The mission of the Cornett Lab is to understand how, where, and why lysine methylation regulates cellular processes. Toward this goal, we use in vitro and cellular biochemistry, chemical biology, and proteomics approaches to map lysine methylation signaling networks and study the regulators of lysine methylation.
Lysine methylation was discovered more than a half-century ago, but functional studies of this PTM did not intensify until the early 2000s when lysine methylation on histone proteins was connected to transcriptional regulation. Since then, significant effort has been devoted to the study of lysine methylation signaling, primarily on histone proteins. However, over the last decade, advances in mass spectrometry have revealed nearly 5,000 unique sites of lysine methylation on over 3,000 human proteins. In this same time, steady progress has revealed several ways in which lysine methylation directly regulates the function of non-histone proteins. However, a small fraction of the known methylation sites are connected to a KMT or KDM, and an even smaller fraction (by our estimates, only ~1%) are functionally annotated (Fig. 1A). Even the known 5,000 sites are likely an under-representation of the entire lysine methylome. Recent in silico work to assess lysine methylation proteome-wide predicts nearly 50,000 sites of lysine methylation on non-histone proteins (Fig. 1A). How many sites are methylated and how lysine methylation on non-histone proteins affects cellular and biological functions are major gaps in our knowledge.
Lysine methylation occurs when one (monomethylation - Kme1), two (dimethylation - Kme2), or three (trimethylation - Kme3) methyl groups are transferred from the universal methyl donor, S-adenosylmethionine (SAM), to a substrate. On histones, different forms of lysine methylation (Kme1, Kme2, Kme3) can recruit different reader proteins, ultimately having different effects. In humans, lysine methyltransferases fall into two classes: the SET domain containing family and seven-β-strand (7BS) family. The SET family primarily contains the lysine specific methyltransferases whereas the 7BS family consist of methyltransferases that target many different biomolecules including DNA, RNA, and proteins, including several that methylate lysine. We recently catalogued all the known KMTs from both families and orphan SET family members, which includes 60 human KMTs. Out of these, 21 have reported histone substrates, 6 have non-histone substrates, 14 have both histone and non-histone substrates, and 19 have no reported substrates. Many of the reported histone substrates are controversial and lack evidence in cells. It is critical that we determine the substrate specificity of KMTs to help delineate which substrates are physiologically relevant substrates and their functions in cellular processes.
The long-term goal of our research program is to determine how lysine methylation regulates protein function. Within this broad framework, we strive to identify biological processes that are regulated by lysine methylation, the substrate specificity of KMTs and KDMs, and how dysregulation of lysine methylation signaling networks contribute to human disease and developmental disorders. We have recently developed new strategies to overcome two critical barriers that have been slowing progress toward this goal: connecting KMTs/KDMs to their physiological substrates and mapping lysine methylation. Over the next five years, we will use these new approaches to advance our understanding of lysine methylation using two different biological systems as models.
Current Research Funding
Regulation of non-histone protein function by lysine methylation
1R35GM147023-01 (PI: Cornett)
Funding period: 09/21/2022 – 08/31/2027
Hanquier, J. N., Sanders, K., Berryhill, C. A., Sahoo, F. K., Hudmon, A., Vilseck, J. Z., & Cornett, E. M. (2022). Substrate selectivity of the PRDM9 lysine methyltransferase domain. bioRxiv. https://doi.org/10.1101/2022.10.12.511945
Chen, Q., Bates, A. M., Hanquier, J. N., Simpson, E., Rusch, D. B., Podicheti, R., Liu, Y., Wek, R. C., Cornett, E. M., & Georgiadis, M. M. (2022). Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing. Journal of Biological Chemistry, 298(5), 101894. https://doi.org/10.1016/j.jbc.2022.101894
Cornett, E. M., Ferry, L., Defossez, P.-A., & Rothbart, S. B. (2019). Lysine Methylation Regulators Moonlighting outside the Epigenome. Molecular Cell, 75(6), 1092–1101. https://doi.org/10.1016/j.molcel.2019.08.026
Cornett, E. M., Dickson, B. M., Krajewski, K., Spellmon, N., Umstead, A., Vaughan, R. M., Shaw, K. M., Versluis, P. P., Cowles, M. W., Brunzelle, J., Yang, Z., Vega, I. E., Sun, Z.-W., & Rothbart, S. B. (2018). A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity. Science Advances, 4(11), eaav2623. https://doi.org/10.1126/sciadv.aav2623