SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation

Epigenetics Chromatin. 2017 Feb 23;10:8. doi: 10.1186/s13072-017-0115-7. eCollection 2017.

Abstract

Background: Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone 4 lysine 20 (H4K20me3) in pluripotency and development are largely unknown.

Results: Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation. SMYD5-bound regions are enriched with repetitive DNA elements. Knockdown of SMYD5 results in a global decrease of H4K20me3 levels, a redistribution of heterochromatin constituents including H3K9me3/2, G9a, and HP1α, and de-repression of endogenous retroelements. A loss of SMYD5-dependent silencing of heterochromatin nearby genic regions leads to upregulated expression of lineage-specific genes, thus contributing to the decreased self-renewal and perturbed differentiation of SMYD5-depleted ES cells.

Conclusions: Altogether, these findings implicate a role for SMYD5 in regulating ES cell self-renewal and H4K20me3-marked heterochromatin.

Keywords: ChIP-Seq; Chromatin; Differentiation; Embryoid body; Embryonic stem cells; Epigenetics; Gene expression; Genomics; H4K20me3; Heterochromatin; Histone methyltransferase; LINE; LTR; Pluripotent; RNA-Seq; Repetitive DNA; SMYD5; Self-renewal.

MeSH terms

  • Animals
  • Cell Differentiation / physiology*
  • Cell Self Renewal / physiology*
  • Chromatin Immunoprecipitation
  • Chromosomal Proteins, Non-Histone / chemistry
  • Chromosomal Proteins, Non-Histone / metabolism
  • DNA Methylation
  • Embryoid Bodies / metabolism
  • Embryoid Bodies / pathology
  • Heterochromatin / metabolism*
  • Histone-Lysine N-Methyltransferase / antagonists & inhibitors
  • Histone-Lysine N-Methyltransferase / genetics
  • Histone-Lysine N-Methyltransferase / metabolism*
  • Histones / genetics
  • Histones / metabolism*
  • Interspersed Repetitive Sequences / genetics
  • Mice
  • Mice, SCID
  • Microscopy, Fluorescence
  • Mouse Embryonic Stem Cells / cytology
  • Mouse Embryonic Stem Cells / metabolism
  • Protein Binding
  • RNA Interference
  • RNA, Small Interfering / metabolism
  • Teratoma / pathology
  • Transcription Factors / metabolism
  • Tumor Suppressor Proteins / antagonists & inhibitors
  • Tumor Suppressor Proteins / genetics
  • Tumor Suppressor Proteins / metabolism*

Substances

  • Chromosomal Proteins, Non-Histone
  • Heterochromatin
  • Histones
  • RNA, Small Interfering
  • Transcription Factors
  • Tumor Suppressor Proteins
  • heterochromatin-specific nonhistone chromosomal protein HP-1
  • Smyd5 protein, mouse
  • Histone-Lysine N-Methyltransferase