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. 2021 Jan 5;22:14. doi: 10.1186/s13059-020-02251-5

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — MicroRNAs antagonize codon optimality effect on mRNA stability during the MZT. a Sinaplot showing the codon optimality distribution (Table S5) for the top 1000 most unstable maternal genes during zebrafish and Xenopus MZT. The stability was defined based on the log₂-fold change of early (2 h) vs late time points (fish = 6 h, Xenopus = 9 h) in fish (Additional file 1: Fig. S1a-b) and Xenopus [33]. The genes were divided into groups based on the numbers or seed type of miR-430/427. The content of optimal codons increases with the miR-430 regulation strength (p = 2 × 10⁻⁴ zebrafish, p = 2 × 10⁻³ Xenopus, linear regression). The p value was obtained by comparing the difference in the mean level of optimal codons (PLS1) between genes with and without miR-430/427 sites using a linear model. b Heatmap of miR-430 enrichment in the 3′UTR as a function of mRNA stability and codon optimality level. The miR-430 enrichment was estimated with a generalized linear model. Unstable mRNAs enriched in optimal codons temp to contain miR-430 sites (e.g., smarca2). c Scatter plot comparing the RNA stability, during MZT, of ortholog genes in zebrafish (Additional file 1: Fig. S1a-b) and Xenopus [33]. d Scatter plot comparing the content of optimal codons in zebrafish and Xenopus for ortholog genes [22]. e Sinaplot showing the codon optimality distribution for unstable mRNAs in panel a that are orthologs (n = 280). Messenger RNAs were divided into four categories according to the presence or absence of miR-430/-427 seeds in both species. The orthologous mRNA with miR-430/-427 seeds in both species are the most enriched in optimal codons (p = 0.0868, one-way ANOVA test)