To study the function of chromatin regulators in hybrid gene expression, the histone deacetylase gene OsHDT1 was over-expressed or inactivated by RNAi in an elite rice parent. Digital analysis of gene expression using high throughput sequencing technology revealed several differential gene expression patterns in the hybrid, including additivity, nonadditivity and overdominance, etc. Alteration of OsHDT1 levels affected many genes specifically in the hybrid. In addition, we show that increased OsHDT1 could suppress overdominance gene expression, providing evidence of overdominance gene action in heterosis. These results not only support the overdominance hypothesis to explain heterosis, but also provide evidence that variation in the levels of single trans-acting regulatory proteins such as chromatin factors is important to establish differential gene expression pattern in the hybrid. High throughput sequencing technology was used to analyse gene differencial expression of 15 days old rice seedling of 5 samples, MH63(MH), ZS97(ZS), SY63(SY,hybrids of MH and ZS), overexpression of OsHDT1 in SY(FU), RNAi of OsHDT1 in SY(FR).