Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei

Mol Cell Proteomics. 2018 Oct;17(10):2018-2033. doi: 10.1074/mcp.RA118.000924. Epub 2018 Jul 18.


Cells organize their actions partly through tightly controlled protein-protein interactions-collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the protein-protein interactions in intact human nuclei. Overall, we identified ∼8,700 crosslinks, of which 2/3 represent links connecting distinct proteins. From these data, we gain insights on interactions involving histone proteins. We observed that core histones on the nucleosomes expose well-defined interaction hot spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build low-resolution models of their binding mode to the nucleosome. For HMGN2, the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS, and modeling. Excitingly, the analysis of crosslinks carrying posttranslational modifications allowed us to extract how specific modifications influence nucleosome interactions. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.

Keywords: Chromatin function or biology; Histone interaction network – PTM interplay; Histone variant specific interactions; Histones; Mass Spectrometry; Nuclear interactome; Protein Cross-linking; Protein-Protein Interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Cell Nucleus / metabolism*
  • Cross-Linking Reagents / metabolism*
  • Histones / metabolism*
  • Humans
  • Mass Spectrometry / methods*
  • Models, Molecular
  • Nuclear Proteins / metabolism
  • Nucleosomes / metabolism
  • Protein Binding
  • Protein Interaction Maps
  • Protein Processing, Post-Translational
  • Reproducibility of Results


  • Cross-Linking Reagents
  • Histones
  • Nuclear Proteins
  • Nucleosomes

Associated data

  • PDB/1AN4
  • PDB/1EQZ
  • PDB/2PYO
  • PDB/1KX5
  • PDB/3JCT
  • PDB/3GJ0
  • PDB/1I2M
  • PDB/3MVD