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

UID: 10653

Author(s): Kidder, Benjamin L.

Description: Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary: This SuperSeries is composed of the SubSeries GSE94033 and GSE94085.

Article summary that correlates to the GEO: "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.
"...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.
Altogether, these findings implicate a role for SMYD5 in regulating ES cell self-renewal and H4K20me3-marked heterochromatin."

Subject of Study

Subject(s)

Access via GEO
BEDGRAPH and RPKM files of expression and genome binding/occupancy profiling by high throughput sequencing
Accession #: GSE94086

Access via BioProject
Additional information about overall initiative
Accession #: PRJNA368813
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus and BioProject databases provide open access to these files.
Associated Publications: Ren W, Fan H, Grimm S, et al. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nature Communications. 2021; 12:2490.

Kidder BL, Hu G, Cui K, Zhao K. SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation. Epigenetics Chromatin. 2017;10:8. Published 2017 Feb 23.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system
Dataset Format(s): TAR, RPKM, BEDGRAPH
Data Tool(s): RNA Seq

ChIP Seq
Dataset Size: 873.3 MB

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