Cited by 253Genomics and Chromatin DynamicsEpigenetics and DNA MethylationChromatin Remodeling and Cancer

Detection of histone modifications at specific gene loci in single cells in histological sections

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Gomez, Delphine, Shankman, Laura S, Nguyen, Anh T, Owens, Gary K·2013·Nature Methods

Abstract

Chromatin immunoprecipitation assays have contributed greatly to our understanding of the role of histone modifications in gene regulation. However, they do not permit analysis with single-cell resolution, thus confounding analyses of heterogeneous cell populations. Here we present a method that permits visualization of histone modifications of single genomic loci with single-cell resolution in formaldehyde-fixed paraffin-embedded tissue sections based on combined use of in situ hybridization and proximity ligation assays. We show that dimethylation of lysine 4 of histone H3 (H3K4me2) at the MYH11 locus is restricted to the smooth muscle cell (SMC) lineage in human and mouse tissue sections and that the mark persists even in phenotypically modulated SMC in atherosclerotic lesions that show no detectable expression of SMC marker genes. This methodology has promise for broad applications in the study of epigenetic mechanisms in complex multicellular tissues in development and disease.

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  • Lineage tracing studies have unambiguously demonstrated that VSMCs contribute substantially to plaque formation in murine models of atherosclerosis, generating 30-70% of all plaque cells.

    “Lineage tracing studies have unambiguously demonstrated that VSMCs contribute substantially to plaque formation in murine models of atherosclerosis, generating 30-70% of all plaque cells 11,18-20,22,23 .”

    From Vascular smooth muscle cells in atherosclerosis (2019) · cites this paper as [18]

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Authors
Gomez, D., Shankman, L. S., Nguyen, A. T., & Owens, G. K.
Affiliations
University of Virginia (US)
Corresponding author
Owens, Gary K
Venue
Nature Methods
Published
2013-01-13
Volume
10
Issue
2
Pages
171-177
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W2092430017
Cited by
253
References
38
Citations by year
2026: 8 · 2025: 10 · 2024: 13 · 2023: 17 · 2022: 24 · 2021: 30 · 2020: 22 · 2019: 25 · 2018: 18 · 2017: 14 · 2016: 20 · 2015: 19 · 2014: 23 · 2013: 10
FWCI
10.69
Type
journal article
Language
en
Open access
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Heart, Lung, and Blood Institute (R01HL038854, R01HL087867, R01HL057353, R01HL098538, R01HL121008, T32HL007284)
  • National Cancer Institute (P30CA044579)
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 › Chromatin Remodeling and Cancer
Keywords
histone modifications, H3K4 dimethylation, proximity ligation assay, in situ hybridization, smooth muscle cells, atherosclerosis
MeSH terms
Animals, Fixatives, Formaldehyde, Histones, Humans, Lysine, Male, Methylation, Paraffin Embedding, In Situ Hybridization, Myosin Heavy Chains, Cell Lineage, Myocytes, Smooth Muscle, Epigenesis, Genetic, Chromatin Immunoprecipitation, Atherosclerosis, Mice

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