Classification of Maternal mRNA Decay Pathways in Zebrafish

(A) A schematic representation of maternal mRNA decay pathways in zebrafish.

(B) Bright field pictures (upper panels) and in situ hybridization to detect gstm mRNA (lower panels, purple) in wild-type, miR-430 MO-injected, and α-amanitin-injected embryos.

(C) Left: a Venn diagram of the result of the RNA sequencing analysis. Right: pie charts representing subclasses of maternal genes whose mRNAs are degraded during MZT. The numbers show genes in each subclass.

(D) qRT-PCR analysis of wild-type and α-amanitin-injected embryos. mRNA levels at 0 hpf were set to one. The graph represents an average of three independent injection experiments. The error bars show SD.

(E) In situ hybridization to detect mRNAs of M-decay genes suv39h1a (upper panels) and pus1 (lower panels) in wild-type and α-amanitin-injected embryos. See also Figure S1.

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Cotranslational Deadenylation and Degradation of M-Decay mRNAs

(A-C) Cumulative plots showing the distributions of 5′ UTR (A), ORF (B), and 3′ UTR (C) length in all genes (black), Z-decay genes (blue), M-decay genes (orange), and stable genes (gray). The x axis shows the length of each region on a log10 scale. The y axis shows the cumulative fraction. The median length (upper left) and the p values compared with all genes (lower right, two-sided Kolmogorov-Smirnov test) are shown.

(D) Results of the time course PAT assay of EGFP reporter mRNAs injected at the one-cell stage. The developmental stages are shown above as hpf. Lanes labeled as A0 show 3′ UTR fragments without a poly(A) tail.

(E) GFP fluorescence of embryos injected with GFP reporter mRNA and control MO or EGFP MO (upper panel, green). The fluorescence of coinjected rhodamine-dextran is shown as an injection control (lower panel, red).

(F) Results of the time course PAT assay of suv39h1a and vasa mRNAs in embryos injected with control MO or suv39h1a MO.

(G) In situ hybridization detecting suv39h1a mRNA in control MO- or suv39h1a MO-injected embryos.

(H) qRT-PCR analysis of MO-injected embryos. The mRNA levels at 0 hpf were set to one. The graphs represent the averages of three independent injection experiments. The error bars show SD. See also Figures S3 and S4.