Fig. 2: DMS mapping of chromosomal-encoded tRNAs reveals in vitro versus in vivo, and in vivo isodecoder differences.
The parameters used here are: DMS signal = DMdiff (+DMS) – DMdiff(–DMS). a Heatmap showing the in vitro and in vivo positional DMS signals for the most abundant tRNA isodecoder in each anticodon family. Native modifications30 that are incompletely removed by demethylases are marked with “X”. tRNA positions are according to the standard tRNA nomenclature, and residues missing in specific tRNAs are marked in gray. b Box-whisker plots of DMS signal differences for each A and C residue in every tRNA using the formula (x – in vitro), where x = in vitro (1), or in vivo (2) in D, T, anticodon, variable loops, and the 3’ unpaired CCA regions. P-values are calculated with standard two-sided Wilcox rank-sum test; ****: p < 10-4. The exact P-values for each box-whisker plot are as follows: D-loop = 1.6 × 10–26, anticodon loop p = 1.3 × 10–31, variable loop p = 1.3 × 10–20, T loop = 1.9 × 0–21, CCA p = 4.9 × 10–05. In each box-whisker plot, the maxima represent the first quantiles, the middle lines represent the medians, the minima represent the 75th quantiles, the crosses in the center represent the means, and the whiskers represent the standard deviation. c Secondary structures of two tRNASer(AGA) isodecoders with different tRNAScan scores33: Ser-AGA-1, 90.4, and Ser-AGA-4, 78.8, overlaid with in vivo DMS signals. Sequence differences are indicated as circled nucleotides. d Tertiary structures of Ser-AGA-1 and Ser-AGA-4 overlaid with in vivo DMS signals (modified from the E site tRNA in the human 80S ribosome, PDB: 6Z6M)90. e Secondary structures of two tRNAVal(UAC) isodecoders with different tRNAScan scores33: Val-UAC-1, 82.9, and Val-UAC-4, 68.7, overlaid with in vivo DMS signals. Sequence differences are indicated as circled nucleotides. f Tertiary structures of Val-UAC-1 and Val-UAC-4 overlaid with in vivo DMS signals (modified from the tRNAVal in the human METTL1-WDR4-tRNA(Val) complex, PDB: 8CTI)91.
