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| Status |
Public on Jul 22, 2024 |
| Title |
A developmental mechanism to Regulate Alternative Polyadenylation in an Adult Stem Cell Lineage [3'seq_OEs] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Alternative Cleavage and Polyadenylation (APA) often results in production of mRNA isoforms with either longer or shorter 3’UTRs from the same genetic locus, potentially impacting mRNA translation, localization and stability. Developmentally regulated APA can thus make major contributions to cell-type-specific gene expression programs as cells differentiate. During Drosophila spermatogenesis, approximately 500 genes undergo APA when proliferating spermatogonia differentiate into spermatocytes, producing transcripts with shortened 3’ UTRs, leading to profound stage-specific changes in the proteins expressed. The molecular mechanisms that specify usage of upstream polyadenylation sites in spermatocytes are thus key to understanding the changes in cell state. Here, we show that upregulation of PCF11 and Cbc, the two components of Cleavage Factor II (CFII), orchestrates APA during Drosophila spermatogenesis. Knock down of PCF11 or cbc in spermatocytes caused dysregulation of APA, with many transcripts normally cleaved at a proximal site in spermatocytes now cleaved at their distal site, as in spermatogonia. Forced overexpression of CFII components in spermatogonia switched cleavage of some transcripts to the proximal site normally used in spermatocytes. Our findings reveal a developmental mechanism where changes in expression of specific cleavage factors can direct cell-type-specific APA at selected genes.
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| Overall design |
We performed 3'seq on control bam-/- flies (nosGal4/Y;+/+;bam86,bamGal4/bam1) and compared to bam mutant fies in which either cbc alone, or PCf11 alone or cbc plus PCF11 were overexpressed via the Gal4-UAS system. Libraries were performed in duplicates. Per each library roughly 150 pairs of testes were used.
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| Contributor(s) |
Gallicchio L, Matias NR |
| Citation(s) |
39111825 |
| |
| Submission date |
Jul 18, 2024 |
| Last update date |
Oct 21, 2024 |
| Contact name |
Lorenzo Gallicchio |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Stanford University
|
| Department |
developmental Biology
|
| Lab |
Fuller
|
| Street address |
Campus Drive W
|
| City |
Stanford |
| State/province |
california |
| ZIP/Postal code |
94033 |
| Country |
USA |
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| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA1137373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE272580_UASPCF11_PolyAminer_Out.PolyA-miner.log.txt.gz |
811 b |
(ftp)(http) |
TXT |
| GSE272580_UASPCF11_PolyAminer_Out_APACountMatrix4DEGs.txt.gz |
19.7 Kb |
(ftp)(http) |
TXT |
| GSE272580_UASPCF11_PolyAminer_Out_APA_BBstats.txt.gz |
37.9 Kb |
(ftp)(http) |
TXT |
| GSE272580_UASPCF11_PolyAminer_Out_PolyA-miner.Results.txt.gz |
48.6 Kb |
(ftp)(http) |
TXT |
| GSE272580_UAScbc-PCF11_PolyAminer_Out.PolyA-miner.log.txt.gz |
823 b |
(ftp)(http) |
TXT |
| GSE272580_UAScbc-PCF11_PolyAminer_Out_APACountMatrix4DEGs.txt.gz |
19.9 Kb |
(ftp)(http) |
TXT |
| GSE272580_UAScbc-PCF11_PolyAminer_Out_APA_BBstats.txt.gz |
37.8 Kb |
(ftp)(http) |
TXT |
| GSE272580_UAScbc-PCF11_PolyAminer_Out_PolyA-miner.Results.txt.gz |
48.0 Kb |
(ftp)(http) |
TXT |
| GSE272580_UAScbc_PolyAminer_Out.PolyA-miner.log.txt.gz |
803 b |
(ftp)(http) |
TXT |
| GSE272580_UAScbc_PolyAminer_Out_APACountMatrix4DEGs.txt.gz |
19.8 Kb |
(ftp)(http) |
TXT |
| GSE272580_UAScbc_PolyAminer_Out_APA_BBstats.txt.gz |
37.5 Kb |
(ftp)(http) |
TXT |
| GSE272580_UAScbc_PolyAminer_Out_PolyA-miner.Results.txt.gz |
47.8 Kb |
(ftp)(http) |
TXT |
| GSE272580_bam_vs_Spermatocytes.bed.gz |
11.6 Kb |
(ftp)(http) |
BED |
| GSE272580_genes_bed.bed.gz |
247.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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