Fig. 1: Transfer RNA anticodon pools are maintained largely stable across cell types despite extensive reprogramming of tRNA repertoires during differentiation.
From: Selective gene expression maintains human tRNA anticodon pools during differentiation
a, Schematic of hiPSC differentiation into NPC, neurons and CM. b, Representative fluorescence microscopy images (from at least three independent experiments) of immunostaining for cell type-specific marker proteins and DAPI. CTNT, cardiac troponin T; ACTN2, ɑ-actinin-2. Scale bars, 10 µm. c, Gene expression heatmaps for known cell type- and proliferative state-specific markers in hiPSC, NPC, neuron and CM cultures (n = 2 biological replicates). Standardized Z scores were calculated using DESeq2-normalized RNA-Seq gene counts across samples. d, Schematic depicting tRNA classification. Distinct tRNA transcripts sharing an anticodon are called isodecoders and collectively constitute anticodon families. Members of different anticodon families that carry the same amino acid belong to the same isotype. e, Principal component (PC) analysis of variance-stabilizing-transformed count data for tRNA transcripts from DESeq2 for each cell line (n = 2 biological replicates; variance explained by each principal component in parentheses). f, Heatmap of tRNA transcript expression dynamics showing only differentially expressed transcripts in at least one differentiated cell line relative to hiPSC (Benjamini–Hochberg-adjusted Wald test, Padj ≤ 0.05). Hierarchically clustered expression heatmap showing the scaled Z score of normalized unique transcript counts in hiPSC, NPC, neurons and CM (n = 2 biological replicates; left). Differential expression for NPC, neurons and CM relative to hiPSC reported as log2-tranformed fold changes (middle). Base mean normalized to the tRNA transcript across all samples (right). g, Principal component analysis as in e calculated from variance-stabilizing-transformed count data summed by tRNA anticodon. h, Heatmap as in f for count data summed by tRNA anticodon. Anticodon families previously38 associated with proliferating (P) or differentiated (D) cells are shown. Source numerical data and unprocessed blots are provided.
