Epigenetic control of endogenous retroviruses and their immune recognition in differentiated human cells

Endogenous retroviruses (ERVs) have accumulated in vertebrate genomes and contribute to the complexity of gene regulation. ERVs are beneficial to their hosts because their promoters can drive temporal and spatial expression of cellular genes. Aberrantly activated ERVs, however, can be detrimental. ERV transcription is therefore controlled by multiple epigenetic modifiers. One ERV repression pathway involves KAP1 and Krüppel-associated box domain-zinc finger proteins (KZNFs), which recruit KAP1 to ERVs and other repetitive sequences early in development. Little is known, in contrast, about the regulation of ERVs in differentiated cells, particularly in humans. In this thesis, we aimed firstly to address the question of whether KAP1 and related epigenetic factors are necessary to repress ERVs in differentiated human cells. Secondly, we sought to assess the impact of ERV reactivation on the innate immune system. We found through KAP1 knockout and mRNA-sequencing analyses that KAP1 represses ERVs and ZNFs, both of which overlap with KAP1 binding sites and silent chromatin marks in multiple cell types. Furthermore, this pathway is functionally conserved in primary human peripheral blood mononuclear cells (PBMCs). We show that cytosine methylation that acts on KAP1-regulated loci is necessary to prevent immune reactivity of ERVs and other retrotransposons that can mimic viruses by producing immunostimulatory nucleic acids. While KAP1 depletion alone leads to activation of several chemokines, it is not sufficient for global induction of interferon-stimulated genes. Therefore, we depleted key epigenetic complexes that KAP1 collaborates with including the HUSH complex comprising MPP8, Periphilin and Tasor. We identified MPP8 to play a dominant role in preventing aberrant immune activation in human cells. MPP8 is a chromodomain protein implicated in the spread of heterochromatin. In sum, these data indicate that the KAP1-KZNF pathway and MPP8 are central to genome stability and the control of viral mimicry in differentiated human cells.