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| Item Type: | Article |
|---|---|
| Title: | reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells |
| Creators Name: | Kinkley, S. and Helmuth, J. and Polansky, J.K. and Dunkel, I. and Gasparoni, G. and Froehler, S. and Chen, W. and Walter, J. and Hamann, A. and Chung, H.R. |
| Abstract: | 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. |
| Keywords: | Data Processing, Histone Post-Translational Modifications, Immunochemistry, Statistical Methods |
| Source: | Nature Communications |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 7 |
| Page Range: | 12514 |
| Date: | 17 August 2016 |
| Official Publication: | https://doi.org/10.1038/ncomms12514 |
| PubMed: | View item in PubMed |
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