Fig. 8

The 3′ end sequences of a diverse group of mRNAs are shortened during the early development of zebrafish. (A) A schematic diagram of the detection of mRNA 3′ ends by 3′ end RNA sequencing. Left: Zebrafish embryos at 0 and 4 hpf were collected and extracted for RNA purification. Right: Total RNAs were reverse-transcribed using an oligo(dT) primer. After removing the RNA template, second-strand DNAs were synthesized by random priming. (B) Tracks of 3′ end RNA sequencing plotted on the 3′ genomic region of tktb and pycr1b from embryos at 0 and 4 hpf. The terminal exon is presented. The numbers of reads were 1062 (0 hpf) and 1372 (4 hpf) in tktb and 4392 (0 hpf) and 12378 (4 hpf) in pycr1b. (C) Tracks of 3′ end sequencing plotted on the 3′ genomic region of chek1, cotl1, and btbd10b from embryos at 0 and 4 hpf. The total numbers of reads were 505 (0 hpf) and 361 (4 hpf) in chek1, 17 (0 hpf) and 44 (4 hpf) in cotl1, and 809 (0 hpf) and 1217 (4 hpf) in btbd10b. The details with P values are shown in table S2. (D) Summary of 3′ end RNA sequencing of 568 genes with the number of mRNAs with shortened (red) and unchanged (blue) 3′ end between 0 and 4 hpf.