Wilson Thomas Stuart, Noberini Roberta, Moysidou Eirini, Ojukwu Ifeyinwa, Milan Marta, Jiang Ming, Kelly Gavin, Howell Michael, Bonaldi Tiziana, Scaffidi Paola
Cancer Epigenetics , The Francis Crick Institute, London, NW1 1AT, United Kingdom.
Nuclear Proteomics, Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy.
Nucleic Acids Res. 2025 Apr 10;53(7). doi: 10.1093/nar/gkaf297.
The molecular control of epigenetic information relies on hundreds of proteins of diverse function, which cooperate in defining chromatin structure and DNA methylation landscapes. While many individual pathways have been characterized, how different classes of epigenetic regulators interact to build a resilient epigenetic regulatory network (ERN) remains poorly understood. Here, we show that most individual regulators are dispensable for somatic cell fitness, and that robustness emerges from multiple layers of functional cooperation and degeneracy among network components. By disrupting 200 epigenetic regulator genes, individually or in combination, we generated network-wide maps of functional interactions for representative regulators. We found that paralogues represent only a first layer of functional compensation within the ERN, with intra- or inter-class interactions buffering the effects of perturbation in a gene-specific manner: while CREBBP cooperates with multiple acetyltransferases to form a subnetwork that ensures robust chromatin acetylation, ARID1A interacts with regulators from across all functional classes. When combined with oncogene activation, the accumulated epigenetic disorder exposes a synthetic fragility and broadly sensitizes ARID1A-deficient cells to further perturbation. Our findings reveal homeostatic mechanisms through which the ERN sustains somatic cell fitness and uncover how the network remodels as the epigenome is progressively deregulated in disease.
表观遗传信息的分子控制依赖于数百种功能各异的蛋白质,它们协同作用以定义染色质结构和DNA甲基化图谱。虽然许多单独的途径已被表征,但不同类别的表观遗传调节因子如何相互作用以构建一个有弹性的表观遗传调节网络(ERN)仍知之甚少。在这里,我们表明大多数单独的调节因子对于体细胞适应性并非必需,并且稳健性源于网络组件之间多层的功能合作和简并性。通过单独或组合破坏200个表观遗传调节基因,我们生成了代表性调节因子的全网络功能相互作用图谱。我们发现旁系同源物仅代表ERN内功能补偿的第一层,类内或类间相互作用以基因特异性方式缓冲扰动的影响:虽然CREBBP与多种乙酰转移酶合作形成一个确保稳健染色质乙酰化的子网络,但ARID1A与所有功能类别的调节因子相互作用。当与癌基因激活相结合时,累积的表观遗传紊乱会暴露出合成脆弱性,并使ARID1A缺陷细胞广泛地对进一步的扰动敏感。我们的研究结果揭示了ERN维持体细胞适应性的稳态机制,并揭示了随着表观基因组在疾病中逐渐失调,网络是如何重塑的。