The transcription termination site of the ribosomal RNA operon in yeast

Veldman, Geertruida M.; Klootwijk, J.; jonge, Petrus de; Leer, Robert J.; Planta, Rudi J.

doi:10.1093/nar/8.22.5179

Cited by 72 publications

(38 citation statements)

References 22 publications

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“…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.…”

Section: Discussionmentioning

confidence: 91%

“…-*, 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).…”

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confidence: 99%

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

Parker¹,

Bond²

1989

Mol. Cell. Biol.

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Human rRNA precursors from normal or stressed HeLa cells were studied by Si nuclease mapping of unlabeled RNA and by antisense RNase mapping of RNA from cells that had been labeled in vivo with[32p]PO4. Heating cells to 43°C decreased the amount of newly synthesized rRNA to less than 5% of the control level and led to greater than 95% inhibition of transcription termination at a region 355 to 362 nucleotides downstream of the 3' end of 28S rRNA, with readthrough continuing into the next transcription unit. Heating of cells to 42°C led to 60% inhibition of termination at this site; 50% of transcripts that extended into the nontranscribed spacer ended in a region 200 to 210 nucleotides upstream of the polymerase I (Pol I) initiation site. This is presumed to be the human upstream transcription termination site because of the absence of RNAs with a 5' end corresponding to this region, the location relative to the Pol I initiation site (which is similar to the location of upstream terminators in other species), and the fact that it is 15 to 25 nucleotides upstream of the sequence GGGTTGACC, which has an 8-of-9 base identity with the sequence 3' of the downstream termination site. Surprisingly, treatment of cells with sodium arsenite, which also leads to the induction of a stress response, did not inhibit termination. Pol I initiation was decreased to the same extent as termination, which lends support to the hypothesis that termination and initiation are coupled. Although termination was almost completely inhibited at 43°C, the majority of the recently synthesized rRNAs were processed to have the correct 3' end of 28S. This finding suggests that 3'-end formation can involve an endonucleolytic cut and is not solely dependent on exonucleolytic trimming of correctly terminated rRNAs.

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Section: Discussionmentioning

confidence: 91%

mentioning

confidence: 99%

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

Parker¹,

Bond²

1989

Mol. Cell. Biol.

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“…Neither does it in yeast 29S RNA [2,5]. However, rRNA in yeast takes place at the level of nucleoprotein particles whereas neither RNAase III nor RNAase M5 action requires additional proteins [38,39].…”

Section: Discussionmentioning

confidence: 99%

“…Terminal labelling of DNA fragments 5'-End labelling was performed with [y-32P]ATP and polynucleotide kinase as described previously [2,5]. 3'-End labelling was performed by filling in the protruding ends with [a-32P]dATP (400 Ci/mmol, the Radiochemical Centre, Amersham) as described by Levis et al [6].…”

Section: Materials and Methods Isolation Of Dna And Dna Fragmentsmentioning

confidence: 99%

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

et al. 1981

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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 We also describe the existence of a significant base complementarity between sequences in the 5'-terminal region of 26S rRNA and the 3'-terminal region of 5.8S rRNA. We suggest that base pairing between these sequences contributes to the binding between 5.8S and 26S rRNA. INTRODUCTION The RNA constituents of the ribosome in yeast are all encoded in a repeating unit of about 9000 base pairs [1]. This repeating unit contains two separate transcription units, one for 5S rRNA and one for 17S, 5.8S and 26S rRNA. The primary transcript of the latter is a common 37S precursor RNA which is processed in a number of steps into the respective mature rRNAs [1]. This processing is carried out on nucleoprotein (pre-ribosomal) particles rather than on the naked RNA and includes both modification and nucleolytic cleavage

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“…As the 3'-terminal sequences of the large ribosomal rRNAs from yea6t and X.Ztaevi cytoplasmic ribosomes (14,15) and from mouse and human mitochondrial ribosomes (16,17) have recently been sequenced, we checked if these may have common structural features with the 3'-terminus of bacterial 23S rRNAs.…”

Section: Introductionmentioning

confidence: 99%

The 3′-terminal region of bacterial 23S ribosomal RNA: structure and homology with the 3′-terminal region of eukaryotic 28S rRNA and with chloroplast 4.5S rRNA

1981

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The sequence of the 110 nucleotide fragment located at the 3'-end of E.coli, P.vuZgaiz and A.puncata 23S rRNAs has been determined. The homology between the E.coti and P.vutga&ii6 fragments is 90%, whereas that between the E.coti and A.punctata fragments is only 60%. The three rRNA fragments have sequences compatible with a secondary structure consisting of two hairpins. Using chemical and enzymatic methods recently developed for the study of the secondary structure of RNA, we demonstrated that one of these hairpins and part of the other are actually present in the three 3'-terminal fragments in solution. This supports the existence of these two hairpins in the intact molecule. Indeed, results obtained upon limited digestion of intact 23S RNA with T1 RNasewere in good agreement with the existence of these two hairpins.We observed that the primary structures of the 3'-terminal regions of yea6t 26S rRNA and X.&aeviZ 28S rRNA are both compatible with a secondary structure similar to that found at the 3'-end of bacterial 23S rRNAs. Furthermore, both tobacco and wheW chloroplast 4.5S rRNAs can also be folded in a similar way as the 3'-terminal region of bacterial 23S rRNA , the 3'-end of chloroplast 4.5S rRNAs being complementary to the 5'-end of chloroplast 23S rRNA. This strongly reinforces the hypothesis that chloroplast 4.5S rRNA originates from the 3'-end of bacterial 23S rRNA and suggests that this rRNA may be base-paired with the 5'-end of chloroplast 23S rRNA. Invariant oligonucleotides are present at identical positions in the homologous secondary structures of E.Cofi 23S, yea6t 26S , X.Ztaevi 28S and Whew and tobacco 4.5S rRNAs. Surprisingly, the sequences of these oligonucleotides are not all conserved in the 3'-terminal regions of A.putctata or even P.Vuwga&lZ 23S rRNAs. Results obtained upon mild methylation of E.colL 50S subunits with dimethylsulfate strongly suggest that these invariant oligonucleotides are involved in RNA tertiary structure or in RNA-protein interactions.

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The transcription termination site of the ribosomal RNA operon in yeast

Cited by 72 publications

References 22 publications

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

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

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

The 3′-terminal region of bacterial 23S ribosomal RNA: structure and homology with the 3′-terminal region of eukaryotic 28S rRNA and with chloroplast 4.5S rRNA

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