Fig. 1

SLAM-seq T>C conversion depends on s4-UTP presence and transcription. A Representation of experimental set up and SLAM-seq principle applied in early zebrafish development. Injected embryos are collected at ~6h post-injection and after RNA alkylation, libraries were prepared and sequenced. s4-UTP-incorporated reads should present T>C mutations. Maternal mRNAs are expected to show background labeling (unlabeled) levels while zygotic mRNAs are expected to have T>C conversions (labeled). B Representative screenshots from genome tracks at cul3a 3′UTR from alignment files of SLAM-seq samples: (top) non-injected, (middle) injected with 75mM s4-UTP, and (bottom) co-injected with Alpha amanitin. T>C transitions highlighted in blue and V>N (non-T to any nucleotide) highlighted in brown. Coverage graphs on top of their respective tracks. C Histogram showing total number of expressed genes in each bin of mean T>C conversion rates normalized by 3′UTR base for all groups. Arbitrary cutoff of 0.01 was used to estimate number of false positives in control samples. Bonferroni corrected p-values highlighted from one-sided Kolmogorov-Smirnov tests. D Sinaplots showing mean zygotic component score (labeled reads/total reads) for different groups of genes in all SLAM-seq conditions. Number of expressed genes in each category (>5 CPMs, counts per million, nd = non-detected) is shown below each group. Bonferroni-corrected p-values from one-sided Wilcoxon tests as follows: *** < 0.0001, ** < 0.001, * < 0.05, ns ≥ 0.05