title: An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations.
abstract: 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.
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.
authors.forename: Julie
authors.initials: J
authors.lastname: Brind'Amour
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.
authors.forename: Sheng
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hudson
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.
authors.forename: Carol
authors.initials: C
authors.lastname: Chen
authors.affiliation: 1] Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 [2] Biomedical Research Centre, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.
authors.forename: Mohammad M
authors.initials: MM
authors.lastname: Karimi
authors.affiliation: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Lorincz
mesh_terms: D000818:Animals; D016477:Artifacts; D002469:Cell Separation; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D053595:Embryonic Stem Cells / Q000378:metabolism; D005260:Female; D005434:Flow Cytometry; D056726:Genetic Association Studies; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D008297:Male; D051379:Mice; D008836:Micrococcal Nuclease / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods; D012737:Sex Factors
chemical_list: D006657:Histones; D008836:Micrococcal Nuclease