypomethylation was activation of an interferon-based innate immune response. Mechanistically, I tie this response to derepression of pericentromeric satellite transcripts and I demonstrate that these aberrant transcripts are recognized through the MDA5-MAVS dsRNA-sensing machinery, which is normally associated with an innate immune response to viruses. Additional preliminary studies indicate increased incidence of DNA damage and tumor formation in zbtb24 mutants suggesting that pericentromeric 5mC is likely important for genome stability. Taken together, this thesis describes the first viable animal model of ICF Syndrome, reveals a function for ICF-gene zbtb24 in the long-term maintenance of pericentromeric DNA methylation and identifies roles for pericentromeric DNA methylation in preventing autoimmunity and maintaining genome integrity.