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| Status |
Public on Aug 13, 2024 |
| Title |
Widespread regulation of the maternal transcriptome by Nanos in Drosophila |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The translational repressor Nanos (Nos) regulates a single target, maternal hunchback (hb) mRNA, to govern abdominal segmentation in the early Drosophila embryo. Nos is recruited specifically to sites in the 3'-UTR of hb mRNA in collaboration with the sequence-specific RNA-binding protein Pumilio (Pum); on its own, Nos has no binding specificity. Nos is expressed at other stages of development, but very few mRNA targets that might mediate its action at these stages have been described. Nor has it been clear whether Nos is targeted to other mRNAs in concert with Pum or via other mechanisms. In this report, we identify mRNAs targeted by Nos via two approaches. In the first method, we identify mRNAs depleted upon expression of a chimera bearing Nos fused to the nonsense mediated decay (NMD) factor Upf1. We find that, in addition to hb, Upf1-Nos depletes ~2600 mRNAs from the maternal transcriptome in early embryos. Virtually all of these appear to be targeted in a canonical, hb-like manner in concert with Pum. In a second, more conventional approach, we identify mRNAs that are stabilized during the maternal zygotic transition (MZT) in embryos from nos- females. Most (86%) of the 1185 mRNAs regulated by Nos are also targeted by Upf1-Nos, validating use of the chimera. Previous work has shown that 60% of the maternal transcriptome is degraded in early embryos. We find that maternal mRNAs targeted by Upf1-Nos are hypo-adenylated and inefficiently translated at the ovary-embryo transition; they are subsequently degraded in the early embryo, accounting for 59% of all destabilized maternal mRNAs.We suggest that the late ovarian burst of Nosrepresses a large fraction of the maternal transcriptome, priming it for later degradation by other factors during the MZT in the embryo.
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| Overall design |
To identify mRNAs targeted by Nos we took two approaches. In the first method, we identify mRNAs depleted upon expression of a chimera bearing Nos fused to the nonsense mediated decay factor Upf1. In addition to Upf1-Nos and wild type embryos, we also prepared triplicate samples from 3 more experimental embryos: Upf1, Nos, and Upf1-NosL7.
In a second one, we took a more conventional approach and identify mRNAs that are stabilized during the maternal zygotic transition in embryos from nos- females compared to wild type w strain.
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| Contributor(s) |
Marhabaie M, Wharton TH, Yun-Kim S, Wharton RP |
| Citation missing |
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| Submission date |
Apr 15, 2024 |
| Last update date |
Aug 13, 2024 |
| Contact name |
Mohammad Marhabaie |
| Organization name |
Nationwide Children's Hospital
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| Street address |
700 Children's Dr
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platforms (1) |
| GPL21306 |
Illumina HiSeq 4000 (Drosophila melanogaster) |
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| Samples (27)
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| GSM8208921 |
Upf1-NosL7, cycle9, rep1 |
| GSM8208922 |
Upf1-NosL7, cycle9, rep2 |
| GSM8208923 |
Upf1-NosL7, cycle9, rep3 |
| GSM8208924 |
Upf1-Nos, cycle9, rep1 |
| GSM8208925 |
Upf1-Nos, cycle9, rep2 |
| GSM8208926 |
Upf1-Nos, cycle9, rep3 |
| GSM8208927 |
Upf1, cycle9, rep1 |
| GSM8208928 |
Upf1, cycle9, rep2 |
| GSM8208929 |
Upf1, cycle9, rep3 |
| GSM8208930 |
Nos, cycle9, rep1 |
| GSM8208931 |
Nos, cycle9, rep2 |
| GSM8208932 |
Nos, cycle9, rep3 |
| GSM8208933 |
w, 0-1h, rep1 |
| GSM8208934 |
w, 0-1h, rep2 |
| GSM8208935 |
w, 0-1h, rep3 |
| GSM8208936 |
nos, 0-1h, rep1 |
| GSM8208937 |
nos, 0-1h, rep2 |
| GSM8208938 |
nos, 0-1h, rep3 |
| GSM8208939 |
w, 2-3h, rep1 |
| GSM8208940 |
w, 2-3h, rep2 |
| GSM8208941 |
w, 2-3h, rep3 |
| GSM8208942 |
nos, 2-3h, rep1 |
| GSM8208943 |
nos, 2-3h, rep2 |
| GSM8208944 |
nos, 2-3h, rep3 |
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| Relations |
| BioProject |
PRJNA1100568 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE264028_sorted_embryos_45_ENSMBL_6_22_96_genes_TPM_matrix.tsv.gz |
386.4 Kb |
(ftp)(http) |
TSV |
| GSE264028_sorted_embryos_45_ENSMBL_6_22_96_genes_counts_matrix.tsv.gz |
356.7 Kb |
(ftp)(http) |
TSV |
| GSE264028_sorted_embryos_45_ENSMBL_6_22_96_transcripts_TPM_matrix.tsv.gz |
700.9 Kb |
(ftp)(http) |
TSV |
| GSE264028_sorted_embryos_45_ENSMBL_6_22_96_transcripts_counts_matrix.tsv.gz |
838.5 Kb |
(ftp)(http) |
TSV |
| GSE264028_unsorted_embryos_46_w_vs_nos_ENSMBL_6_22_96_genes_TPM_matrix.tsv.gz |
384.3 Kb |
(ftp)(http) |
TSV |
| GSE264028_unsorted_embryos_46_w_vs_nos_ENSMBL_6_22_96_genes_counts_matrix.tsv.gz |
350.3 Kb |
(ftp)(http) |
TSV |
| GSE264028_unsorted_embryos_46_w_vs_nos_ENSMBL_6_22_96_transcripts_TPM_matrix.tsv.gz |
698.8 Kb |
(ftp)(http) |
TSV |
| GSE264028_unsorted_embryos_46_w_vs_nos_ENSMBL_6_22_96_transcripts_counts_matrix.tsv.gz |
834.7 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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