Quantitative sub-cellular metabolomic measurements can yield crucial insights into the roles of metabolites in cellular processes, but are subject to multiple confounding factors. We developed Stable Isotope Labeling of Essential nutrients in cell Culture - Sub-cellular Fractionation (SILEC-SF), which uses isotope labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-Coenzyme A thioesters in sub-cellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing we identified the branched chain amino acid (BCAA) isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.

中文翻译：

---

定量亚细胞酰基辅酶A分析揭示了不同的核调控

定量亚细胞代谢组学测量可以对代谢物在细胞过程中的作用产生重要的见解，但会受到多种混杂因素的影响。我们开发了细胞培养中必需营养素的稳定同位素标记 - 亚细胞分馏 (SILEC-SF)，它使用同位素标记的内标对照，在整个分馏和加工过程中都存在，以通过液体量化亚细胞区室中的酰基辅酶 A 硫酯色谱-质谱法。我们在一系列样品类型中测试了 SILEC-SF，并检查了对氧张力、细胞分化和营养可用性的分区反应。将 SILEC-SF 应用于核隔室的挑战性分析揭示了与细胞溶胶不同的核酰基辅酶 A 谱，具有显着的丙酰辅酶A核富集。使用同位素示踪，我们将支链氨基酸 (BCAA) 异亮氨酸鉴定为核丙酰辅酶 A 和组蛋白丙酰化的主要代谢来源，从而揭示了代谢与表观基因组之间的串扰的新机制。