Figure 4. Landscape of tRNA and rRNA modifications.
(A) All annotated mammalian tRNA modifications were pulled from Modomics (http://modomics.genesilico.pl/). Blue residues have no modification annotated while yellow residues are modified in at least one mammalian cytosolic tRNA (Bos taurus Homo sapiens, Mus musculus, Oryctolagus cuniculus, Ovis aries, Rattus norvegicus). The anticodon, a hot spot of modification, is highlighted in red. m1A58, the first tRNA modification shown to be reversible, is circled. Modifications that occur in the variable loop were left out for simplicity. m2G -N2-methylguanosine; m22G - N2N2-dimethylguanosine; m1G - 1-methylguanosine; ac4C - N4-acetylcytidine; m1A - 1-methyladenosine; D - dihydrouridine; acp3U - 3-(3-amino-3-carboxypropyl)uridine; m3C - 3-methylcytidine; I - inosine; m1I - 1-methylinosine; mcm5U - 5-methoxycarbonylmethyluridine; mcm5s2U - 5-methoxycarbonylmethyl-2-thiouridine; Q - queuosine; galQ - galactosyl-queuosine; manQ - mannosyl-queuosine; f5Cm - 5-formyl-2’-O-methylcytidine; t6A- N6-threonylcarbamoyladenosine; ms2t6A - 2-methylthio-N6-threonylcarbamoyladenosine; m6t6A - N6-methyl-N6-threonylcarbamoyladenosine; i6A - N6-isopentenyladenosine; o2yW - peroxywybutosine; yW - wybutosine; m1Ψ - 1-methylpseudouridine; Ψm - 2’-O-methylpseudouridine; m7G - 7-methylguanosine; m5C - 5-methylcytidine; m2A - 2-methyladenosine; m5U - 5-methyluridine.
B) All annotated Homo sapiens rRNA modifications recorded in Modomics (http://modomics.genesilico.pl/) were mapped onto the cryo-EM structure of the human ribosome (4ug0). An E- site tRNA (green) is shown for orientation. 2’-O-methylations are shown in blue, pseudouridylations are shown in yellow, and base modifications are shown in red. For simplicity, 2’-O-methyl-seudouridine is shown in blue. The rRNA ribbon diagram shows the prevalence of modification (~2% of total RNA residues). As the surface rendering incorporating ribosomal proteins shows, the large majority of the modifications are buried within the core of the ribosome.