Cited by 123Genomics and Chromatin DynamicsEpigenetics and DNA MethylationGenomics and Phylogenetic Studies

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

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Steiner, Florian A., Talbert, Paul B., Kasinathan, Sivakanthan, Deal, Roger B., Henikoff, Steven·2012·Genome Research

Abstract

An understanding of developmental processes requires knowledge of transcriptional and epigenetic landscapes at the level of tissues and ultimately individual cells. However, obtaining tissue- or cell-type-specific expression and chromatin profiles for animals has been challenging. Here we describe a method for purifying nuclei from specific cell types of animal models that allows simultaneous determination of both expression and chromatin profiles. The method is based on in vivo biotin-labeling of the nuclear envelope and subsequent affinity purification of nuclei. We describe the use of the method to isolate nuclei from muscle of adult Caenorhabditis elegans and from mesoderm of Drosophila melanogaster embryos. As a case study, we determined expression and nucleosome occupancy profiles for affinity-purified nuclei from C. elegans muscle. We identified hundreds of genes that are specifically expressed in muscle tissues and found that these genes are depleted of nucleosomes at promoters and gene bodies in muscle relative to other tissues. This method should be universally applicable to all model systems that allow transgenesis and will make it possible to determine epigenetic and expression profiles of different tissues and cell types.

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  • Purification of a homogeneous population of fluorescently tagged nuclei in animal models has demonstrated six-fold increased sensitivity for cell-type specific identification of down-regulated genes.

    “Purification of a homogeneous population of fluorescently tagged nuclei in animal models has also demonstrated six-fold increased sensitivity for cell-type specific identification of down-regulated genes51.”

    From Neuron Enriched Nuclear Proteome Isolated from Human Brain (2013) · cites this paper as [51]

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Authors
Steiner, F. A., Talbert, P. B., Kasinathan, S., Deal, R. B., & Henikoff, S.
Affiliations
  • Fred Hutch Cancer Center (US)
  • Howard Hughes Medical Institute (US)
Venue
Genome Research
Published
2012-01-04
Volume
22
Issue
4
Pages
766-777
ISSN
1088-9051 (ISSN-L)
OpenAlex
W2163482547
Cited by
123
References
50
Citations by year
2026: 3 · 2025: 2 · 2024: 2 · 2023: 1 · 2022: 7 · 2021: 8 · 2020: 5 · 2019: 4 · 2018: 12 · 2017: 10 · 2016: 11 · 2015: 13 · 2014: 22 · 2013: 13 · 2012: 10
Type
posted content
Language
en
Open access
Licence
other-oa
Locations
  • Genome Research (publishedVersion, other-oa)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
  • Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by-nc)
Funders
  • National Science Foundation
  • Howard Hughes Medical Institute
  • Fred Hutchinson Cancer Research Center
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • National Institutes of Health
  • National Human Genome Research Institute
  • National Institute of General Medical Sciences (T32GM007266)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
nucleosome occupancy, chromatin profiling, tissue-specific gene expression, epigenetics, transgenic animals
MeSH terms
Animals, Cell Nucleus, Chromatin, Drosophila melanogaster, Embryo, Nonmammalian, Luminescent Proteins, Mesoderm, Microscopy, Fluorescence, Muscles, Nucleosomes, Helminth Proteins, Genome, Caenorhabditis elegans, Gene Expression Regulation, Developmental, Gene Expression Profiling, Muscle Development, Drosophila Proteins, Animals, Genetically Modified

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