17The Exon Junction Complex (EJC) regulates many steps in post-transcriptional gene 18 expression and is essential for cellular function and organismal development; however, 19 EJC-regulated genes and genetic pathways during development remain largely 20 unknown. To study EJC function during zebrafish development, we first established that 21 zebrafish EJCs mainly bind ~24 nucleotides upstream of exon-exon junctions, and are 22 also detected at more distant non-canonical positions. We then generated mutations in 23 two zebrafish EJC core genes, rbm8a and magoh, and observed that homozygous 24 mutant embryos show paralysis, muscle disorganization, neural cell death, and motor 25 neuron outgrowth defects. Coinciding with developmental defects, mRNAs subjected to 26 Nonsense-Mediated mRNA Decay (NMD) due to translation termination ≥ 50 nts 27 upstream of the last exon-exon junction are upregulated in EJC mutant embryos.28 Surprisingly, several transcripts containing 3′UTR introns (3′UI) < 50 nts downstream of 29 a stop codon are also upregulated in EJC mutant embryos. These proximal containing transcripts are also upregulated in NMD-compromised zebrafish embryos, 31 cultured human cells, and mouse embryonic stem cells. Loss of function of foxo3b, one 32 of the upregulated proximal 3′UI-containing genes, partially rescues EJC mutant motor 33 neuron outgrowth. In addition to foxo3b, 166 other genes contain a proximal 3′UI in 34 zebrafish, mouse and humans, and these genes are enriched in nervous system 35 development and RNA binding functions. A proximal 3′UI-containing 3′UTR from one of 36 these genes, HNRNPD, is sufficient to reduce steady state transcript levels when fused 37 to a β-globin reporter in HeLa cells. Overall, our work shows that genes with stop 38 codon-proximal 3′UIs encode a new class of EJC-regulated NMD targets with critical 39 roles during vertebrate development.40 84 suggesting that 3′UIs may play an important role in regulating tissue-specific 85 developmental programs via EJC-dependent NMD. However, specific mRNAs, genetic 86 5 pathways, and developmental events that are regulated by 3′UI-dependent NMD 87 remain largely unknown.
88In this work, we establish zebrafish as a model to study EJC developmental 89 functions. As expected from work in human cells, we show that in zebrafish embryos 90 the EJC mainly binds ~24 nts upstream of exon-exon junctions and is also detected on 91 more distant exonic positions. Zebrafish Rbm8a and Magoh are crucial for early 92 zebrafish embryonic development, with muscle and neural lineages being particularly 93 sensitive to the loss of EJC. We find that EJC-dependent NMD is disrupted in rbm8a 94 and magoh mutant embryos. Strikingly, we uncover a class of genes that contain a stop 95 codon-proximal 3′UI (intron within 50 nts of the stop codon) and are upregulated in 96 zebrafish EJC mutant embryos and upf1 morphants. We show that loss of foxo3b, a 97 proximal 3′UI-containing gene whose transcript and protein levels are elevated in EJC 98 mutants, partially...