Valine-restricted diet regulates DNA methylation [ddC S1-END-Seq]. Valine-restricted diet regulates DNA methylation [ddC S1-END-Seq]

The abundancy of intracellular amino acid (AA) levels is precisely sensed by complex machineries to regulate various signaling pathways and control cell functions. Insufficient intracellular AAs may block the release of tRNA molecules from the general control non-derepressible 2 (GCN2), and consequently activate GCN2-ATF4 pathways, which is an indirect mechanism for sensing general AAs levels. Additionally, the intracellular levels of some AAs can be sensed by direct binding to specific sensors. Nowadays, the sensors of arginine and leucine levels are most well-characterized, including CASTor1/2, SLC38A9, Sestrin2 and SAR1B, which regulate the mechanistic target of rapamycin complex 1 (mTORC1) pathway, and couple AA availability to cell growth and metabolism. However, it is still unclear whether and how other types of amino acids are directly sensed to regulate cellular functions except tRNA synthetases. Moreover, epigenetics is known to be regulated by the metabolism of amino acids, but it is incompletely understood how AA abundancy regulates the epigenetics, especially DNA methylation. The long-sought sensor of amino acids for epigenetic regulation has thus far been unknown. Here, we present evidence that valine sensor regulated DNA demethylation. Overall design: ddC S1-END-seq in WT and TDG knockdown HCT116 cells upon valine deprivation

细胞内氨基酸（intracellular amino acid, AA）的丰度可通过复杂的分子机器精准感知，以此调控多种信号通路并控制细胞功能。细胞内氨基酸不足会阻断转运RNA（transfer RNA, tRNA）分子从通用控制非阻遏2（general control non-derepressible 2, GCN2）的释放，进而激活GCN2-ATF4通路，这是感知整体氨基酸水平的间接机制。

此外，部分细胞内氨基酸可通过直接结合特定传感器实现感知。目前研究最为透彻的精氨酸与亮氨酸传感器包括CASTor1/2、SLC38A9、Sestrin2及SAR1B，它们可调控雷帕霉素靶蛋白复合物1（mechanistic target of rapamycin complex 1, mTORC1）通路，将氨基酸可获得性与细胞生长及代谢相耦联。

然而，除氨酰-tRNA合成酶外，其他类型氨基酸是否以及如何通过直接感知来调控细胞功能，目前仍不明确。此外，已知氨基酸代谢可调控表观遗传，但氨基酸丰度如何调控表观遗传（尤其是DNA甲基化）的机制仍未完全阐明。此前长期追寻的、用于表观遗传调控的氨基酸传感器至今仍未被发现。

本研究提供证据表明，缬氨酸传感器可调控DNA去甲基化。

整体实验设计：在缬氨酸剥夺处理下，对野生型（wild type, WT）及TDG敲降的HCT116细胞开展ddC S1-END-seq检测。