Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution

Ronen Sadeh*, Roee Launer-Wachs, Hava Wandel, Ayelet Rahat, Nir Friedman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single-nucleosome resolution. By comparing to a null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than would be expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin.

Original languageAmerican English
Pages (from-to)1080-1088
Number of pages9
JournalMolecular Cell
Issue number6
StatePublished - 15 Sep 2016

Bibliographical note

Publisher Copyright:
© 2016


  • ChIP
  • Rpd3
  • Set2
  • chromatin
  • histone modifications
  • nucleosomes


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