ADNP Exhibits Methyltransferase Activity in Overexpression Systems and Modulates DNA and Histone Methylation

Activity-Dependent Neuroprotective Protein (ADNP) is a putative transcription factor that differentially interacts with proteins involved in chromatin remodeling, thereby controlling neuronal differentiation. The protein contains nine zinc fingers, a bipartite nuclear localization signal (NLS), and a homeobox domain with a heterochromatin protein 1 interaction motif, ensuring nuclear association with DNA and chromatin. De novo variants in ADNP cause autism comorbid with intellectual disability in the Helsmoortel-Van der Aa syndrome. ADNP interacts with components of the SWI/SNF in HEK293T cells but has also been reported as part of the repressive ChAHP complex in mouse embryonic stem cells. Although converging evidence suggests a role in chromatin remodeling, Hi-C experiments failed to detect major alterations in 3D chromatin structure. We therefore investigated ADNP's role in epigenetic regulation and identified the chromatin scaffolding protein WDR5 and HDAC2 as interaction partners. Structural modeling revealed two N-terminal methyltransferase domains, suggesting catalytic activity via SAM to SAH conversion. Immunoprecipitated fractions containing wild-type ADNP exhibited methyltransferase activity, which was reduced by nonsense variants. ADNP was expressed in histone-enriched cerebellar fractions in mice and a Helsmoortel-Van der Aa autopsy case, with male-specific reduction of the H3K79me1 modification. At the DNA level, wild-type ADNP induced CpG hypermethylation. However, most variants caused CpG hypomethylation, supporting a loss-of-function mechanism, while NLS variants showed additional hypermethylation, suggesting a gain-of-function effect linked to apoptosis and microtubule transport. Taken together, we identified an ADNP-WDR5-HDAC2 protein complex involved in epigenetic regulation, with ADNP exhibiting methyltransferase activity in overexpression systems.