In Schizosaccharomyces pombe, there are two aconitases, Aco1 and Aco2, involved in the Krebs cycle in mitochondria. Interestingly, Aco2 is localized to nucleus as well. Here, we investigated the nuclear role of Aco2 by deleting its nuclear localization signal. The aco2 Delta NLS mutation suppressed the gene-silencing defects of RNAi mutants at the centromere, where heterochromatin formation depends on RNAi pathway. In Delta ago1, the aco2 Delta NLS mutation restored heterochromatin through elevating Chp1 binding. Aco2 physically interacted with Chp1 via the N-terminal chromodomain that binds to methylated his tone H3K9. In the sub-telomeric region, where heterochromatin forms independent of RNAi pathway, the single aco2 Delta NLS mutation caused extra gene silencing via elevating Chp1 binding, without increasing histone methylation. The anti-silencing effect did not require the catalytic function of aconitase. Taken together, Aco2 functions as an epigenetic regulator of gene expression, through associating with chromodomain of Chp1 to maintain heterochromatin. (C) 2019 The Authors. Published by Elsevier Inc.