Systematic imaging reveals features and changing localization of mRNAs in Drosophila development
- Max Planck Institute of Molecular Cell Biology and Genetics, Germany
- University of Veterinary Medicine Vienna, Austria
- Janelia Research Campus, Howard Hughes Medical Institute, United States
Figures
Figure 1 with 2 supplements
Summary of the fluorescent in situ hybridization (FISH) screen in ovaries.
(A) Summary of key numbers of the screen. For each of the 6091 FISH experiments, we annotated the signal as no signal, ubiquitous, or specific. Specific and some ubiquitous signals were imaged. (B) …
Figure 1—figure supplement 1
Experimental outline and database features.
(A) Overview of the experimental procedure for transcriptome and genome-wide in situ hybridization experiments and evaluation. (B) Screenshot of the publicly available Dresden ovary table, DOT, and …
Figure 1—figure supplement 2
GO-term enrichment analysis for gene sets.
GO-terms associated with ubiquitous, subcellular, cellular, nuclear, oocyte enriched, anterior and posterior gene sets. Shown is also analysis of all ‘localization competent’ mRNAs. Bar plots show …
Figure 2 with 1 supplement
Summary of cellular and nuclear expression patterns.
(A,C) Exemplary FISH experiments for the cellular (A) and nuclear (C) expression sets. RNA is shown in green and the DNA (labelled with DAPI) is shown in magenta. Scale bars: 30 μm. (A) tutl is …
Figure 2—figure supplement 1
FISH screen results and controls.
(A) Estimate of false-positive/negative rate of the in situ screen using comparison with the independent transcriptomics data. A gene was classified as falsely positive if it was annotated as …
Figure 3 with 5 supplements
Localized mRNAs show gene set specific features.
(A) Linear hierarchy plot (Tomancak et al., 2007) showing stage- and tissue-specific re-expression of the ovary gene sets in embryogenesis. (B) Protein interaction analysis per gene set revealed …
Figure 3—figure supplement 1
Ovary gene sets have specific expression patterns during embryogenesis.
Linear hierarchy (Tomancak et al., 2007) plot showing at which embryonic stage and in which tissue the oogenesis gene sets are re-expressed during embryogenesis. Each colour-coded bar represents …
Figure 3—figure supplement 2
Gene features of subcellular enriched mRNAs.
(A) Boxplots showing the median mRNA expression measured by 3Pseq per gene set in early and full ovaries and in 0–2 hr embryos. At the onset of embryogenesis, the cellular mRNAs were almost as low …
Figure 3—figure supplement 3
Embryo localized mRNAs also have long, conserved 3′UTRs.
Distributions of median 3′UTR length (A) and conservation of the 3′UTR sequence (B, across 24 Drosophila species) for embryo gene sets. Shown are genes that are ubiquitously expressed during …
Figure 3—figure supplement 4
Cytoplasmic but not nuclear mRNA localization requires the cytoskeleton.
(A) Localization of anterior and posterior mRNAs is lost upon microtubule depolymerization by colchicine. Shown are the anterior mRNAs fs(1)K10 and milt (examples for diffuse-anterior and …
Figure 3—figure supplement 5
Posterior mRNA localization is impaired in posterior localization pathway mutants.
(A) Localization of the novel posterior candidate mRNAs vkg, TwdlG, PI3K21B, and zpg is lost in egg-chambers that prematurely depolymerize the microtubules (flies homozygous for SpireRP), are mutant …
Figure 4
mRNA localizations change across time-points.
(A) Schematic of changing mRNA distributions in germline cells (nurse cells, oocyte) in stage 4–7 and stage 9–10 egg-chambers. (A′) Exemplary mRNAs that show diverging combinations of mRNA …
Figure 5 with 1 supplement
mRNA expression is stable during oogenesis.
(A) Changing localization of ZnT35C, exu, aret, Dok, Bsg25D and ssp mRNAs across time-points (see Figure 4) does not coincide with a change in transcript expression: the expressed 3′UTRs (sampled by …
Figure 5—figure supplement 1
The transcriptome shows little variation over the course of oogenesis.
(A) Scatterplot showing high correlation (Pearson Correlation 0.71) between RNAseq and 3Pseq sequencing results. (B) Stage-specific sequencing reveals that ∼5500 genes (grey) were detected by both …
Figure 6 with 1 supplement
mRNA localizations are changing across cell types and within cells over time.
(A) In the oocyte, most mRNAs of the subcellular category also have phases with ubiquitous mRNA distribution. (B) The number of localized mRNAs in the oocyte varies over oogenesis time points. mRNAs …
Figure 6—figure supplement 1
Changing localization of mRNAs in ovaries and embryos.
(A) Expanded dendrogram from Figure 6C including the data for the first two time-points of embryogenesis (Lecuyer et al., 2007). mRNAs at the anterior (minus category) and posterior (plus category) …
Additional files
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Supplementary file 1
Gene set definitions. Definition of Gene Sets used in this analysis from the ovary and the embryo (Lecuyer et al., 2007) FISH annotation matrices.
- https://doi.org/10.7554/eLife.05003.019
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Supplementary file 2
Differentially expressed genes (early/late). Genes showing significant differential expression (padj <0.1) from early to late ovaries. Upregulated genes show log2FolgChange >0, downregulated genes show log2FolgChange ≤0.
- https://doi.org/10.7554/eLife.05003.020
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Supplementary file 3
Differentially expressed genes (late/full). Genes showing significant differential expression (padj <0.1) from late to full ovaries. Upregulated genes show log2FolgChange >0, downregulated genes show log2FolgChange ≤0.
- https://doi.org/10.7554/eLife.05003.021
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Supplementary file 4
Differentially expressed genes (full/0–2h embryos). Genes showing significant differential expression (padj <0.1) from full ovaries to 0–2 hr embryos. Upregulated genes show log2FolgChange >0, downregulated genes show log2FolgChange ≤0.
- https://doi.org/10.7554/eLife.05003.022
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Supplementary file 5
Differential isoform expression (early/late). Transcripts that are differentially expressed from early to late ovaries.
- https://doi.org/10.7554/eLife.05003.023
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Supplementary file 6
Differential isoform expression (late/full). Transcripts that are differentially expressed from late to full ovaries.
- https://doi.org/10.7554/eLife.05003.024
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Supplementary file 7
Changes in 3′UTR length. Shown are the mean-weighted changes in 3′UTR length across oogenesis. Values >0 indicate 3′UTR lengthening, Values <0 indicate 3′UTR shortening. Only changes affecting >200 nt are shown.
- https://doi.org/10.7554/eLife.05003.025
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Supplementary file 8
Effect of colchicine on oocyte mRNAs. Summary of experiments on colchicine treated egg-chambers; Shown are gene/clone name, localization in wild-type egg-chambers and mRNA appearance upon microtubule depolymerization. Data is available publicly at the DOT, the Dresden Ovary Table (http://tomancak-srv1.mpi-cbg.de/DOT/main.html).
- https://doi.org/10.7554/eLife.05003.026
