mRNA poly(A)-tail changes specified by deadenylation broadly reshape translation in Drosophila oocytes and early embryos
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, United States
- Massachusetts Institute of Technology, United States
- Harvard-MIT Division of Health Sciences and Technology, United States
- Whitehead Institute for Biomedical Research, United States
Figures
Figure 1 with 1 supplement
Transient coupling between poly(A)-tail length and translational efficiency in embryos.
(A) Time line of the developmental transitions probed in this study, illustrating the presence of maternal and zygotic mRNAs (pink and purple, respectively). (B) Relationship between mean …
Figure 1—figure supplement 1
Dynamics of translational regulation during the OET and early embryonic development.
Distinct patterns of TE changes during the OET and early embryonic development. TE values (log2) for mRNAs in stage 14 oocytes, 0–1 hr embryos, and 2–3 hr embryos that had ≥10.0 RPM in the RNA-seq …
Figure 2 with 2 supplements
Coupling between poly(A)-tail length and translational efficiency in oocytes.
Relationship between mean poly(A)-tail length and TE in either oocytes at the indicated stage or activated eggs (top), and the relationship between tail-length and TE changes observed between …
Figure 2—figure supplement 1
Widespread translational regulation during oocyte maturation.
(A) Relationship between TEs in stage 11 and stage 14 oocytes. TE values (log2) were median centered (median values in stage 11 and stage 14 oocytes, –0.5153 and –0.1318, respectively). Results are …
Figure 2—figure supplement 2
Uncoupled behavior observed for a subset of mRNAs between the last stages of oocyte maturation.
(A) The relationship between the tail-length and TE changes observed between stage 14 oocytes relative to stage 13 oocytes, redrawn from Figure 2, highlighting in blue mRNAs that had tail-length …
Figure 3
Dynamics of translational regulation during oocyte maturation.
(A) Distinct patterns of TE changes during oocyte maturation. TE values (log2) for mRNAs in oocytes from stages 11 through 14 that had ≥10.0 RPM in the RNA-seq data for all samples, and ≥10.0 RPM in …
Figure 4
TEs and Poly(A) tail lengths of selected mRNAs during oocyte maturation and egg activation.
(A) Relationship between net tail-length and TE changes observed after oocyte maturation, highlighting the behavior of cyclin B, cyclin B3, and fizzy. The TE data for stage 14 oocytes were from Kronj…
Figure 5 with 1 supplement
Widespread impact of Wispy on poly(A)-tail length but not TE.
(A) Comparison of mean poly(A)-tail lengths in wild-type and wispy-mutant stage 13 oocytes (left) and in wild-type cleavage-stage embryos and wispy-mutant laid eggs (right). Plotted are mean …
Figure 5—figure supplement 1
Impact of Wispy on the poly(A)-tail lengths, mRNA recovery, and RPFs.
(A) The plots from Figure 5A, highlighting mRNAs encoding ribosomal proteins in red (Supplementary file 3). (B) Relationship between mean poly(A)-tail length and TE at the indicated developmental …
Figure 6 with 1 supplement
Widespread translational regulation by PAN GU primarily attributable to changes in poly(A)-tail length.
(A) Relationship between the TE changes in wild-type activated eggs relative to wild-type stage 14 oocytes and those in wild-type activated eggs relative to png-mutant activated eggs. TE fold-change …
Figure 6—figure supplement 1
Perturbation of tail-length and TE during egg activation in png-mutant samples.
(A) Comparison of mean poly(A)-tail lengths and TEs between wild-type and png-mutant stage 14 oocytes, and between wild-type and png-mutant activated eggs. TE values (log2) were median centered …
Figure 7 with 2 supplements
Translational regulation by Smaug primarily explained by changes in poly(A)-tail length.
(A) Relationship between mean tail-length changes and TE changes during the OET for wild-type 0–1 hr embryos (left) and smg-mutant 0–1 hr embryos (right), comparing wild-type or smg-mutant 0–1 hr …
Figure 7—figure supplement 1
Smaug-dependent translational repression of Smaug binding targets, primarily explained by changes in poly(A)-tail length.
Shown is the relationship between mean tail-length changes and TE changes during the OET for wild-type and smg-mutant 0–1 hr embryos (left and right, respectively), highlighting mRNAs previously …
Figure 7—figure supplement 2
Relationship between poly(A)-tail length changes and TE changes throughout development, plotting absolute rather than relative tail-length changes.
Shown are the relationships between the absolute differences in mean tail-length and TE changes observed between stages; otherwise, as in the corresponding panels from Figures 1, 2, 4, 5, 6, and 7.
Author response image 1
Author response image 2
Additional files
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Supplementary file 1
Relationships between RNA-seq, ribosome profiling, and PAL-seq measurements for wild-type samples at different developmental stages.
The Spearman correlation coefficients for all unique pairwise combinations of stages are shown. For the RNA-seq or ribosome-profiling comparisons, all mRNAs with ≥10.0 RPM in both samples of the respective datasets being compared were included. For the PAL-seq comparisons, all mRNAs with ≥100 poly(A) tags in both samples being compared were included.
- https://doi.org/10.7554/eLife.16955.016
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Supplementary file 2
Processed RNA-seq, ribosome-profiling, and PAL-seq data.
Each of the 16 spreadsheets of this file reports the data for the indicated sample. Within each sheet, the initial Refseq ID is the dm6 Refseq ID that was selected for each gene on the basis of being the longest annotated isoform of that gene. For many genes, the 3' end of this gene model was extended to include the most distal isoform supported by PAL-seq data. RPKM is reads per kilobase per million mapped reads. Descriptions of the analyses include the measurement cutoffs applied to RNA-seq, ribosome profiling, and PAL-seq data, as applicable. The 8th and 9th columns specify whether a 10 RPM cutoff for RNA-seq or ribosome profiling data was met, and the 10th column specifies whether a 100 tag cutoff for PAL-seq data was met. All transcripts with a 3' UTR that overlapped a snoRNA or snRNA were excluded from analysis, as indicated in the final column.
- https://doi.org/10.7554/eLife.16955.017
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Supplementary file 3
Lists of mRNAs highlighted in figures.
This file lists mRNAs that are highlighted in Figures 6 and 7, and Figure 2−figure supplement 1C, Figure 2−figure supplement 2, Figure 5−figure supplement 1, and Figure 7−figure supplement 1.
- https://doi.org/10.7554/eLife.16955.018
