The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells. The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells

While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns in normal, immortalized human fibroblasts. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signaling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated, producing double-stranded RNA; 2) this triggered activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable knockdown systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression in the absence of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing even in the absence of DNA methylation. Overall design: Stable knockdowns of Ubiquitin Like With PHD And Ring Finger Domains 1 UHRF1 were generated in hTERT-immortalised adult fibroblasts using shRNA. WThTERT-1604 cells were used in triplicate as a control. Genome wide methylation and transcriptional levels were assayed using the Illumina 450k BeadChip and subsequently analysed using bioinformatic approaches. Genes targets of relevant interest identified through bioinformatic mining were validated using wet lab approaches.