Figure 2. ME31B and PABP bind similar mRNAs in 0–1 hr embryos.

(A) Enrichment of Act5C transcripts in PABP and ME31B immunoprecipitations. Extracts from 0 to 1 hr embryos were immunoprecipitated with the indicated antibodies (control pull-downs, black; PABP or ME31B pull-downs, red). In the case of PABP, complexes were immunoprecipitated with Fab1; ME31B was precipitated from eGFP-ME31B embryos with anti-GFP antibodies. The percent of Act5C mRNA pulled down was quantified by RT-qPCR, primed by oligo(dT) (in the case of PABP) or random-hexamers (in the case of ME31B). Numbers reflect the fold enrichment of Act5C in PABP or ME31B immunoprecipitations relative to the control immunoprecipitations. (B) Distribution of PABP enrichment values transcriptome-wide, as determined by RIP-seq. For mRNAs of each gene that satisfied the expression cut-offs, PABP binding was calculated. Highlighted is the binding for Act5C. (C) As in (B), except for ME31B binding values. (D) Comparison of PABP and ME31B binding in 0–1 hr embryos. (E) Comparison of PABP and ME31B binding in S2 cells.

Figure 2—figure supplement 1. ME31B and PABP bind similar transcripts in the early embryo.

(A) Comparison of total RNA abundance in 0–1 hr embryos. Shown is a scatter plot comparing the FPKM abundance for each gene expressed above cut-off in 0–1 hr wild-type and eGFP-ME31B embryos. (B) As in (A), except for ME31B and PABP immunoprecipitations. Shown is a scatter plot comparing the FPKM abundance for each gene expressed above cut-off in PABP and ME31B immunoprecipitations from 0 to 1 hr wild-type and eGFP-ME31B embryos, respectively. (C) As in (A), except for S2 cells transfected with eGFP-ME31B. The red dot highlights me31B. (D) As in (B), except for S2 transfected with eGFP-ME31B.

Figure 2—figure supplement 2. ME31B and PABP binding as measured by RT-qPCR and RNA-sequencing.

(A) A comparison of ME31B binding as determined by RT-qPCR and RNA-sequencing in 0–1 hr embryos. Plotted is the ME31B binding for the five indicated genes, as measured by RIP-seq, and the percent of total RNA immunoprecipitated, as measured by RT-qPCR. RT-qPCR measurements were an average of 3–4 independent, biological replicates with the error bars denoting standard deviation. (B) As in (A), except for PABP binding. (C) Enrichment of Act5C transcripts in ME31B immunoprecipitations in different biological replicates, summarized in (A). Extracts from 0–1 hr eGFP-ME31B embryos were immunoprecipitated with IgG or anti-GFP antibodies. The percent of Act5C mRNA pulled down was quantified by random-hexamer-primed RT-qPCR. Numbers reflect the fold enrichment of Act5C in ME31B immunoprecipitations relative to the control immunoprecipitations. (D) As in (C), except for smg. (E) As in (C), except for PABP immunoprecipitation of Act5C. (F) As in (C), except for PABP immunoprecipitation of smg.