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Degradation of casein mRNA in the presence and absence of prolactin. Cultured mammary cells were given radioactive RNA precursors (pulse) and after a given time were washed and given nonradioactive precursors (chase). The casein RNA synthesized during the pulse time was then isolated and its radioactive labelmeasured. In the absence of prolactin, the newly synthesized casein mRNA decayed rapidly, with a half-life of 1.1 hours. When the same experiment was done in a medium containing prolactin, the half-life was extended to 28.5 hours. (After Guyette et al. 1979.)

Metabolic pathways for RNA and DNA precursors biosynthesis: a palimpsest from the RNA to DNA world transition? The biosynthetic pathways for purine and pyrimidine nucleotides both start with ribose 5-monophosphate. The formation of the four bases requires several amino-acids, formate and carbamyl-phosphate. Nucleotide monophosphates (NMP) are converted into RNA precursors (NTP) by NMP kinases (k) and NDP kinases (K). These reactions probably are relics of the RNA-protein world. DNA precursors are produced from NDP and/or NTP by ribonucleotide reductases (RNR), except for dTTP, which results from methylation of dUMP. dTMP is produced from dUMP by Thymidylate synthases (ThyA or ThyX) and converted into dTTP by the same kinases that convert NMP into NTP. dUMP can be produced either by dUTPAse or by dCTP deaminase. In the U-DNA world, it could have been also produced by degradation of U-DNA. The mode of dTMP production clearly suggests that U-DNA was an evolutionary intermediate between RNA and T-DNA. Some viruses contain U-DNA, whereas others contain HMC-DNA (HMC= hydroxymethyl-cytosine). Transformation of C into HMC occurs at the level of dCMP, and conversion of dCMP into dHMCMP is catalyzed by a dCMP hydroxy-methyl transferase (dCMP HM transferase), which is homologue to ThyA (See refs. 11, 14, and 19 for more details).

Exemplary 4-thiouracil (4-TU) labeling of total RNA in S. cerevisiae and H. volcanii : (a) Workflow summary of 4-TU labeling. 4-thiouracil labeling and biotinylation workflow is briefly depicted. Growing cells (see Subheading 3.1.) are pulse labeled with 4-thiouracil as described in Subheading 3.2. After RNA extraction (see Subheading 3.3), sulfhydryl groups are specifically biotinylated in the presence of methylthiosulfonate activated Biotin derivate (MTS-Biotin) (see Subheading 3.4). After biotinylation RNA are separated by gel electrophoresis and visualized as described in Subheading 3.5 and below. (b and c) Exemplary 4-TU labeling applied on the eukaryotic model organism S. cerevisiae . The indicated yeast cells, wild-type (WT), cells depleted for the small and large ribosomal subunit biogenesis factors Pwp2 (GAL::PWP2) and Pol5 (GAL::POL5), respectively [39, 40] were labeled for 20 min with 4-thiouracil as indicated in Subheading 3.2. Labeled total RNA were separated by denaturing agarose (b) or polyacrylamide (c) gel electrophoresis, respectively. Biotinylated RNA was detected as described in Subheading 3.5. Ribosomal RNA precursors (35S, 27S, and 20S rRNA) and mature ribosomal RNA (25S, 18S, 5.8 and 5S rRNA) are indicated. Please note that depletion of the small ribosomal subunit biogenesis factor, Pwp2, for 14 h leads to the reduction of small ribosomal subunit pre- and mature rRNAs (20S and 18S rRNA, respectively) [39]. In contrast depletion of the large ribosomal subunit biogenesis factor, Pol5, for 9 h leads to the reduction of the common large ribosomal subunit precursor and corresponding mature rRNA (27S, 25S, and 5.8S, respectively) [39–41]. Additional application examples using this protocol and S. cerevisiae is described in [41]. (d) Exemplary 4-TU labeling applied on the archaeal model organism H. volcanii . Haloferax volcanii wildtype cells were labeled for 3 h with 4-thiouracil as indicated in Subheading 3.2. Labeled total RNA was separated by denaturing agarose electrophoresis. Biotinylated RNA was detected as described in Subheading 3.5. Mature ribosomal RNA (23S, 16S, and 5S rRNA) observed in these conditions are indicated. Additional application examples using this protocol and H. volcanii has been described previously [36]