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

转录活性常染色质和抑制的异染色质的空间分布不是随机的，并使基因组的功能区室化。特别是，沉默的异染色质活跃地被隔离在核周边，而活跃的常染色质位于中央。然而，3D染色质分布本身的功能在很大程度上仍然是未知的，主要是由于不能选择性地扰乱染色质空间组织，同时保持其他核过程不变。在这个建议中，我们将利用蛔虫C。elegans是迄今为止唯一鉴定出高度特异性的异染色质核周锚（称为CEC-4）的生物体，其在全球范围内损害异染色质的空间分布，并揭示了组织完整性和生物体健康的后果。尽管空间基因组定位的全基因组损伤，切除cec-4不会改变转录全局和cec-4突变体显示在最佳生长条件下没有表型，除非挑战与异位转录刺激。这提出了一个有趣的可能性，即染色质的空间区室化在协调对非编程线索的转录反应中起作用。有趣的是，在自然环境中生长的动物不断暴露在环境压力下，这会引起深刻的基因表达变化。然而，环境线索如何影响基因组的空间组织，以及这是否对应激反应有重要贡献，目前尚不清楚。我们的初步数据表明，当动物暴露于环境压力时，常染色质和异染色质的准确空间分离确实是功能性的。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突变体和野生型动物暴露于环境应激，并测量i）基因组-核纤层相互作用，ii）染色质可及性和iii）基因表达，在应激期间和恢复时，在两种不同的组织中，使我们能够确定生物体内不同的细胞类型如何响应相同的环境提示。有趣的是，在几个物种中，早期生活压力暴露可以影响以后生活中发生的事件，其机制在很大程度上仍然未知。在这项工作中，我们将确定在异染色质空间分布受损时的应激反应中失调的基因，并确定它们在恢复最佳生长条件后对以后生活中发育和衰老的影响。为了实现我们的目标，我的团队将采用显微镜，分子和遗传方法的组合。由于包括人类在内的所有生物体都不断暴露在不断变化的环境中，因此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.