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. 2016 Jul 30;5:e16955. doi: 10.7554/eLife.16955

Figure 2. 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 adjacent stages (bottom). TE values (log2) were median centered (median values in stage 11, 12, 13, and 14 oocytes and activated eggs were –0.6641, –0.9006, –1.38, –0.2523, and –0.0158, respectively). TE fold-change values (log2) were median centered for each comparison (median values, –0.1961, –0.3969, 1.0886, and 0.2123 from left to right). The TE data for stage 14 oocytes and activated eggs were from Kronja et al. (2014b), and the plot of mean poly(A)-tail length and TE for the stage 14 oocyte is redrawn from Figure 1B. Otherwise, these panels are as in Figure 1B.

DOI: http://dx.doi.org/10.7554/eLife.16955.004

Figure 2.

Figure 2—figure supplement 1. Widespread translational regulation during oocyte maturation.

Figure 2—figure supplement 1.

(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 plotted for all mRNAs that had ≥10.0 RPM in the RNA-seq data of both samples and ≥10.0 RPM in the ribosome profiling data of at least one of the two samples and >0.0 RPM in the other. The median-centered TE fold-change values (log2) of stage 14 relative to stage 11 (median, 0.0147) were used to identify mRNAs that were ≥2-fold up- or downregulated in stage 14 oocytes, which are highlighted in red and blue, respectively; otherwise as in Figure 1B. (B) Relationship between the change in protein level (Kronja et al., 2014a) and change in TE observed after oocyte maturation. TE and protein fold-change (log2) values were median centered (median values of 0.1236 and 0.0474, respectively). Results are plotted for all mRNAs that had ≥10.0 RPM in the RNA-seq data, ≥10.0 RPM in the ribosome profiling of one of the two samples and >0.0 RPM in the other, and proteins with ≥2 unique peptides in each of three independent mass spectrometry experiments. (C) Relationship between tail-length and TE changes observed after oocyte maturation, redrawn from Figure 4A, but highlighting points for mRNAs with a TE ≤0.1 in stage 11 oocytes in blue (Supplementary file 3) and those for cyclin B, cyclin B3, and fizzy in yellow, green, and purple, respectively. The dashed line indicates a TE increase of 10 fold.
DOI: http://dx.doi.org/10.7554/eLife.16955.005
Figure 2—figure supplement 2. Uncoupled behavior observed for a subset of mRNAs between the last stages of oocyte maturation.

Figure 2—figure supplement 2.

(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 decreases of at least 29% (log2 fold change of –0.5), and in red mRNAs encoding proteasome subunits (Supplementary file 3). (B) The relationship between tail length and TE observed in stage 13 and 14 oocytes (left and right, respectively) analyzed as in Figure 2 but plotting results for only the mRNAs examined in panel A and highlighting the same sets of mRNAs as in panel A. TE values (log2) were median centered (median values for stage 13 and 14 oocytes, –1.2409 and –0.0779, respectively).
DOI: http://dx.doi.org/10.7554/eLife.16955.006