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Series GSE94085 Query DataSets for GSE94085
Status Public on Jun 12, 2017
Title SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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 lysine 20 (H4K20me3) in pluripotency and development are largely unknown. 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 accelerated differentiation of SMYD5-depeleted ES cells. Altogether, these findings implicate a role for SMYD5 in regulating ES cell self-renewal and H4K20me3-marked heterochromatin.
Overall design RNA-Seq of undifferentiated and differentiated murine shLuc and shSmyd5 ES cells
Contributor(s) Kidder BL, Zhao K
Citation(s) 28250819
Submission date Jan 26, 2017
Last update date May 15, 2019
Contact name Benjamin L Kidder
Organization name Wayne State University
Department Oncology
Lab Laboratory of Epigenomics
Street address 4100 John R St
City Detroit
State/province MI
ZIP/Postal code 48201
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (10)
GSM2468428 mES_shLuc_ctrl (RNA-Seq)
GSM2468429 mES_shSmyd5 (RNA-Seq)
GSM2468430 EB_24h_shLuc_ctrl (RNA-Seq)
This SubSeries is part of SuperSeries:
GSE94086 SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation
BioProject PRJNA368814
SRA SRP097856

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Supplementary file Size Download File type/resource
GSE94085_RAW.tar 157.8 Mb (http)(custom) TAR (of BEDGRAPH, RPKM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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