Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome

Aicardi-Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE). AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4) and SAMHD1 (AGS5). However, the identity and source of such immunogenic nucleic acid species remain undefined. Using genome-wide approaches, we show that fibroblasts from AGS patients with AGS1-5 mutations are burdened by excessive loads of RNA:DNA hybrids. Using MethylC-seq, we show that AGS fibroblasts display pronounced and global loss of DNA methylation and demonstrate that AGS-specific RNA:DNA hybrids often occur within DNA hypomethylated regions. Altogether, our data suggest that RNA:DNA hybrids may represent a common immunogenic form of nucleic acids in AGS and provide the first evidence of epigenetic perturbations in AGS, furthering the links between AGS and SLE. DNA-RNA immunoprecipitation (DRIP-seq) was performed on control 1, control 3, AGS1 P1, AGS1 P2, AGS2 P1, AGS2 P2, AGS4 P1, AGS4 P2, AGS5 P1 and AGS5 P2. MethylC-seq was performed on control 1, control 2, AGS1 P1, AGS2 P1, AGS4 P1 and AGS5 P1. Reduced representation bisulfite sequencing (RRBS) was performed on GM12697 and AGS2 LCL cell lines. RNA-seq was performed on 2 biological replicates each of control 1, AGS1 P1, AGS2 P1, AGS2 P2, AGS4 P1, AGS4 P2 and AGS5 P1.