Glc7/PP1 dephosphorylates histone H3T11 to regulate autophagy and telomere silencing in response to nutrient availability

How cells adapt their gene expression to nutritional changes remains poorly understood. Histone H3T11 is phosphorylated by pyruvate kinase to repress gene transcription. Here, we identify the protein phosphatase 1 (PP1), Glc7 as the enzyme that specifically dephosphorylates H3T11. We also characterize two novel Glc7-containing subcomplexes and reveal their roles in regulating gene expression upon glucose starvation. Specifically, the Glc7-Sen1 subcomplex dephosphorylates H3T11 to activate the transcription of autophagy-related genes. The Glc7-Rif1-Rap1 subcomplex dephosphorylates H3T11 to derepress the transcription of telomere-proximal genes. Upon glucose starvation, Glc7 expression is up-regulated and more Glc7 translocates into the nucleus to dephosphorylate H3T11, leading to induction of autophagy and derepressed transcription of telomere-proximal genes. Furthermore, the functions of PP1/Glc7 and the two Glc7-containing subcomplexes are conserved in mammals to regulate autophagy and telomere structure. Collectively, our results reveal a novel mechanism to regulate gene expression and chromatin structure in response to glucose availability. ChIP-Seq analysis. Yeast strain were grown in 200 ml YPD or SD-C media at 30°C until OD600 of ~0.7-1.0. The crosslinking was performed in 1% formaldehyde and quenched by adding 10 ml of 2.5 M glycine. Cells were harvested, washed once with cold TBS + PMSF, lysed in FA-SDS buffer (40 mM HEPES-KOH pH7.5, 1 mM EDTA pH8.0, 0.1% SDS, 1% Triton X-100, 0.1% Na deoxycholate, 1 mM PMSF, 2 μg/ml leupeptin, 1 μg/ml pepstatin A, protease inhibitor cocktail, phosphatase inhibitor cocktail). Chromatin was sonicated to an average size of ~500 bp and then subjected to immunoprecipitation with antibodies pre-bound to Protein G Dynabeads (Invitrogen) at 4°C overnight. The beads were washed successively with FA buffer, FA buffer + 1 M NaCl, FA buffer + 0.5 M NaCl, TEL buffer (10 mM Tris pH8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% Na deoxycholate) and TE buffer (10 mM Tris pH7.4, 1 mM EDTA). The eluted DNA/protein complex was treated with 20 µg Proteinase K at 55°C for 1 h followed by treatment at 65°C overnight. After removing RNA by RNase (Roche), the DNA was purified with ethanol precipitation and sequenced . Yeast strains WT (BY4741 in Open Biosystem) and Rif1-FLAG were the in same group, yeast strains Sen1-FLAG and Glc7-FLAG cultured both in YPD medium and SD-C medium were the other group.