Arabidopsis RPD3-type histone deacetylases form multiple plant-specific complexes that are required for preventing overexpression of stress-induced genes (ChIP-Seq)

Although the Arabidopsis thaliana RPD3-type histone deacetylases have been known to form SIN3 histone deacetylase complexes that are conserved in eukaryotes, it is unknown whether they also form other types of histone deacetylase complexes. Here, we performed affinity purification followed by mass spectrometry and demonstrated that the Arabidopsis RPD3-type histone deacetylases HDA6 and HDA19 can interact with several previously uncharacterized proteins and form three types of plant-specific histone deacetylase complexes, which we named SANT, ESANT, and ARID. RNA-seq indicated that HDA6 and HDA19 function together with other components of the histone deacetylase complexes and co-regulate the expression of a number of genes. HDA6 and HDA19 have been thought to repress gene transcription by histone deacetylation. We found that the histone deacetylase complexes can also repress gene expression via certain histone-deacetylation-independent mechanisms. In the mutants of the histone deacetylase complexes, the expression of a number of stress-induced genes was up-regulated. Several mutants of the histone deacetylase complexes showed severe retardation in growth. Considering that the growth retardation is thought to be a trade-off for the increase of stress tolerance, we predict that the histone deacetylase complexes identified in this study prevent overexpression of stress-induced genes and thereby ensure normal growth of plants under non-stress conditions. Examination of H3Ac levels in wild type and eight mutants grown under long day conditions.

尽管已知拟南芥（Arabidopsis thaliana）的RPD3型组蛋白去乙酰化酶可形成在真核生物中保守的SIN3型组蛋白去乙酰化复合物，但目前尚不清楚其是否还能形成其他类型的组蛋白去乙酰化复合物。本研究通过亲和纯化结合质谱分析，证实拟南芥的RPD3型组蛋白去乙酰化酶HDA6与HDA19可与多种此前未被表征的蛋白质相互作用，并形成三类植物特异性组蛋白去乙酰化复合物，我们将其分别命名为SANT、ESANT及ARID复合物。RNA测序（RNA-seq）结果显示，HDA6与HDA19可与该组蛋白去乙酰化复合物的其他组分协同发挥功能，共同调控大量基因的表达。此前学界普遍认为HDA6与HDA19通过组蛋白去乙酰化作用抑制基因转录，而本研究发现，这类组蛋白去乙酰化复合物还可通过某些不依赖组蛋白去乙酰化的机制实现基因表达抑制。在该组蛋白去乙酰化复合物的突变体中，大量胁迫诱导基因的表达出现上调。多款该复合物的突变体表现出严重的生长迟缓表型。鉴于生长迟缓被认为是胁迫耐受性提升的权衡效应，我们推测本研究鉴定出的组蛋白去乙酰化复合物可通过抑制胁迫诱导基因的过度表达，从而保障植物在非胁迫条件下的正常生长。本研究还检测了长日照条件下培养的野生型植株与8株突变体的组蛋白H3乙酰化（H3Ac）水平。