TRR 81: Chromatin Changes in Differentiation and Malignancies

细胞在正常发育和疾病期间的分化受染色质结构的变化支配，染色质结构在几个水平上表现出来以确定基因活性。在更局部的水平上，基因嵌入在活性或抑制性染色质结构中。这些状态之间的变化是由DNA结合转录因子调节的，这些转录因子将组蛋白修饰酶和核小体重塑酶募集到染色质。在更全球的水平上，结构蛋白驱动染色质折叠和环形成，并建立染色体接触来调节更大的基因组区域。局部和全局染色质调控紧密相连，TRR 81在我们理解肌肉和神经元分化过程中传递发育信号的途径如何与组蛋白修饰酶相互作用以改变染色质结构方面取得了实质性进展。我们揭示了染色质重塑分子在不同发育环境中的分子功能，包括心脏发育和精子发生。此外，驱动染色体构象的因素和机制，拓扑结构相关的结构域和增强子-启动子-相互作用，在不同的细胞系统中被发现。最后，我们对X染色体失活和精子发生过程中染色质致密化的分子机制的理解有了显著的进展，这一扩展应用的重点是利用新的和完善的方法，使“分化和肿瘤中的染色质变化”以前所未有的细节水平得到解决。其中包括开发小分子来调节染色质调节剂，改进CRISPR方法以精确改变基因组DNA，以及将染色质调节剂靶向特定的基因组位点。已经引入了新的测序方法，其中一些是由TRR 81成员发明的，以探测大距离的染色质接触。关键技术的灵敏度和分辨率已经大大提高，使得小数量甚至单个细胞的表观基因组分析成为可能。TRR 81的优势之一是将这些技术应用于多个互补模型，以研究导致染色质变化的正常和病理机制。分化模型包括精子发生、免疫细胞及其通过信号传导的活化、造血干细胞及其分化、允许向神经和肌肉谱系分化的ES细胞和细胞系、脑类器官培养物和癌细胞。疾病模型包括肿瘤形成、神经发育综合征、炎症、肌肉营养不良和血红蛋白病。TRR 81项目将促进我们对健康和患病细胞分化的表观遗传机制的理解，并为未来开发新的治疗方法提供基础。

Differentiation of cells during normal development and disease is governed by changes to chromatin structure that manifest at several levels to determine gene activity. At a more local level, genes are embedded in active or repressive chromatin structures. Changes between these states are modulated by DNA binding transcription factors recruiting histone modifying and nucleosome remodelling enzymes to chromatin. At a more global level, structural proteins drive chromatin folding and loop formation and establish chromosomal contacts to regulate larger genomic regions. Local and global chromatin regulation are tightly interconnected.The TRR81 has made substantial progress in our understanding of how pathways transmitting developmental signals interface with histone modifying enzymes to change chromatin structure during muscle and neuronal differentiation. We unraveled molecular functions of chromatin remodellers in diverse developmental contexts, including heart development and spermatogenesis. In addition, factors and mechanisms driving chromosome conformation, topologically associated domains and enhancer-promoter-interactions, were uncovered in different cell systems. Finally, our understanding of the molecular mechanisms underlying global chromatin compaction during X-chromosome inactivation and spermatogenesis has been significantly advanced.The focus of this extension application is the utilization of new and refined methods allowing “Chromatin Changes in Differentiation and Malignancies” to be addressed at unprecedented levels of detail. Among these are the development of small molecules to modulate chromatin regulators, improved CRISPR methods to precisely change genomic DNA and targeting of chromatin regulators to specific genomic loci. Novel sequencing approaches have been introduced, some of which invented by TRR81 members, to probe chromatin contacts over large distances. Sensitivity and resolution of key techniques have been dramatically improved such that analyses of the epigenomes of small numbers or even single cells have become possible. Finally, super resolution microscopy is continuously being refined by the TRR81.One of the strengths of the TRR81 is to apply these techniques to multiple, complementary models to investigate normal and pathological mechanisms that lead to chromatin changes. The differentiation models include spermatogenesis, immune cells and their activation by signalling, hematopoietic stem cells and their differentiation, ES cells and cell lines that allow differentiation towards neural and muscle lineages, cerebral organoid cultures and cancer cells. Disease models include tumor formation, neurodevelopmental syndromes, inflammation, muscle dystrophy and hemoglobinopathies. The TRR81 projects proposed will advance our understanding of epigenetic mechanisms underlying differentiation in healthy and in diseased cells and will provide the basis for the future development of novel therapeutic approaches.