The impact of microbial metabolites on the chromatin landscape and gene regulation

项目摘要 人类生理和疾病的许多方面都与肠道微生物群的状态密切相关，但 确定微生物组在细胞水平上发挥作用的机制仍然是一个悬而未决的问题。 微生物分解膳食纤维，从而产生短链脂肪酸(SCFAs)，如 代谢副产品。这些发酵反应在胃肠道中创造了一个环境， 高浓度的单链脂肪酸，然后可以作用于邻近的宿主细胞。最近，SCFA已经被 被检测为组蛋白的化学修饰，称为组蛋白酰基标记，表明部分 这些代谢物进入细胞核，沉积在染色质上。虽然某些组蛋白酰基标记已经被 据报道，正向调控转录，包括研究得很好的组蛋白乙酰化，其机制 较新的酰基标记，如组蛋白丁酰化，其功能作用在很大程度上是未知的。此外，SCFA如何 是否在细胞内被调控进入细胞核并作用于染色质尚不确定。在小鼠的肠道里， 组蛋白上的特殊酰基修饰与微生物的存在呈正相关。此外, 抗生素治疗降低了组蛋白酰化标记的水平，这表明选择的组蛋白酰化标记是依赖的 在微生物区系上。这种组蛋白酰基标记对微生物区系的依赖以组织特有的方式发生， 在盲肠观察到的差异最大，盲肠是小肠和大肠相交的地方。现在我们的目标是 为了确定依赖于微生物区系的特定染色质酰基标记对基因表达的作用 老鼠内脏作为一个模型系统。我们假设SCFA是以组蛋白酰化形式写在染色质上的 一种调节方式，调节关键转录程序以响应微生物环境。至 针对这一假设，选择组蛋白酰基标记在基因调控中的机制功能将是 调查后，通过使用小鼠肠道作为模型来研究这些组蛋白标记。此外, 将全面定义依赖于微生物区系的染色质酰基标记和代谢物。 最后，还将确定代谢酶对组蛋白酰基标记的调节。一起， 这些目标的完成将扩大我们对新组蛋白标记的生理作用的理解，以及 还将提供对微生物群如何影响染色质景观的机械洞察。此外， 这项建议将通过染色质阅读器蛋白的募集来阐明组蛋白酰基标记的功能 转录的下游调控。

Project Summary Many aspects of human physiology and disease are closely tied to the state of the gut microbiome, yet determining mechanisms by which the microbiome exerts effects at the cellular level is still an open question. Microbes break down dietary fiber, which results in the generation of short chain fatty acids (SCFAs) as metabolic byproducts. These fermentation reactions create an environment in the gastrointestinal tract with high concentrations of SCFAs, which can then act on neighboring host cells. Recently, SCFAs have been detected as chemical modifications on histone proteins, called histone acyl marks, suggesting that a portion of these metabolites enter the nucleus for deposition onto chromatin. While certain histone acyl marks have been reported to positively regulate transcription, including the well-studied histone acetylation, the mechanistic functional role of newer acyl marks such as histone butyrylation are largely unknown. In addition, how SCFAs are regulated in the cell to enter the nucleus and act on chromatin is undetermined. In the mouse intestine, particular acyl modifications on histones are positively correlated with the presence of microbes. In addition, antibiotic treatment reduces levels of histone acyl marks, suggesting select histone acyl marks are dependent on the microbiota. This dependency of histone acyl marks on the microbiota occurs in a tissue-specific manner, with the highest differences observed in the cecum, where the small and large intestines intersect. Now we aim to determine the function of specific microbiota-dependent chromatin acyl marks on gene expression using the mouse gut as a model system. We hypothesize that SCFAs are written onto chromatin as histone acylations in a regulated manner, which mediate key transcriptional programs in response to the microbial environment. To address this hypothesis, the mechanistic function of select histone acyl marks in gene regulation will be investigated, through the use of the mouse gut as a model to study these histone marks. In addition, microbiota-dependent chromatin acyl marks and metabolites will be defined in a comprehensive manner. Lastly, the regulation of histone acyl marks by metabolic enzymes will also be determined. Together, completion of these aims will expand our understanding of the physiological roles of novel histone marks, and will also provide mechanistic insight into how the microbiome impacts the chromatin landscape. Furthermore, this proposal will elucidate the functions of histone acyl marks through chromatin reader protein recruitment and downstream regulation of transcription.