阿拉伯芥LDL1/2與HDA6參與生物時鐘中心節律調節

Abstract

摘要 在真核生物系統中，組蛋白修飾藉由改變染色體結構而扮演一個調控基因表達的重要角色。其中組蛋白的乙醯化（acetylation）和組蛋白H3K4的甲基化（H3K4 methylation）是啟動基因表達的重要修飾之一，而組蛋白去乙醯化酶（HDACs）以及H3K4去甲基化酶（H3K4 demethylases）皆是抑制基因表達的重要酵素。在酵母及動物系統中已經發現 HDACs 和 Lysine-Specific Demethylase 1（LSD1）在同一個蛋白複合體參與調控基因表達。我們也發現了在阿拉伯芥中的 LSD1-LIKE 1（LDL1） 以及 LDL2 會直接與 HDA6 蛋白交互作用，表示他們可能也會共同調控基因表達。進一步我們利用 ChIP-seq 發現了1895個基因為LDL1 和 HDA6 的共同靶基因。透過 Gene Ontology（GO）分析，我們發現這些LDL1 和 HDA6 的共同靶基因大多參與植物開花以及生長發育的負向調控。在hda6/ldl1/ldl2植物中也發現了延遲開花以及生長遲緩的表現型。 我們在 GO 分析中也發現 LDL1 和 HDA6 的共同靶基因包括許多生物時鐘基因。生物時鐘在植物生長發育階段都扮演重要調控角色。目前已發現許多轉錄因子參與調控生物時鐘，形成一個複雜的回饋調節網路。生物時鐘之中心節律有幾個主要轉錄因子，包括在清晨大量表達的 CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) 、 LHY (LATE ELONGATED HYPOCOTYL) 以及在傍晚大量表達的TOC1 (TIMING OF CAB EXPRESSION 1)，它們彼此互相抑制並在每日形成一個循環。前人研究中指出組蛋白修飾在生物時鐘中心節律的調控扮演重要角色，但其調控機制仍未被清楚瞭解。我們發現 LDL1、LDL2 以及 HDA6 可以和生物時鐘中心節律的轉錄因子 CCA1、 LHY 交互作用，並透過組蛋白修飾來調控 TOC1。這個的結果對於組蛋白修飾如何參與調控生物時鐘之中心節律，提供了一個新的可能的調控機制。

Abstract Histone modification and DNA methylation are important epigenetic marks in eukaryotic cells. The functional consequences of histone modifications can directly cause structural changes to chromatin to activate or repress gene expression. Histone acetylation and H3K4 methylation are important gene activation markers. Histone deacetylases (HDACs) and H3K4 demethylases can act as important transcription corepresser. In yeast and animal systems, HDACs and H3K4 Lysine-Specific Demethylase 1 (LSD1) can interact with each other and they were identified as the core components of several multi-protein complexes. In this research, we found that LSD1-LIKE 1 (LDL1) and LDL2 can interact with the histone deacetylase HDA6 in Arabidopsis. Furthermore, 1895 co-targeted genes of HDA6 and LDL1 were identified by using ChIP-sequencing assays. These co-targeted genes were significantly associated with negative regulation of many different biological processes including growth, flowering and circadian rhythm in the Gene Ontology (GO) analysis. hda6/ldl1/ldl2 triple mutant plants displayed delayed growth rate and strong late flowering phenotypes. Together, these results indicated that the HDA6-LDL1/2 complex generally act as an positive regulator of plant growth and development. In Arabidopsis, the circadian clock central oscillator genes are important cellular components for generating and maintaining circadian rhythms. Recent studies indicate that histone modifications play an important role in the regulation of the central oscillators. However, the regulatory relationship between histone modifications and the circadian clock genes remains largely unclear. In this study, we found that HDA6, LDL1 and LDL2 can interact with morning genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) to repress the expression of evening gene TIMING OF CAB EXPRESSION 1 (TOC1) by histone demetylation and deacetylaion. These results provide new insight into the molecular mechanism of how the circadian clock central oscillator genes are regulated through histone modifications.