大豆種子萌發之表觀遺傳調控機制
Epigenetic regulation of soybean seed germination
計畫主持人：臺大-植物所 吳克強、中研院-農生中心 林哲揚
此合作研究計畫的研究目標是探討表觀遺傳機制在調控大豆和阿拉伯芥種子萌發及其他植物發育過程中的作用。我們發現，阿拉伯芥中的H3K9甲基轉移酶KYP/SUVH5/6通過與AS1-AS2相互作用，改變KNAT1和KNAT2基因上的組蛋白H3乙酰化和H3K9二甲基化，從而參與葉片的發育。此外，阿拉伯芥的端粒重複序列結合因子（TRBs）影響PRC2及JMJ14的活性，通過H3K27me3的沉積和H3K4me3的去除來抑制目標基因的表達。我們還發現，在種子萌發過程中，各種編碼組蛋白變體和組蛋白伴侶蛋白的基因被上調，這可能促進幼苗的生長。活性基因標誌H3K4me3除了調控大豆基因體中的基因活動外，還可能在休眠和萌發過程中維持染色質結構。在種子萌發期間，大豆基因體中的特定順式元件和鄰近基因主要由H3K9ac調控，而在幼苗中則主要由H3K27ac調控。此外，組蛋白去乙酰化酶在大豆與阿拉伯芥種子萌發控制不同基因群，導致這兩種物種的種子在種子萌芽時期，有不同的突變表徵。在阿拉伯芥，我們發現一個特定組蛋白去乙酰化酶基因會造成幼苗喪失根的向地性。這些研究可以幫助我們了解各種表觀遺傳修飾如何參與植物基因表達調控，從而揭示植物生長發育的表觀遺傳調控機制，為作物品質改良提供參考。研究成果發表在Commun Biol（6:219）、Nat Commun（14:1736）和Plant Physiol（196:1939）等期刊。
The goal of this collaborative research is to investigate the role of epigenetic machineries in regulating seed germination and other plant developmental processes in soybean and Arabidopsis. We found that the Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from KNAT1 and KNAT2 loci. Arabidopsis telomeric repeat binding factors (TRBs) coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal. We also found that a variety of genes encoding histone variants and histone chaperones with specific functions are up-regulated during germination to potentially promote seedling growth. Active gene mark H3K4me3 may contribute to maintaining chromatin structure during dormancy and germination in addition to controlling gene activities in the soybean genome. Specific cis-element and nearby gene sets in the soybean genome are mainly regulated by H3K9ac during germination and predominantly by H3K27ac in seedling. Our studies provide new insights into the functional interplay between transcriptinal factors and histone modification proteins and lead to broadening the knowledge about the transcriptional control of plant developmental processes at the chromatin level. Furthermore, histone deacetylases regulate different gene sets during seed germination in soybean and Arabidopsis, leading to distinct mutant phenotypes in the two species. In Arabidopsis, we identified a specific histone deacetylase gene that causes a loss of root gravitropism in seedlings. The accomplishment of this project contributed to both basic and applied sciences - to conceive how plants regulate gene expression in development and environment, and to develop molecular strategies useful in breeding programs to improve crop traits. The relevant research was published in Commun Biol (6:219), Nat Commun (14:1736), and Plant Physiol (196:1939).
We have established robust pipelines for processing and analyzing NGS datasets, including RNA-seq, ChIP-seq, and BS-seq to integrate multiple dimensions of omics data. Together, these tools provide strong support for multi-omics analysis and, most importantly, in uncovering biologically meaningful insights.