Omics · study · 2026
ac4C-RIP-seq in Control, NAT10 KD, NAT10 and Xrp1 KD in Drosophila
Listed in NCBI GEO
In our study, we investigated the role of the ac4C RNA modification enzyme NAT10 in Drosophila development.
Description
We found that knockdown of NAT10 led to a global reduction of ac4C levels on rRNA and impaired the assembly of the 40S ribosomal subunit and triggered a ribosome biogenesis stress response. This response was associated with increased cell apoptosis, cell competition, and reduced translational efficiency.
Through genetic and transcriptomic analyses, we demonstrated that the developmental defects and transcriptional changes observed upon NAT10 knockdown were largely dependent on the upregulation of Xrp1, a key sensor of ribosome assembly stress. To explore the ac4C epitranscriptomic landscape and its functional implications in mRNA, we performed ac4C-RIP-seq in third instar larvae from three genotypes: Dats-GAL4/+ (control), Dats-GAL4 > UAS-NAT10-RNAi, and Dats-GAL4 > UAS-NAT10-RNAi Xrp1-RNAi.
Read the rest (2 more)
Our results revealed that ac4C modifications were widely distributed across the 5’UTR, CDS, and 3’UTR regions of mRNAs, with relatively higher enrichment in the 3’UTR.Integrated analysis of RNA-seq and ac4C-RIP-seq data revealed that the majority of differentially expressed genes upon NAT10 knockdown were not direct targets of ac4C modification. This indicates that the loss of ac4C on mRNAs has a limited direct impact on the transcriptome.
Instead, the observed transcriptional alterations and developmental defects are primarily attributable to ribosome biogenesis stress.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE299nnn/GSE299446 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299446 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1274458 ncbi.nlm.nih.gov/bioproject/PRJNA1274458 ↗
project · from NCBI GEO
Topics
- Stated by source
- Drosophila melanogaster · Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 65%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE299446 | 12 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:7227 | 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 |