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Fig. 2 | Genome Biology

Fig. 2

From: Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability

Fig. 2

Codon optimality is the major determinant of mRNA stability. a Diagram depicting the maternal to zygotic transition in zebrafish. b Scatter plots of predicted and observed mRNA stability, during MZT, for maternal mRNAs in zebrafish and Xenopus. The gradient of color represents the content of optimal codons [22]. The predicted mRNA stability correlates with the proportion of optimal codons (p < 2 × 10−16, Pearson correlation). The mRNA stability median of mRNAs enriched in optimal (red) or non-optimal (blue) codons, as well as mRNAs with miR-430/-427 target sites in the 3′UTR (green) are shown. c Codon content explains most of the mRNA decay during MZT. The x-axis shows the fraction of coding genes that can be regulated by different mRNA stability pathways. For microRNAs, this fraction corresponds to the number of seed sites (GCACTT) in the 3′UTR, and for m6A, the fraction is the number of target genes reported [10]. The y-axis shows the Bayesian model comparison weights [32]. These weights represent which model is more likely to predict unobserved data better, higher values indicate stronger regulatory effects

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