Omics · study · 2026
Effect of knockout of H3mm15 on gene expression during spermatogenesis [RNA-seq]
Listed in NCBI GEO
Histone variants play crucial roles in gene expression regulation, cell differentiation, and other biological processes in different tissues.
Description
We previously identified fourteen histone H3 variants in mice, including H3mm6-18, but the function remains unknown. H3mm15 is relatively highly expressed in the testis.
Here we study the effects of deletion of H3mm15 on gene expression during spermatogenesis in mouse testis. Deletion of H3mm15 resulted in disordered gene expression on germ cells when they were spermatogonia, with the greatest impact on preleptotene and also on subsequent processes. We also used Photo-Isolation-Chemistry (PIC), a spatial-omics method for transcriptome profiling of region of interest, for investigating the effects of loss of H3mm15 on gene expression in STRA8-positive cells (preleptotene) in mouse testis.
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Deletion of H3mm15 led to downregulation of genes related to chromosome segregation and chromatin remodeling, and upregulation of genes related to spermatid development and sperm motility in STRA8-positive cells. For further analysis of H3mm15 function, we generated EGFP tagged H3mm15 overexpressed cells and H3.3 overexpressed cells as control. We here performed gene expression profiling on these cells.
We performed serum starvation treatment and H2O2 treatment for the histone variant overexpressed cells and wild-type cell as control, and performed gene expression profiling on these cells before and after treatment. As a result, H3mm15 overexpressed cells showed modest changes on gene expression regulation compared to H3.3. We also performed epigenetics profiling, including H3mm15 or H3.3 genomic region, DNA methylation and chromatin accesibility on these cells.
Our results showed that both H3.3 and H3mm15 were preferentially incorporated into promoter region, and H3mm15 showed more enrichment than H3.3. In addition, both H3.3 and H3mm15 overexpressed cells showed similar histone modification levels.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE290nnn/GSE290629 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290629 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1229445 ncbi.nlm.nih.gov/bioproject/PRJNA1229445 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 65%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE290629 | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:10090 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |