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Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode-ChIP-Seq

  • Deepani W. Poramba-Liyanage
  • Tessy Korthout
  • Fred van LeeuwenEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2049)

Abstract

The assembly and regulation of chromatin requires coordinated activity of multiple mechanisms. Many factors feed into signaling networks that control the epigenome of a cell. It is this complexity that makes understanding the layers of epigenetic regulation a challenge. Genetic screens have been indispensable for studying chromatin processes. However, they can be laborious and the readout for chromatin changes is often indirect. Epi-ID is a screening strategy in yeast that enables the direct assessment of chromatin status in thousands of gene mutants in parallel. Epi-ID takes advantage of DNA sequences called DNA barcodes that are introduced into a library of yeast knockout mutants at a common chromosomal location in the genome. Chromatin immunoprecipitation on pools of barcoded mutant strains followed by barcode counting by high throughput sequencing will report on the abundance of the chromatin mark of interest in each mutant strain. Epi-ID is applicable to a wide range of chromatin proteins and modifications that are present and can be immunoprecipitated at or around the barcoded region.

Key words

Epi-ID Chromatin DNA barcodes ChIP barcode sequencing Yeast genetic screen 

Notes

Acknowledgments

The authors thank the RHPC facility of the Netherlands Cancer Institute for providing computational resources and Hanneke Vlaming and Kitty Verzijlbergen for developing the Epi-ID technology. This work was supported by the Dutch Cancer Society (KWF2009-4511 and NKI2014-7232) and the Netherlands Organisation for Scientific Research (NWO-VICI-016.130.627). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Deepani W. Poramba-Liyanage
    • 1
  • Tessy Korthout
    • 1
  • Fred van Leeuwen
    • 1
    Email author
  1. 1.Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands

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