Functional glycoproteomics by integrated network assembly and partitioning

Griffin, M. E.; Thompson, J. W.; Xiao, Y.; Sweredoski, M. J.; Jensen, E. H.; Koldobskaya, Y.; Schacht, A. L.; Kim, T. D.; Choudhry, P.; Lomenick, B.; Garbis, S. D.; Moradian, A.; Hsieh-Wilson, L. C.

doi:10.1101/2023.06.13.541482

bioRxiv · 10.1101/2023.06.13.541482

Functional glycoproteomics by integrated network assembly and partitioning

Griffin, M. E.·Thompson, J. W.·Xiao, Y.·Sweredoski, M. J.·Jensen, E. H.·Koldobskaya, Y.·Schacht, A. L.·Kim, T. D.·Choudhry, P.·Lomenick, B.·Garbis, S. D.·Moradian, A.·Hsieh-Wilson, L. C.

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Abstract

The post-translational modification (PTM) of proteins by O-linked {beta}-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describe Networking of Interactors and SubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.

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Griffin, M. E., Thompson, J. W., Xiao, Y., Sweredoski, M. J., Jensen, E. H., Koldobskaya, Y., Schacht, A. L., Kim, T. D., Choudhry, P., Lomenick, B., Garbis, S. D., Moradian, A., Hsieh-Wilson, L. C.. 2023-06-14. Functional glycoproteomics by integrated network assembly and partitioning. https://doi.org/10.1101/2023.06.13.541482

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