SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription

Blank, Maximilian F.; Chen, Sifan; Poetz, Fabian; Schnölzer, Martina; Voit, Renate; Grummt, Ingrid

Previous studies have revealed that the protein content of the nucleolus is dynamic, showing decrease, no changes, or accumulation of specific proteins after inhibition of transcription, viral infection or DNA damage (23) (24) (25) (26) (27) . To functionally characterize SIRT7-interacting proteins, we purified Flag/HA-tagged SIRT7 from HEK293T cells and analyzed associated proteins by mass spectrometry (Supplementary Figure S1A ). Using stringent inclusion criteria, 357 proteins (≥2 unique peptides) were identified, the majority residing in the nuclear and nucleolar compartment (Supplementary Table S2 ). Consistent with previous studies (14) (15) (16) , the SIRT7 interactome was enriched in nucleolar proteins, such as nucleolin, nucleophosmin, MYBBP1A, DHX9, DDX21 and ribosomal proteins. In addition to previously reported SIRT7 interacting proteins, a large part of SIRT7-associated proteins identified by our mass spectrometry analysis was novel (Supplementary Figure S1B and Table S2 ). Classification of proteins revealed prominent groups with functions in transcription, translation, RNA maturation, chromatin organization, DNA repair, and intracellular transport ( Figure 1A ). The largest fraction comprised proteins with roles in RNA metabolism and ribosome biogenesis, such as pre-ribosomal factors (PRFs) and small nucleolar ribonucleoprotein particles (snoRNPs) involved in pre-rRNA folding, processing and posttranscriptional modifications. Proteins with functions in Pol II transcription, such as RPB2 and cyclin-dependent kinase 9 (CDK9) and mRNA processing factors were also identified, suggesting that SIRT7 is involved in both transcriptional and post-transcriptional processes (Supplementary Table S3 ).