The loss of ATRX/DAXX complex disturbs rDNA heterochromatinization and promotes development of glioma

Background Ribosomal DNA (rDNA) transcription by the RNA polymerase I (Pol I) is a rate-limited step for ribosome synthesis, which is critical for cell growth, cell differentiation, and tumorigenesis. Meanwhile rDNA transcription is modulated by DNA methylation and histone epigenetic modification. Though with great progress in epigenetic research recently, it still remains much uncertain about the relationship of histone variant epigenetic modification and rDNA transcription. Results In this study, epigenetic profiles of silent rDNA in next-generation sequencing datasets were examined. We found that the chaperone of histone variant H3.3, the alpha-thalassemia/mental retardation X-linked syndrome protein (ATRX)/death domain-associated protein (DAXX) complex, and methyltransferase SET domain bifurcated 1 (Setdb1, also known as ESET) help maintain H3.3K9me3 modifications among the promoter and coding regions of silent rDNA. Our experiments further confirmed that DAXX depletion leads to the conversion of silent rDNA into upstream binding factor-bound active rDNA and the release of rDNA transcriptional potency. Support for this model is provided by data from a low-grade glioma in which ATRX is lost and a higher level of ribosomal biosynthesis, nucleolus activity, and proliferation are observed. Conclusions We demonstrate a model of epigenetic regulation for rDNA with roles for the ATRX/DAXX complex and H3.3/H3K9me3 modifications identified. Thus, loss of ATRX/DAXX may represent a driving force for tumorigenesis due to its contribution to the release of rDNA transcriptional potency.