reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells

Kinkley S et al.

The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4(+) memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP-seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action.

Bioruptor Plus
Microplex Library Preparation kit

Share this article

August, 2016


Products used in this publication

  • cut and tag antibody icon
    H3K27ac Antibody
  • cut and tag antibody icon
    H3K27me3 Antibody
  • cut and tag antibody icon
    H3K4me3 Antibody
  • ChIP kit icon
    MicroPlex Library Preparation Kit v2 (12 indexes)
  • Bioruptor Plus Sonication Device
    Bioruptor® Plus sonication device


  • APHL 2024
    Milwaukee, Wisconsin, USA
    May 6-May 9, 2024
 See all events


 See all news

The European Regional Development Fund and Wallonia are investing in your future.

Extension of industrial buildings and new laboratories.

       Site map   |   Contact us   |   Conditions of sales   |   Conditions of purchase   |   Privacy policy   |   Diagenode Diagnostics