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Series GSE130696 Query DataSets for GSE130696
Status Public on Nov 13, 2020
Title H4K20me3 methyltransferase SUV420H2 shapes the three-dimensional chromatin landscape of pluripotent embryonic stem cells [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Heterochromatin, which is a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification, H4K20me3, or the histone methyltransferase, SUV420H2, regulate embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we report that depletion of SUV420H2 leads to a near complete loss of H4K20me3 genome-wide, dysregulated gene expression, and delayed ES cell differentiation. SUV420H2-bound regions are enriched with repetitive DNA elements, which are de-repressed in SUV420H2 knockout ES cells. Moreover, SUV420H2 regulation of H4K20me3-marked heterochromatin controls chromatin architecture, including fine-scale interactions between gene regulatory elements in pluripotent ES cells. SUV420H2 plays a critical role in stabilizing the three-dimensional (3D) chromatin landscape of ES cells, where loss of SUV420H2 results in A/B compartment switching, perturbed chromatin insulation, and altered chromatin interactions of pericentric heterochromatin, indicative of localized decondensation. In addition, depletion of SUV420H2 resulted in compromised interactions between H4K20me3 and gene regulatory regions. Together, these findings describe a novel role for SUV420H2 in regulating the chromatin landscape of ES cells.
Overall design RNA-Seq of undifferentiated and differentiated murine WT, SUV420H2 KO, and SUV420H1/H2 DKO ES cells.
Contributor(s) Kidder BL
Citation(s) 33144397
Submission date May 03, 2019
Last update date Nov 13, 2020
Contact name Benjamin L Kidder
Organization name Wayne State University
Department Oncology
Lab Laboratory of Stem Cell Epigenomics
Street address 4100 John R St
City Detroit
State/province MI
ZIP/Postal code 48201
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM3747837 WT_mESC_rep1
GSM3747838 WT_mESC_rep2
GSM3747839 SUV420H2_KO_mESC_rep1
This SubSeries is part of SuperSeries:
GSE130725 H4K20me3 methyltransferase SUV420H2 shapes the three-dimensional chromatin landscape of pluripotent embryonic stem cells
BioProject PRJNA541013
SRA SRP194976

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Supplementary file Size Download File type/resource
GSE130696_RAW.tar 248.0 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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