The antithetical regulation of cardiac ␣-and -myosin heavy chain (MHC) genes by thyroid hormone (T3) is not well understood but appears to involve thyroid hormone interaction with its nuclear receptor and MHC promoters as well as cis-acting noncoding regulatory RNA (ncRNA). Both of these phenomena involve epigenetic regulations. This study investigated the extent that altered thyroid state induces histone modifications in the chromatin associated with the cardiac MHC genes. We hypothesized that specific epigenetic events could be identified and linked to cardiac MHC gene switching in response to a hypothyroid or hyperthyroid state. A hypothyroid state was induced in rats by propylthiouracil treatment (PTU), whereas a hyperthyroid (T3) was induced by T3 treatment. The left ventricle was analyzed after 7 days for MHC pre-mRNA expression, and the chromatin was assessed for enrichment in specific histone modifications using chromatin immunoprecipitation quantitative PCR assays. At both the ␣-MHC promoter and the intergenic region, the enrichment in acetyl histone H3 at K9/14 (H3K9/14ac) and trimethyl histone H3 at K4 (H3K4me3) changed in a similar fashion. They were both decreased with PTU treatment but did not change under T3, except at a location situated 5= to the antisense intergenic transcription start site. These same marks varied differently on the -MHC promoter. For example, H3K4me3 enrichment correlated with the -promoter activity in PTU and T3 groups, whereas H3K9/14ac was repressed in the T3 group but did not change under PTU. Histone H3K9me was enriched in chromatin of both the intergenic and ␣-MHC promoters in the PTU group, whereas histone H4K20me1 was enriched in chromatin of -MHC promoter in the normal control and T3 groups. Collectively, these findings provide evidence that specific epigenetic phenomena modulate MHC gene expression in altered thyroid states. gene transcription; epigenetic regulation; chromatin immunoprecipitation quantitative polymerase chain reaction; noncoding RNA; Sprague-Dawley rats TWO MYOSIN HEAVY CHAIN (MHC) isoforms are expressed in the myocardium, designated as the ␣-and -MHC. Cardiac MHC phenotype is a major determinant of contractility, mechanical performance, and energy turnover of the heart (59). For example, hearts rich in ␣-MHC expression have high contractility, whereas those rich in -MHC expression have slow speed of contraction but are more energy efficient (1). The normal control adult rodent heart expresses predominantly the ␣-MHC gene, but this can be readily altered by several pathophysiological conditions. For example, hypothyroidism, diabetes, pressure overload, and caloric deprivation enhance the -MHC gene expression and repress the ␣-MHC expression, whereas thyroid hormone treatment produces the opposite effect (4, 48). During these MHC transformations, the MHC genes are regulated in an antithetical fashion; i.e., as one isoform's transcription increases, the other decreases in a coordinated fashion.