Conserved abundance and topological features in chromatin-remodeling protein interaction networks

Mihaela E. Sardiu, Joshua M. Gilmore, Brad D. Groppe, Damir Herman, Sreenivasa R. Ramisetty, Yong Cai, Jingji Jin, Ronald C. Conaway, Joan W. Conaway, Laurence Florens, Michael P. Washburn

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

The study of conserved protein interaction networks seeks to better understand the evolution and regulation of protein interactions. Here, we present a quantitative proteomic analysis of 18 orthologous baits from three distinct chromatin-remodeling complexes in Saccharomyces cerevisiae and Homo sapiens. We demonstrate that abundance levels of orthologous proteins correlate strongly between the two organisms and both networks have highly similar topologies. We therefore used the protein abundances in one species to cross-predict missing protein abundance levels in the other species. Lastly, we identified a novel conserved low-abundance subnetwork further demonstrating the value of quantitative analysis of networks. Synopsis Quantitative proteomic analysis of a yeast and human chromatin remodeling protein interaction network demonstrates the conservation of protein content, abundance, and topology in this network. This allowed cross-species prediction of missing values and led to the discovery of a conserved low-abundance subnetwork. The abundance of proteins within INO80, TIP60/NuA4, and SRCAP/SWR complexes are conserved between S. cerevisiae and H. sapiens. The yeast and human chromatin remodeling networks have a similar network topology. Affinity purifications of new associations of orthologous yeast and human proteins pulled down components of multiple chromatin remodeling complexes. Quantitative proteomic analysis of a yeast and human chromatin remodeling protein interaction network demonstrates the conservation of protein content, abundance, and topology in this network. This allowed cross-species prediction of missing values and led to the discovery of a conserved low-abundance subnetwork.

Original languageEnglish (US)
Pages (from-to)116-126
Number of pages11
JournalEMBO Reports
Volume16
Issue number1
DOIs
StatePublished - Jan 1 2015
Externally publishedYes

Keywords

  • human
  • multidimensional protein identification technology
  • quantitative proteomics
  • topological data analysis
  • yeast

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics

Fingerprint

Dive into the research topics of 'Conserved abundance and topological features in chromatin-remodeling protein interaction networks'. Together they form a unique fingerprint.

Cite this