Asparagine starvation suppresses histone demethylation through iron depletion

Abstract

Nutrient availability can impact epigenome to modify gene expression and dictate cell fate decision (Etchegaray and Mostoslavsky, 2016; Kinnaird et al., 2016). -ketoglutarate is an indispensable substrate for the Jumonji family of histone demethylases (JHDMs) mediating most of the cellular demethylation reactions on histone subunits (Schvartzman et al., 2018). Since -ketoglutarate is an intermediate of the tricarboxylic acid (TCA) cycle and a product of transamination, its intracellular levels are regulated by the metabolism of several amino acids (Baksh et al., 2020; Carey et al., 2015; Raffel et al., 2017; Vardhana et al., 2019). Here we show that asparagine starvation suppresses global histone demethylation. This process is neither due to the change of expression of histone modifying enzymes, nor due to the change of intracellular level of -ketoglutarate. Rather, asparagine starvation reduces intracellular pool of labile iron (Fe2+), which is a key cofactor for the JHDMs to function. Mechanistically, asparagine starvation post-transcriptionally suppresses the expression of iron responsive element binding protein 2 (IREB2), an iron sensing protein, which then reduces the mRNA expression of the transferrin receptor (TFRC), a major carrier for iron uptake (Hentze et al., 2010). Furthermore, iron supplementation to the culture medium restores histone demethylation and alters global gene expression to accelerate cell death under conditions of asparagine starvation. Collectively, our results uncover that suppression of iron-dependent histone demethylation is part of the cellular adaptive response to asparagine starvation.