The metabolic aspects of macroH2A histone variants

Abstract

The histone variant macroH2A is the only structural chromatin component containing a macrodomain. In vertebrates, two genes and one event of alternative splicing give rise to three macroH2A proteins that differ in their macrodomains. As histone variants, macroH2A proteins contribute to the protein content of chromatin (Buschbeck & Hake, 2017). On the other hand, the capacity to bind ADP-ribose via its macrodomain is limited to the splice variant macroH2A1.1 (Kustatscher et al., 2005). As a consequence, macroH2A1.1, but not macroH2A1.2 or macroH2A2, binds auto-ADP-ribosylated PARP1 (Timinszky et al., 2009). Since the alternative splicing of the exon 5 affects the binding pocket of macroH2A1.2, as a consequence it cannot bind ADP-ribose (Kustatscher et al., 2005) and it remains an orphan protein. In the first study presented here, we investigated the evolution of the macrodomain-containing histone variant macroH2A1.1, an integral chromatin component that limits nuclear NAD+ consumption by inhibiting PARP1. We found that macroH2A originated in pre-metazoan protists. The crystal structure of the macroH2A macrodomain from the protist Capsaspora allowed us to identify highly conserved principles of ligand binding and pinpoint key residue substitutions, selected for during the evolution of the vertebrate stem lineage. Metabolic characterization of the Capsaspora life cycle indicated that the metabolic function of macroH2A was associated with non-proliferative stages. Taken together, we provide insight into the evolution of a chromatin element involved in compartmental NAD regulation, relevant for understanding of its metabolism and potential therapeutic applications. In the second study, we described the structurally relevant elements for ligand binding by the orphan macroH2A isoform, macroH2A1.2. Furthermore, using targeted and untargeted approaches on the verge of in silico, in vitro and in cellulo approaches, we detected phospholipids as the first putative physiological ligands of macroH2A1.2. We further observed a behavioral phenotype in macroH2A1.2 knock-out mice and report for the first time the upregulation of macroH2A1.2 expression in the differentiated cells, more specifically in differentiated neurons. We postulate that macroH2A1.2 might have a binding-pocket related role in the regulation of behavior, similarly to what was observed for PPARα in hypothalamus, whereby it regulates animal behavior depending on the binding of its phospholipid ligands (Chakravarthy et al., 2007; Roy et al., 2016).