ENO1 couples HDAC1 to regulate histone lactylation and gene transcription

Histone deacetylases (HDACs) are essential transcriptional regulators that mediate gene expression through the complexes they are involved in. Thus, deciphering the HDAC-associated proteins is key to elucidating the underlying mechanisms. Here we present an efficient tool, termed heterobifunctional molecule-enabled proximity labeling strategy (BimPL), to investigate endogenous HDAC neighboring proteins in living cells. Leveraging BimPL and quantitative proteomics, we enable the robust capture of several known HDAC complexes as well as numerous putative HDAC interactors such as glycolytic enzyme enolase-1 (ENO1). Through biochemical studies and CUT&Tag analysis, we uncovered that nuclear ENO1 interacts with HDAC1, which in turn blunts the activity of HDAC1 via locally generated phosphoenolpyruvate (PEP), thereby mediating histone lysine lactylation (Kla) and gene transcription. Our study offers a versatile tool for systematic exploring endogenous protein complexes, as well as provides insight into the unidentified function of ENO1 in the regulation of histone Kla and liver tumor progression. We implemented CUT&Tag assays in HepG2 cells to determine the impact of ENO1/HDAC1-mediated histone lactylation on gene transcription. To this end, the cells were immunoprecipitated by H4K12la, ENO1 or HDAC1 antibodies, respectively, followed by high-throughput sequencing.