PRISMA: Protein Interaction Screen on Peptide Matrix reveals interaction footprints and modifications- dependent interactome of intrinsically disordered C/EBPb


  • G. Dittmar
  • D. Perez Hernandez
  • E. Kowenz-Leutz
  • M. Kirchner
  • G. Kahlert
  • R. Wesolowski
  • K. Baum
  • M. Knoblich
  • M. Hofstätter
  • A. Muller
  • J. Wolf
  • U. Reimer
  • A. Leutz


  • iScience


  • iScience 13: 351-370


  • CCAAT enhancer binding protein beta (C/EBPβ) is a pioneer transcription factor that specifies cell differentiation. C/EBPβ is intrinsically unstructured, a molecular feature common to many proteins involved in signal processing and epigenetics. The structure of C/EBPβ differs depending on alternative translation initiation and multiple post-translational modifications (PTM). Mutation of distinct PTM sites in C/EBPβ alters protein interactions and cell differentiation, suggesting a C/EBPβ PTM indexing code determines epigenetic outcomes. Herein, we systematically explored the interactome of C/EBPβ using an array technique based on spot-synthesized C/EBPβ-derived linear tiling peptides with and without PTM, combined with mass spectrometric proteomic analysis of protein interactions (PRISMA). We identified interaction footprints of ∼1300 proteins in nuclear extracts, many with chromatin modifying, remodeling and RNA processing functions. The results suggest C/EBPβ acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes directing cell fate and function.