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A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes.

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Author(s)

  • EK Papachristou
  • K Kishore
  • AN Holding
  • K Harvey
  • TI Roumeliotis
  • CSR Chilamakuri
  • S Omarjee
  • KM Chia
  • A Swarbrick
  • E Lim
  • F Markowetz
  • M Eldridge
  • R Siersbaek
  • CS D'Santos
  • JS Carroll

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Publication details

JournalNature Communications
DatePublished - 13 Jun 2018
Issue number1
Volume9
Number of pages1
Pages (from-to)2311
Original languageEnglish

Abstract

Understanding the dynamics of endogenous protein-protein interactions in complex networks is pivotal in deciphering disease mechanisms. To enable the in-depth analysis of protein interactions in chromatin-associated protein complexes, we have previously developed a method termed RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins). Here, we present a quantitative multiplexed method (qPLEX-RIME), which integrates RIME with isobaric labelling and tribrid mass spectrometry for the study of protein interactome dynamics in a quantitative fashion with increased sensitivity. Using the qPLEX-RIME method, we delineate the temporal changes of the Estrogen Receptor alpha (ERα) interactome in breast cancer cells treated with 4-hydroxytamoxifen. Furthermore, we identify endogenous ERα-associated proteins in human Patient-Derived Xenograft tumours and in primary human breast cancer clinical tissue. Our results demonstrate that the combination of RIME with isobaric labelling offers a powerful tool for the in-depth and quantitative characterisation of protein interactome dynamics, which is applicable to clinical samples.

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© 2018, The Author(s).

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