THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [RNA-seq]

Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. To decipher the epigenome influence on the formation of all levels of the nuclear organization, we studied tomato mutants defective for DDM1, a chromatin remodeler determining for the constitutive heterochromatin establishment. We observed that the ddm1 mutant exhibited weakened compartmentalization with lower insulation, more inter-compartment contacts and an increase in long-range contacts. This disorganization is accompanied by a reconfiguration of the epigenome, ultimately resulting in a reprogramming of its transcriptome. By integrating all our data, we have shown that this redistribution of the epigenome is linked to the global disorganization of the nucleus notably via new interactions mediated by H3K27me3, and is also related to new interactions between genes and/or TEs which display the same epigenetic characteristics. Altogether, our results strongly suggest that epigenetic features drive the formation of distinct compartments by playing a segregating role between active and inactive chromatin, becoming an essential characteristic for the identity of genes and TEs in terms of genome organization. Overall design: To assess the effect of the epigenome reconfiguration on transcriptome reprogramming, we performed RNA-seq analyses in WT and mutant. Then, we performed DESeq2 analysis and found differentially expressed genes in ddm1.

细胞核三维基因组组织参与从转录到细胞核自身完整性在内的诸多生命过程，且在生物体生命周期的全阶段均发挥关键作用，因此对其开展研究的重要性日益凸显。相较于由核苷酸序列所定义的线性基因组，三维基因组组织同时受表观基因组调控，但目前学界对表观基因组如何操控细胞核三维结构的分子机制仍知之甚少。
为解析表观基因组对细胞核各级组织形成的影响，本研究针对DDM1（一种调控组成型异染色质建立的染色质重塑因子）功能缺陷的番茄突变体展开实验。研究结果显示，ddm1突变体的染色质区室化作用减弱：染色质绝缘能力下降，区室间接触频次增加，同时长距离染色质接触频次上升。这种基因组组织紊乱伴随表观基因组的重构，最终引发转录组重编程。
通过整合所有实验数据，本研究证实表观基因组的重分布与细胞核全局紊乱存在显著关联，其中以H3K27me3（三甲基化组蛋白H3第27位赖氨酸）介导的新型染色质相互作用尤为关键；此外，该表观基因组重分布还与具备相同表观遗传特征的基因和/或转座因子（TE，Transposable Element）之间的新型相互作用密切相关。
综上，本研究结果有力表明，表观遗传特征通过在活跃染色质与非活跃染色质之间发挥分隔作用，驱动了特异性染色质区室的形成，这一机制是基因组组织层面上决定基因与转座因子（TE）身份的核心特征。
实验整体设计：为评估表观基因组重构对转录组重编程的影响，本研究对野生型（WT，Wild Type）及ddm1突变体开展RNA测序（RNA-seq）分析；随后通过DESeq2生物信息学分析，筛选得到ddm1突变体中的差异表达基因。