Antisense transcription is prevalent in mammalian genomes, yet the function of many antisense transcripts remains elusive. We have previously shown that the fibroblast growth factor 2 (FGF2) gene is regulated endogenously by an overlapping antisense gene called Nudix-type motif 6 (NUDT6). However, the molecular mechanisms that determine the balance of FGF2 and NUDT6 transcripts are not yet well understood. Here we demonstrate that there is a strong negative correlation between FGF2 and NUDT6 across 7 different cell lines. Small interfering RNA-mediated knockdown of NUDT6 causes an increase in nascent FGF2 transcripts, including a short FGF2 variant that lacks sequence complementarity with NUDT6, indicating the involvement of transcriptional mechanisms. In support of this, we show that changes in histone acetylation by trichostatin A treatment, histone deacetylase inhibition, or small interfering RNA knockdown of the histone acetyltransferase CSRP2BP, oppositely affect NUDT6 and FGF2 mRNA levels. A significant increase in histone acetylation with trichostatin A treatment was only detected at the genomic region where the 2 genes overlap, suggesting that this may be an important regulatory region for determining the balance of NUDT6 and FGF2. Knockdown of the histone demethylase KDM4A similarly causes a shift in the balance of NUDT6 and FGF2 transcripts. Expression of CSRP2BP and KDM4A correlates positively with NUDT6 expression and negatively with FGF2 expression. The results presented here indicate that histone acetylation and additional chromatin modifiers are important in determining the relative levels of FGF2 and NUDT6 and support a model in which epigenetic remodeling contributes to their relative expression levels.