GCN5-ADA2 Recruits ATP-Citrate Lyase (ACL) and Forms Condensates to Modulate Acetylation at H3K9 for Functional Genes in Rice Meristem

The SAGA complex is a highly conserved histone acetyltransferase (HAT) complex in eukaryotes, playing crucial role in regulating gene transcription throughout organismal development. The complex consists of two core components: GCN5, the HAT subunit, and ADA2, which primarily functions as an adaptor, facilitating interactions between GCN5 and other proteins and enhancing the complex's accessibility to nucleosomes. Beyond its well-established roles, we discovered that, in rice, ADA2 possesses an evolutionary conserved intrinsically disordered region (IDR) that directs the SAGA complex to form nuclear condensates. Moreover, we identified a physical interaction between ADA2 and ATP-citrate lyase subunit A2 (ACLA2), leading to the formation of a GCN5-ADA2-ACLA2 (GAA) complex. Both GCN5 and ACLA2 exhibit phase separation in vivo, a process that is dependent on ADA2. Within these condensates, ACL contributes to the production and enrichment of acetyl-CoA, thereby promoting histone acetylation. Genetic evidence showed that knock-out or suppression of the three indicated genes collectively resulted in diminished meristem zones at both root tips and inflorescences, accompanied by a significant reduction in genomic H3K9 acetylation and transcriptional attenuation of essential genes for meristem function. In summary, our findings unveiled a novel mechanism for HAT in modulating gene transcription and plant development, in which the GAA complex phase separates and enriches acetyl-CoA metabolites within the nuclear puncta to facilitate the acetylation of histones at target genes. Overall design: Transcriptome detection by RNA-seq for rice root tips and inflorescence meristems in wild type and the three indicated mutants/RNAi backgrounds. Genomic binding detection for the three components of GAA complex via CUT&Tag. Genomic histone H3 K9 acetylation detection of root tips for wild type and the three indicated mutants/RNAi backgrounds.

SAGA复合物是真核生物中高度保守的组蛋白乙酰转移酶（histone acetyltransferase, HAT）复合物，在生物体发育全程的基因转录调控中发挥关键作用。该复合物包含两个核心组分：作为HAT亚基的GCN5，以及主要发挥衔接蛋白功能的ADA2；ADA2可介导GCN5与其他蛋白的相互作用，并提升复合物对核小体的可及性。
除其已被广泛证实的经典功能外，本研究在水稻中发现，ADA2含有进化保守的内在无序区域（intrinsically disordered region, IDR），可指导SAGA复合物形成核凝聚体。此外，我们还鉴定出ADA2与ATP-柠檬酸裂解酶亚基A2（ATP-citrate lyase subunit A2, ACLA2）之间存在物理相互作用，进而形成GCN5-ADA2-ACLA2（GAA）复合物。GCN5与ACLA2均可在体内发生相分离，且该过程依赖于ADA2。在这些核凝聚体中，ATP-柠檬酸裂解酶（ACL）可催化乙酰辅酶A的生成与富集，从而促进组蛋白乙酰化。
遗传学实验证实，同时敲除或抑制上述三个基因，会导致水稻根尖与花序的分生组织区域缩小，同时伴随基因组H3K9乙酰化水平显著降低，以及分生组织功能必需基因的转录减弱。
综上，本研究揭示了组蛋白乙酰转移酶调控基因转录与植物发育的全新机制：GAA复合物通过相分离在核凝集中富集乙酰辅酶A代谢物，以促进靶基因位点的组蛋白乙酰化。
整体实验设计：对野生型及上述三个突变体/RNA干扰（RNAi）背景的水稻根尖与花序分生组织开展RNA-seq转录组检测；通过CUT&Tag技术检测GAA复合物三个组分的基因组结合位点；对野生型及上述三个突变体/RNAi背景的水稻根尖进行基因组组蛋白H3 K9乙酰化水平检测。