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| Status |
Public on Dec 13, 2022 |
| Title |
Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters [ATAC-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Cell fate decisions are closely associated with changes in gene expression programs. A large number of post-translational modifications of core histones contribute to controlling the expression of genes. A modification that is closely correlated with open chromatin and gene transcription is methylation of lysine 4 of histone H3 (H3K4). It is catalyzed by methyltransferases of the KMT2 family, which require interaction with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, for catalytic activity. Ash2l is required for organismal development and for tissue homeostasis in the mouse. In mouse embryo fibroblasts (MEFs), the loss of Ash2l results in downregulated gene expression, which provokes a senescence phenotype. We now find that both H3K4 mono- and tri-methylation (H3K4me1 and me3, respectively) are deregulated. H3K4me3 is lost while H3K4me1 is increased at promoters upon knockout of Ash2l. In particular, loss of H3K4me3 at promoters correlates with downregulation of gene expression, which is particularly obvious at CpG island promoters. Ash2l loss results in an increase of histone H3 loading at promoters, paralleled by enhanced chromatin compaction. This is accompanied by an increase of repressing and a decrease of activating histone marks. One of the sequence-specific transcription factors with altered binding upon depletion of Ash2l is CTCF. It is lost from some promoter-associated sites, but gained binding in other regions of the genome. This suggests that in addition to the well-known effects on H3K4 methylation upon depleting KMT2 complex components, Ash2l loss affects chromatin compaction. Whether the decrease of H3K4me3 promotes chromatin compaction at promoters or whether these are independent consequences of Ash2l loss remains to be determined. We suggest that both contribute mechanistically to gene repression and thus to the observed cellular effects.
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| Overall design |
One mouse embryo fibroblast line with floxed exon 4 of Ash2l (congruent to KO2 in ChIPseq experiments for H3K4me1/3 from the same study) were used. The cell line express Cre-ER and were immortalized using shArf. Cells were treated -/+ 4-hydroxytamoxifen for 7 days. ATAC-seq was performed with engineered hyperactive Tn5-Transposase for accessibility analysis. For both treating conditions, two technical replicates were prepared.
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| Contributor(s) |
Barsoum M, Stenzel AT, Bochyńska A, Kuo C, Tsompanidis A, Sayadi Boroujeni R, Bussmann P, Lüscher-Firzlaff J, Costa IG, Lüscher B |
| Citation(s) |
36513698 |
| |
| Submission date |
May 31, 2022 |
| Last update date |
Jan 05, 2023 |
| Contact name |
Mirna Barsoum |
| E-mail(s) |
mirna.barsoum@rwth-aachen.de
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| Phone |
00492418088915
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| Organization name |
Uniklinik RWTH Aachen
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| Department |
Institute of Biochemistry and Molecular Biology
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| Lab |
Bernhard Lüscher
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| Street address |
Pauwelsstrasse 30
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| City |
Aachen |
| State/province |
North Rhine Westphalia |
| ZIP/Postal code |
52074 |
| Country |
Germany |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE205233 |
Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters. |
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| Relations |
| BioProject |
PRJNA844129 |
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