Histone deacetylase 4 (HDAC4) is a member of class IIa histone deacetylases (class IIa HDACs) and is believed to possess a low intrinsic deacetylase activity. However, HDAC4 sufficiently represses distinct transcription factors (TFs) such as the myocyte enhancer factor 2 (MEF2). Transcriptional repression by HDAC4 has been suggested to be mediated by the recruitment of other chromatin-modifying enzymes, such as methyltransferases or class I histone deacetylases. However, this concept has not been investigated by an unbiased approach.

Therefore, we studied the histone modifications H3K4me3, H3K9ac, H3K27ac, H3K9me2 and H3K27me3 in a genome-wide approach using HDAC4-deficient cardiomyocytes. We identified a general epigenetic shift from a ‘repressive’ to an ‘active’ status, characterized by an increase of H3K4me3, H3K9ac and H3K27ac and a decrease of H3K9me2 and H3K27me3.

In HDAC4-deficient cardiomyocytes, MEF2 binding sites were considerably overrepresented in upregulated promoter regions of H3K9ac and H3K4me3. For example, we identified the promoter of Adprhl1 as a new genomic target of HDAC4 and MEF2. Overexpression of HDAC4 in cardiomyocytes was able to repress the transcription of the Adprhl1 promoter in the presence of the methyltransferase SUV39H1. On a genome-wide level, the decrease of H3K9 methylation did not change baseline expression but was associated with exercise-induced gene expression.

We conclude that HDAC4, on the one hand, associates with activating histone modifications, such as H3K4me3 and H3K9ac. A functional consequence, on the other hand, requires an indirect regulation of H3K9me2. H3K9 hypomethylation in HDAC4 target genes (‘first hit’) plus a ‘second hit’ (e.g., exercise) determines the transcriptional response.

组蛋白去乙酰化酶 4 (HDAC4) 是 IIa 类组蛋白去乙酰化酶 (IIa 类 HDAC) 的成员，被认为具有较低的内在去乙酰化酶活性。然而，HDAC4 足以抑制不同的转录因子 (TF)，例如肌细胞增强因子 2 (MEF2)。HDAC4 的转录抑制被认为是由其他染色质修饰酶的募集介导的，例如甲基转移酶或 I 类组蛋白脱乙酰酶。然而，这一概念尚未通过公正的方法进行调查。

因此，我们使用 HDAC4 缺陷型心肌细胞在全基因组方法中研究了组蛋白修饰 H3K4me3、H3K9ac、H3K27ac、H3K9me2 和 H3K27me3。我们确定了从“抑制”状态到“活跃”状态的一般表观遗传转变，其特征是 H3K4me3、H3K9ac 和 H3K27ac 的增加以及 H3K9me2 和 H3K27me3 的减少。

在 HDAC4 缺陷型心肌细胞中，MEF2 结合位点在 H3K9ac 和 H3K4me3 的上调启动子区域中明显过多。例如，我们将 Adprhl1 的启动子确定为 HDAC4 和 MEF2 的新基因组靶标。心肌细胞中 HDAC4 的过表达能够在甲基转移酶 SUV39H1 存在的情况下抑制 Adprhl1 启动子的转录。在全基因组水平上，H3K9 甲基化的降低并未改变基线表达，但与运动诱导的基因表达有关。

我们得出结论，一方面 HDAC4 与激活组蛋白修饰有关，例如 H3K4me3 和 H3K9ac。另一方面，功能性后果需要对 H3K9me2 进行间接调节。HDAC4 靶基因中的 H3K9 低甲基化（“第一次打击”）加上“第二次打击”（例如，运动）决定了转录反应。