An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

Nat Commun. 2015 Jan 21;6:6033. doi: 10.1038/ncomms7033.


Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has enabled genome-wide epigenetic profiling of numerous cell lines and tissue types. A major limitation of ChIP-seq, however, is the large number of cells required to generate high-quality data sets, precluding the study of rare cell populations. Here, we present an ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP) and sequencing method to generate genome-wide histone mark profiles with high resolution from as few as 10(3) cells. We demonstrate that ULI-NChIP-seq generates high-quality maps of covalent histone marks from 10(3) to 10(6) embryonic stem cells. Subsequently, we show that ULI-NChIP-seq H3K27me3 profiles generated from E13.5 primordial germ cells isolated from single male and female embryos show high similarity to recent data sets generated using 50-180 × more material. Finally, we identify sexually dimorphic H3K27me3 enrichment at specific genic promoters, thereby illustrating the utility of this method for generating high-quality and -complexity libraries from rare cell populations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Artifacts
  • Cell Separation
  • Chromatin Immunoprecipitation / methods*
  • Embryonic Stem Cells / metabolism
  • Female
  • Flow Cytometry
  • Genetic Association Studies
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Histones / chemistry
  • Histones / metabolism
  • Male
  • Mice
  • Micrococcal Nuclease / metabolism
  • Oligonucleotide Array Sequence Analysis / methods
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA / methods
  • Sex Factors


  • Histones
  • Micrococcal Nuclease