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Background  Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) is a systemic autoimmune disease characterized by destructive vascular inflammation. Two prominent ANCA autoantigens are myeloperoxidase (MPO) and proteinase 3 (PR3), and transcription of  MPO  and  PRTN3 , the genes encoding the autoantigens, is associated with disease activity. We investigated whether patients with AAV have alterations in histone modifications, particularly those associated with transcriptional activation, at  MPO  and  PRTN3 .    Results  We identified a network of genes regulating histone modifications that were differentially expressed in AAV patients compared to healthy controls. We focused on four genes ( EHMT1  and  EHMT2 ,  ING4 , and  MSL1 ) and found their expression correlated with expression of  MPO  and  PRTN3 . Methylation of histone H3K9, catalyzed by EHMT1 and EHMT2 and associated with gene silencing, was most depleted at  MPO  and  PRTN3  in patients with active disease and the highest  MPO  and  PRTN3  expression. Acetylation of histone H4K16, modified by complexes containing ING4 and MSL1 and associated with gene activation, was most enriched at  MPO  and  PRTN3  in patients with active disease and the highest  MPO  and  PRTN3  expression. Methylation at H3K4, a mark of transcriptional activation, was enriched at  MPO  and  PRTN3  in patients and healthy controls.    Conclusions    MPO  and  PRTN3  in neutrophils of AAV patients with active disease have a distinct pattern of histone modifications, which implicates epigenetic mechanisms in regulating expression of autoantigen genes and suggests that the epigenome may be involved in AAV pathogenesis.    Electronic supplementary material  The online version of this article (doi:10.1186/s13148-016-0251-0) contains supplementary material, which is available to authorized users.

Histone modification signature at myeloperoxidase and proteinase 3 in patients with anti-neutrophil cytoplasmic autoantibody-associated vasculitis