Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins

Mahmoud Reza Rafiee, Charles Girardot, Gianluca Sigismondo, Jeroen Krijgsveld

Research output: Contribution to journalArticlepeer-review

Abstract

Maintenance of pluripotency is regulated by a network of transcription factors coordinated by Oct4, Sox2, and Nanog (OSN), yet a systematic investigation of the composition and dynamics of the OSN protein network specifically on chromatin is still missing. Here we have developed a method combining ChIP with selective isolation of chromatin-associated proteins (SICAP) followed by mass spectrometry to identify chromatin-bound partners of a protein of interest. ChIP-SICAP in mouse embryonic stem cells (ESCs) identified over 400 proteins associating with OSN, including several whose interaction depends on the pluripotent state. Trim24, a previously unrecognized protein in the network, converges with OSN on multiple enhancers and suppresses the expression of developmental genes while activating cell cycle genes. Consistently, Trim24 significantly improved efficiency of cellular reprogramming, demonstrating its direct functionality in establishing pluripotency. Collectively, ChIP-SICAP provides a powerful tool to decode chromatin protein composition, further enhanced by its integrative capacity to perform ChIP-seq.

Original languageEnglish
Pages (from-to)624-635
Number of pages12
JournalMolecular Cell
Volume64
Issue number3
DOIs
Publication statusPublished - Nov 3 2016

Keywords

  • biotinylation
  • chromatin
  • embryonic stem cells
  • pluripotency
  • protein interactions
  • proteomics
  • reprogramming

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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