A transcriptional biosensor reveals mechanisms of α-ketoglutarate signaling to chromatin

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.

doi:10.1101/2025.04.06.647450

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bioRxiv · 10.1101/2025.04.06.647450

A transcriptional biosensor reveals mechanisms of α-ketoglutarate signaling to chromatin

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Abstract

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.

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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.. 2025-04-07. A transcriptional biosensor reveals mechanisms of α-ketoglutarate signaling to chromatin. https://doi.org/10.1101/2025.04.06.647450

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