Revealing the function of heterochromatin spatial organization in response to early-life environmental challenges in C. elegans

转录活跃的常染色质和被抑制的异染色质的空间分布不是随机的，使基因组能够进行功能划分。特别是，沉默的异染色质主动地隔离在核的外围，而活性常染色质位于中央。然而，3D染色质分布本身的功能在很大程度上仍不清楚，主要是因为无法选择性地扰乱染色质的空间组织，同时保持其他核过程不变。在这项提议中，我们将利用线虫，这是迄今为止唯一发现了高度特异的异染色质核周锚定的生物，称为CEC-4，以破坏全球异染色质的空间分布，并揭示其对组织完整性和生物健康的影响。尽管空间基因组定位在全基因组范围内受到损害，但去除CEC-4并不会改变整体转录，并且CEC-4突变体在最佳生长条件下没有表现出表型，除非受到异位转录刺激的挑战。这提出了一种有趣的可能性，即染色质的空间区隔在协调对非程序化线索的转录反应方面具有功能。有趣的是，在自然环境中生长的动物不断地暴露在环境压力下，这会导致基因表达的深刻变化。然而，环境信号如何影响基因组的空间组织，以及这是否对应激反应起关键作用目前尚不清楚。我们的初步数据表明，当动物暴露在环境压力下时，常染色质和异染色质的准确空间分离确实是有功能的。在这项提案中，我们计划进一步表征环境和3D染色质组织之间的功能相互作用。特别是，我们将使CEC-4突变体和wt动物暴露于环境应激，并测量i)基因组-核板相互作用，ii)染色质可及性和iii)基因在两个不同组织中的表达，使我们能够确定一个生物体内不同类型的细胞如何对相同的环境线索做出反应。有趣的是，在几个物种中，早年的压力暴露会影响生命后期发生的事件，其机制在很大程度上仍不清楚。在这项工作中，我们将识别在异染色质空间分布受损时的应激反应中去调控的基因，并确定它们在恢复最佳生长条件后对生命后期发育和衰老的影响。为了实现我们的目标，我的团队将结合使用显微镜、分子和遗传学方法。由于包括人类在内的所有有机体都会不断地暴露在不断变化的环境中，这项研究的意义可能是巨大的。

The spatial distribution of transcriptionally active euchromatin and repressed heterochromatin is not random and enables a functional compartmentalization of the genome. In particular, silent heterochromatin is actively sequestered at the nuclear periphery, while active euchromatin is centrally located. Yet, the function of 3D chromatin distribution per se remains largely unknown, mainly due to the inability to selectively perturb chromatin spatial organization while leaving other nuclear processes unaltered. In this proposal, we will take advantage of the roundworm C. elegans, the only organism where a highly specific perinuclear anchor of heterochromatin, termed CEC-4, was identified to date, to impair heterochromatin spatial distribution globally and unravel the consequences for tissue integrity and organismal health. Despite a genome-wide impairment of spatial genome positioning, ablating cec-4 does not alter transcription globally and cec-4 mutants display no phenotype under optimal growth conditions unless challenged with an ectopic transcriptional stimulus. This raises the fascinating possibility that the spatial compartmentalization of chromatin is functional in coordinating the transcriptional response to non-programmed cues. Intriguingly, animals growing in their natural context are constantly exposed to environmental stresses, which induce profound gene expression changes. However, how environmental cues affects the spatial organization of the genome and whether this critically contributes to the stress response is currently unknown. Our preliminary data suggest that an accurate spatial segregation of euchromatin and heterochromatin is indeed functional when animals are exposed to environmental stress. In this proposal, we plan to characterize the functional interaction between the environment and 3D chromatin organization further. In particular, we will expose cec-4 mutants and wt animals to environmental stress and measure i) genome-nuclear lamina interactions, ii) chromatin accessibility and iii) gene expression, during stress and upon recovery in two different tissues, allowing us to determine how different cell types within an organism respond to the same environmental cue. Interestingly, in several species an early life stress exposure can influence events that occur later in life, with mechanisms that remain largely unknown. In this work, we will identify genes de-regulated during the stress response when heterochromatin spatial distribution is impaired and determine their impact on development and aging later in life, upon restoration of optimal growth conditions. To achieve our goals, my team will employ a combination of microscopy, molecular and genetic approaches. Because all organisms, including humans, are constantly exposed to a changing environment, the implications of this study are likely to be vast.