Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states

Rong Wu, Anna V Terry, Prim B Singh, David M Gilbert

Research output: Contribution to journalArticle

95 Citations (Scopus)

Abstract

Mono-, di-, and trimethylation of specific histone residues adds an additional level of complexity to the range of histone modifications that may contribute to a histone code. However, it has not been clear whether different methylated states reside stably at different chromatin sites or whether they represent dynamic intermediates at the same chromatin sites. Here, we have used recently developed antibodies that are highly specific for mono-, di-, and trimethylated lysine 9 of histone H3 (MeK9H3) to examine the subnuclear localization and replication timing of chromatin containing these epigenetic marks in mammalian cells. Me1K9H3 was largely restricted to early replicating, small punctate domains in the nuclear interior. Me2K9H3 was the predominant MeK9 epitope at the nuclear and nucleolar periphery and colocalized with sites of DNA synthesis primarily in mid-S phase. Me3K9H3 decorated late-replicating pericentric heterochromatin in mouse cells and sites of DAPI-dense intranuclear heterochromatin in human and hamster cells that replicated throughout S phase. Disruption of the Suv39h1,2 or G9a methyltransferases in murine embryonic stem cells resulted in a redistribution of methyl epitopes, but did not alter the overall spatiotemporal replication program. These results demonstrate that mono-, di-, and trimethylated states of K9H3 largely occupy distinct chromosome domains.

Original languageEnglish
Pages (from-to)2872-81
Number of pages10
JournalMolecular Biology of the Cell
Volume16
Issue number6
DOIs
Publication statusPublished - Jun 2005

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Histone Code
Histones
Methylation
Lysine
Chromatin
Heterochromatin
S Phase
Epitopes
Methyltransferases
Embryonic Stem Cells
Epigenomics
Cricetinae
Chromosomes
Antibodies
DNA

Keywords

  • Animals
  • Antibodies, Monoclonal
  • CHO Cells
  • Cell Line, Tumor
  • Cell Nucleus
  • Cricetinae
  • Cricetulus
  • DNA
  • Epigenesis, Genetic
  • Epitopes
  • Fluorescent Dyes
  • Heterochromatin
  • Histone-Lysine N-Methyltransferase
  • Histones
  • Humans
  • Indoles
  • Lysine
  • Methylation
  • Mice
  • Microscopy, Confocal
  • S Phase
  • Comparative Study
  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

Cite this

Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. / Wu, Rong; Terry, Anna V; Singh, Prim B; Gilbert, David M.

In: Molecular Biology of the Cell, Vol. 16, No. 6, 06.2005, p. 2872-81.

Research output: Contribution to journalArticle

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AU - Gilbert, David M

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N2 - Mono-, di-, and trimethylation of specific histone residues adds an additional level of complexity to the range of histone modifications that may contribute to a histone code. However, it has not been clear whether different methylated states reside stably at different chromatin sites or whether they represent dynamic intermediates at the same chromatin sites. Here, we have used recently developed antibodies that are highly specific for mono-, di-, and trimethylated lysine 9 of histone H3 (MeK9H3) to examine the subnuclear localization and replication timing of chromatin containing these epigenetic marks in mammalian cells. Me1K9H3 was largely restricted to early replicating, small punctate domains in the nuclear interior. Me2K9H3 was the predominant MeK9 epitope at the nuclear and nucleolar periphery and colocalized with sites of DNA synthesis primarily in mid-S phase. Me3K9H3 decorated late-replicating pericentric heterochromatin in mouse cells and sites of DAPI-dense intranuclear heterochromatin in human and hamster cells that replicated throughout S phase. Disruption of the Suv39h1,2 or G9a methyltransferases in murine embryonic stem cells resulted in a redistribution of methyl epitopes, but did not alter the overall spatiotemporal replication program. These results demonstrate that mono-, di-, and trimethylated states of K9H3 largely occupy distinct chromosome domains.

AB - Mono-, di-, and trimethylation of specific histone residues adds an additional level of complexity to the range of histone modifications that may contribute to a histone code. However, it has not been clear whether different methylated states reside stably at different chromatin sites or whether they represent dynamic intermediates at the same chromatin sites. Here, we have used recently developed antibodies that are highly specific for mono-, di-, and trimethylated lysine 9 of histone H3 (MeK9H3) to examine the subnuclear localization and replication timing of chromatin containing these epigenetic marks in mammalian cells. Me1K9H3 was largely restricted to early replicating, small punctate domains in the nuclear interior. Me2K9H3 was the predominant MeK9 epitope at the nuclear and nucleolar periphery and colocalized with sites of DNA synthesis primarily in mid-S phase. Me3K9H3 decorated late-replicating pericentric heterochromatin in mouse cells and sites of DAPI-dense intranuclear heterochromatin in human and hamster cells that replicated throughout S phase. Disruption of the Suv39h1,2 or G9a methyltransferases in murine embryonic stem cells resulted in a redistribution of methyl epitopes, but did not alter the overall spatiotemporal replication program. These results demonstrate that mono-, di-, and trimethylated states of K9H3 largely occupy distinct chromosome domains.

KW - Animals

KW - Antibodies, Monoclonal

KW - CHO Cells

KW - Cell Line, Tumor

KW - Cell Nucleus

KW - Cricetinae

KW - Cricetulus

KW - DNA

KW - Epigenesis, Genetic

KW - Epitopes

KW - Fluorescent Dyes

KW - Heterochromatin

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KW - Mice

KW - Microscopy, Confocal

KW - S Phase

KW - Comparative Study

KW - Journal Article

KW - Research Support, N.I.H., Extramural

KW - Research Support, U.S. Gov't, Non-P.H.S.

KW - Research Support, U.S. Gov't, P.H.S.

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JO - Molecular Biology of the Cell

JF - Molecular Biology of the Cell

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