Identification of Rpl29 as a major substrate of the lysine methyltransferase Set7/9

J Biol Chem. 2018 Aug 17;293(33):12770-12780. doi: 10.1074/jbc.RA118.002890. Epub 2018 Jun 29.


Set7/9 (also known as Set7, Set9, Setd7, and Kmt7) is a lysine methyltransferase that catalyzes the methylation of multiple substrates, including histone H3 and non-histone proteins. Although not essential for normal development and physiology, Set7/9-mediated methylation events play important roles in regulating cellular pathways involved in various human diseases, making Set7/9 a promising therapeutic target. Multiple Set7/9 inhibitors have been developed, which exhibit varying degrees of potency and selectivity in vitro However, validation of these compounds in vivo has been hampered by the lack of a reliable cellular biomarker for Set7/9 activity. Here, we report the identification of Rpl29, a ribosomal protein abundantly expressed in all cell types, as a major substrate of Set7/9. We show that Rpl29 lysine 5 (Rpl29K5) is methylated exclusively by Set7/9 and can be demethylated by Lsd1 (also known as Kdm1a). Rpl29 is not a core component of the ribosome translational machinery and plays a regulatory role in translation efficiency. Our results indicate that Rpl29 methylation has no effect on global protein synthesis but affects Rpl29 subcellular localization. Using an Rpl29 methylation-specific antibody, we demonstrate that Rpl29K5 methylation is present ubiquitously and validate that (R)-PFI-2, a Set7/9 inhibitor, efficiently reduces Rpl29K5 methylation in cell lines. Thus, Rpl29 methylation can serve as a specific cellular biomarker for measuring Set7/9 activity.

Keywords: Lsd1; Rpl29; Set7/9; biomarker; epigenetics; histone methylation; post-translational modification (PTM); ribosome function.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blood Coagulation Factors / genetics*
  • Blood Coagulation Factors / metabolism
  • Cells, Cultured
  • DNA Methylation*
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Gene Expression Regulation*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism*
  • Histones / metabolism*
  • Humans
  • Lysine / chemistry*
  • Male
  • Mice, Knockout
  • Protein Processing, Post-Translational
  • RNA-Binding Proteins
  • Ribosomal Proteins / physiology*
  • Transcription, Genetic


  • Blood Coagulation Factors
  • Histones
  • RNA-Binding Proteins
  • RPL29 protein, human
  • Ribosomal Proteins
  • Rpl29 protein, mouse
  • Histone-Lysine N-Methyltransferase
  • SETD7 protein, human
  • Lysine