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Series GSE129156 Query DataSets for GSE129156
Status Public on Apr 02, 2019
Title Genome-wide maps of H3K9me3 in hematopoietic stem cells from Kdm4a, b, c triple knockout mice
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary The KDM4/JMJD2 are H3K9- and H3K36- specific demethylases, which are considered promising therapeutic targets for the treatment of acute myeloid leukemia (AML) harboring MLL-translocations. Here, we investigate the long-term effects of depleting KDM4 activity on normal hematopoiesis to probe potential side effects of continuous inhibition of these enzymes. Utilizing conditional Kdm4a/Kdm4b/Kdm4c triple-knockout mice we show that KDM4 activity is required for hematopoietic stem cell (HSC) maintenance in vivo. The knockout of the KDM4 demethylases leads to accumulation of H3K9me3 on transcription start sites and the corresponding downregulation of expression of several genes in hematopoietic stem cells. We show that two of these genes, Taf1b and Nom1, are essential for the maintenance of hematopoietic cells. Taken together, our results show that the KDM4 demethylases are required for the expression of genes essential for the long-term maintenance of normal hematopoiesis.
Overall design In this study we map the distribution of H3K9me3 in LSK cells before and after the combined knockout of Kdm4a, b and c.
Conditional Kdm4a, b, c knockout mice were injected with tamoxifen to induce knockout. After two weeks LSK cells were sorted from the bone marrow, fixed in formaldehyde and used in ChIPseq experiments.
Contributor(s) Agger K, Helin K
Citation(s) 31434704
Submission date Apr 01, 2019
Last update date Aug 28, 2019
Contact name Karl Agger
Phone +4522832639
Organization name University of Copenhagen
Department BRIC
Street address Ole Maaloes Vej 5
City Copenhagen
ZIP/Postal code 2200
Country Denmark
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (2)
GSM3701318 H3K9me3 WT LSK cells
GSM3701319 H3K9me3 knockout LSK cells
This SubSeries is part of SuperSeries:
GSE129157 The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance
Reanalysis of GSM1347235
Reanalysis of GSM1347236
BioProject PRJNA530249
SRA SRP190046

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Supplementary file Size Download File type/resource
GSE129156_H3K9me3_H3K4me3_regions.xlsx 333.8 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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