Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins

Cell Rep. 2020 Feb 25;30(8):2463-2471.e5. doi: 10.1016/j.celrep.2020.01.096.

Abstract

Transcription factors and other chromatin-associated proteins are difficult to quantify comprehensively. Here, we combine facile nuclear sub-fractionation with data-independent acquisition mass spectrometry to achieve rapid, sensitive, and highly parallel quantification of the nuclear proteome in human cells. We apply this approach to quantify the response to acute degradation of BET bromodomains, revealing unexpected chromatin regulatory dynamics. The method is simple and enables system-level study of previously inaccessible chromatin and genome regulators.

Keywords: chromatin; data-independent acquisition; proteomics; small molecule degredation; transcription factors.

Publication types

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

MeSH terms

  • Cell Compartmentation*
  • Chromatin / metabolism
  • Humans
  • K562 Cells
  • Kinetics
  • Nuclear Proteins / metabolism*
  • Proteolysis
  • Transcription Factors / metabolism*

Substances

  • Chromatin
  • Nuclear Proteins
  • Transcription Factors