Sternisha, A. C.; Li, H.; Traylor, J. I.; Guo, L.; Jun, J. H.; Zhao, X.; Gajendra, K.; Ouyang, Q.; Schmidt, M.; Fleishman, M.; Shi, D. D.; Savani, M. R.; Xiao, Y.; Lee, J. H.; Zacharias, L. G.; Mathews, T. P.; Gordillo, R.; Kim, Y. J.; Xu, L.; Doench, J. G.; Koduri, V.; Abdullah, K. G.; Banaszynski, L. A.; Agathocleous, M.; DeBerardinis, R. J.; Morrow, E. M.; McBrayer, S. K.

Alpha-ketoglutarate (-KG) is required for chromatin demethylation but mechanisms controlling -KG abundance in the nucleus are poorly defined. Therefore, we designed a biosensor system to monitor this metabolite pool in human cells using an -KG-responsive cyanobacterial transcription factor, NtcA. We then coupled this system with a genetic screen to identify genes that regulate -KG in the nucleus, defining an inter-organelle pathway in which sequential mitochondrial activities of the GPT2 transaminase and SLC25A11 transporter supply nuclear -KG. Using a mouse model of GPT2 deficiency, a human inborn error of metabolism, we found that this pathway controls chromatin methylation in the developing brain. Our work provides a tool to assess -KG signaling to chromatin and a framework for leveraging forward genetics to study nuclear metabolite pools.