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| Status |
Public on Sep 14, 2022 |
| Title |
H3K18la marks active tissue-specific enhancers [Cut & Tag mouse] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We profiled the genome-wide distribution of H3K18la in samples originating from 6 different in vitro and in vivo mouse samples, representing 3 tissues: embryonic stem cells, macrophages and skeletal muscle as well as in human skeletal muscle and compared them to the profiles of other well-established histone modifications as well as gene expression patterns. Globally, we found that H3K18la profiles resemble H3K27ac profiles better than any other investigated hPTM, including H3K4me3, but that they do not copy them. For all samples, H3K18la marked active CGI promoters of highly expressed genes which were remarkably shared across the different mouse tissues and which contained many housekeeping genes. Promoter H3K18la levels correlated positively to both H3K27ac and H3K4me3 levels as well as to gene expression levels. In addition, we found that H3K18la is enriched at tissue-type specific, active enhancers, which are particularly tissue-type-specific, especially when compared to the H3K18la-marked promoter regions. Accordingly, enhancer H3K18la levels correlate positively to the expression of their nearest genes. Additionally, genes closest to enhancers with high H3K18la levels predominantly consist of tissue-type specific marker genes. Overall, we showed that H3K18la is not only a marker for active promoters, but that it also marks active enhancers, and this both in embryonic tissues and differentiated tissues, and both in mouse and in human.
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| Overall design |
We profiled various mouse (embryonic stem cells (ESC), gastrocnemius (GAS), post-ischemia macrophages (PIM), primary myoblasts (MB), primary myotubes (MT) and bone marrow-derived macrophages (BMDM) and human samples (vastus lateralis) for various histone post-translational modifications
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| Contributor(s) |
Galle E, Wong C, Ghosh A, Desgeorges T, De Bock K, von Meyenn F |
| Citation(s) |
36192798 |
| |
| Submission date |
Feb 01, 2022 |
| Last update date |
Oct 27, 2022 |
| Contact name |
Ferdinand von Meyenn |
| E-mail(s) |
ferdinand.vonmeyenn@hest.ethz.ch
|
| Organization name |
ETH Zurich
|
| Department |
Health Sciences and Technology
|
| Lab |
Nutrition and Metabolic Epigenetics
|
| Street address |
Schorenstrasse 16
|
| City |
Schwerzenbach |
| State/province |
Zurich |
| ZIP/Postal code |
8603 |
| Country |
Switzerland |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (41)
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| This SubSeries is part of SuperSeries: |
| GSE195860 |
H3K18la marks active tissue-specific enhancers |
|
| Relations |
| BioProject |
PRJNA802361 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE195856_ADIPO_H3K18la_peaks.bed.gz |
588.8 Kb |
(ftp)(http) |
BED |
| GSE195856_ADIPO_H3K27ac_peaks.bed.gz |
480.3 Kb |
(ftp)(http) |
BED |
| GSE195856_BMDM_H3K18la_peaks.bed.gz |
396.8 Kb |
(ftp)(http) |
BED |
| GSE195856_BMDM_H3K27ac_peaks.bed.gz |
264.9 Kb |
(ftp)(http) |
BED |
| GSE195856_BMDM_H3K27me3_peaks.bed.gz |
247.5 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC-2i_H3K18la_peaks.bed.gz |
418.2 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC-2i_H3K27me3_peaks.bed.gz |
507.2 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC-2i_H3K4me3_peaks.bed.gz |
402.6 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC-ser_H3K27ac_peaks.bed.gz |
316.6 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC_H3K18la_peaks.bed.gz |
391.8 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC_H3K27me3_peaks.bed.gz |
496.3 Kb |
(ftp)(http) |
BED |
| GSE195856_ESC_H3K4me3_peaks.bed.gz |
234.7 Kb |
(ftp)(http) |
BED |
| GSE195856_GAS_H3K18la_peaks.bed.gz |
747.5 Kb |
(ftp)(http) |
BED |
| GSE195856_GAS_H3K27ac_peaks.bed.gz |
717.0 Kb |
(ftp)(http) |
BED |
| GSE195856_GAS_H3K27me3_peaks.bed.gz |
730.4 Kb |
(ftp)(http) |
BED |
| GSE195856_GAS_H3K4me3_peaks.bed.gz |
584.0 Kb |
(ftp)(http) |
BED |
| GSE195856_MB_H3K18la_peaks.bed.gz |
281.0 Kb |
(ftp)(http) |
BED |
| GSE195856_MB_H3K27me3_peaks.bed.gz |
281.3 Kb |
(ftp)(http) |
BED |
| GSE195856_MT_H3K18la_peaks.bed.gz |
697.7 Kb |
(ftp)(http) |
BED |
| GSE195856_MT_H3K27me3_peaks.bed.gz |
388.5 Kb |
(ftp)(http) |
BED |
| GSE195856_PIM_H3K18la_peaks.bed.gz |
646.3 Kb |
(ftp)(http) |
BED |
| GSE195856_PIM_H3K27ac_peaks.bed.gz |
489.3 Kb |
(ftp)(http) |
BED |
| GSE195856_PIM_H3K27me3_peaks.bed.gz |
329.2 Kb |
(ftp)(http) |
BED |
| GSE195856_PIM_H3K4me3_peaks.bed.gz |
527.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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