The structure of the yeast ribosomal RNA genes. 3. Precise mapping of the 18 S and 25 S rRNA genes and structure of the adjacent regions

Abstract

The 5'-terminal of Saccharomyces cerevisiae 18 S and 25 S rRNA are precisely mapped within the sequence of the rDNA repeating unit. The 3'-terminal of 25 S rRNA and 37 S pre-rRNA are located within a 548 bp segment of the rDNA repeating unit by the use of a DNA polymerase I extension technique. The analysis of the rDNA sequences at the structural gene boundaries reveals the presence of oligonucleotide repeats which may be involved in transcription or processing control mechanisms. The sequence of rDNA in the transcription termination region is determined and possible mechanisms shaping the 3'-end of 25 S rRNA are discussed.

Analysis of pre-rRNAs in heat-shocked HeLa cells allows identification of the upstream termination site of human polymerase I transcription.

“…2C. As expected, there was no signal from the 37°C nuclear sample (lane 5). The 42°C nuclear sample (lane 9), however, contained some RNA that gave full-length protection and some that gave a very heterogeneous set of bands approximately 15 2C), no transcription was apparent in this region (data not shown).…”

“…In view of the recent data that Pol I transcription termination occurs several hundred nucleotides downstream of 28S rRNA in all species in which it has been carefully studied, there are two possible ways that the 3' end could be formed: (i) 3' exonucleases, which are prevalent in cells, could digest from the end until a stable RNA structure is reached, or (ii) a processing factor could recognize a sequence at or near the 3' end of 28S rRNA and either directly generate the 3' end or produce an end that would require only a small amount of exonucleolytic trimming. The fact that in several species there is an intermediate with 10 to 30 nucleotides of sequence downstream of the 3' end of 28S rRNA (5,19,26,46) supports the latter theory, although it is possible that those ends are merely regions where an exonuclease pauses because of the secondary structure of the RNA.…”

“…-*, Orientation in pGEM4 such that transcription with SP6 will result in synthesis of a positive-sense (rRNA-like) RNA; <-, orientation such that transcription with T7 polymerase will result in positive-sense RNA. at a position 650 nucleotides downstream of the initiation site (10,24,35); this appears to be an endonucleolytic event that requires a protein factor (10). The second processing event (20) forms the mature 3' end of 28S rRNA; little is known about this event except that in some species a processing intermediate with 7 to 30 nucleotides of downstream sequence has been identified (5,19,26,46).…”

Non‐random distribution of the TY1 elements within nuclear DNA of Saccharomyces cerevisiae

“…Apart from these junctions, the length of fragment B seems to be constant within one strain, but may vary from one strain to the other. Authors in [31] reported a 24 basepair insertion in one cloned fragment B as compared to the sequence of another clone [27], and in our case, the fragment B of strain 309 is about 50 basepairs shorter than those of the other strains (unpublished). Such length variations could represent scars following insertions and excisions of transposable elements; rRNA gene orphons, which might exist in some strains [32], could be the result of transposonmediated translocations.…”

The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript

“…Bayev et al [24] recently mapped the 5'-terminus of 26S rRNA of S. cerevisiae at positions 313 and 314 of the small EcoRI-KpnI fragment derived from the EcoRI fragment A (cf. Figs.…”