Transcription of the ‘non-transcribed’ spacer of<i>Drosophila melanogaster</i>rDNA

Miller, J. Ross; Hayward, David C.; Glover, David M.

doi:10.1093/nar/11.1.11

Cited by 80 publications

(55 citation statements)

References 17 publications

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“…Kohorn and Rae (18) reported that the NTS of Drosophila rDNA contained several repeats of imperfect copies of the promoter region. Miller et al (29) suggested that the role of these repeats is to facilitate initiation and provide a selective advantage to the downstream promoter.…”

Section: Resultsmentioning

confidence: 99%

Additional RNA polymerase I initiation site within the nontranscribed spacer region of the rat rRNA gene.

Cassidy¹,

Yang-Yen²,

Rothblum³

1987

Mol. Cell. Biol.

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We identified and characterized an additional promoter within the nontranscribed spacer (NTS) of the rat ribosomal gene repeat that is capable of supporting initiation of transcription by RNA polymerase I in vitro. Within this promoter there is a sequence of 13 nucleotides which is 100% homologous to nucleotides -18 to -6 (+1 being the frst nucleotide of 45S rRNA) of the major promoter of 45S pre-rRNA and is located between nucleotides -731 and -719. To identify the exact location of the upstream initiation site, the RNA synthesized in vitro from this new promoter was gel isolated and subjected to fingerprint analysis, Southern hybridization, and reverse transcriptase elongation. Based on these analyses, the in vitro-synthesized RNA initiates with an A at nucleotide -713. When compared individually, the upstream promoter was transcribed ninefold less efficiently than the major promoter. When templates which contain both promoters on the same piece of DNA were transcribed, the major promoter was at least 50-fold more efficient.Eucaryotic ribosomal genes are arranged as tandemly repeating units. The transcription units that code for the RNA precursor are flanked by the nontranscribed spacer (NTS) regions. The transcribed portion of the repeat consists of an external transcribed spacer, the region that codes for 18S rRNA, an internal transcribed spacer, the 5.8S coding region, a second internal transcribed spacer, the region that codes for 28S rRNA, and a short 3' external transcribed spacer (23).Besides functioning to direct and regulate transcription, the NTS has been both proposed and shown to have roles in recombination (39), DNA replication (37), and chromatin structure (8).By far the greatest number of studies on the NTS have focused on its role in transcription. The DNA sequences immediately upstream of the rRNA transcription initiation site have been intensively studied by several laboratories. A core promoter region, located between nucleotides -39 and +6, has been identified, and specific nucleotides within this region have been shown to be required for initiation (11, 18, 2,, 25, 38, 43, 47). A second region, the upstream control element or upstream promoter element (between nucleotides 150 and -110), has been demonstrated to stabilize effectively the preinitiation complex (15,19,30,44,45; B. G. Cassidy, R. Haglund, and L. I. Rothblum, Biochim. Biophys. Acta, in press).In yeasts and Xenopus laevis, regions several hundred to several thousand nucleotides upstream of the 5' end of the ribosomal precursor have been shown to have profound effects on promoter utilization and the efficiency of transcription. In yeasts, a polymerase I promoter (42) or enhancer element (9) has an effect on the transcription of the 35S rRNA precursor (10). Two promoter-related elements present in multiple copies in the NTS of X. laevis have also been identified (reviewed in references 7 and 34). These elements, the Bam islands and the 60-or 81-base-pair (60/81-bp) repeats, affect the utilization of the polymerase I promoter and ...

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Section: Resultsmentioning

confidence: 99%

Additional RNA polymerase I initiation site within the nontranscribed spacer region of the rat rRNA gene.

Cassidy¹,

Yang-Yen²,

Rothblum³

1987

Mol. Cell. Biol.

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“…Furthermore, in X.laevis it has been observed that these promoter duplications can give rise to short spacer transcripts (19). In Drosophila also, promoter duplications give rise to spacer transcripts (20)(21)(22)(23).…”

Section: Discussionmentioning

confidence: 99%

The origin of the rRNA precursor fromXenopus borealis, analysedin vivoandin vitro

McStay

Bird

1983

Nucl Acids Res

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We have determined the origin of the major transcript of Xenopus borealis rDNA by the use of an SI nuclease protection assay. The DNA surrounding the origin of this transcript was sequenced, and the region upstream of the origin was shown to have strong sequence homology with that region from X.laevis rDNA. We have also demonstrated faithful transcription from this origin using cloned X.borealis rDNA in an extract derived from X.laevis culture cells. This in vitro transcription was insensitive to lOO1g/ml a-amanatin, suggesting that it was mediated by RNA polymerase 1. INTRODUCTIONThe genes for the large ribosomal RNA's (rRNA) of the genus

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“…The 240-bp repeat in D. melanogaster contains a partial copy of the promoter sequences associated with transcription of the rDNA unit (Kohorn and Rae 1983;Miller et al 1983). However, sequence conservation of this repeat was not higher than most other noncoding sequences of the rDNA unit (Fig.…”

Section: Comparison Of the Consensus Rdna Unit Among Speciesmentioning

confidence: 99%

Sequence variation within the rRNA gene loci of 12 Drosophila species

Stage¹,

Eickbush²

2007

Genome Res.

116

127

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Concerted evolution maintains at near identity the hundreds of tandemly arrayed ribosomal RNA (rRNA) genes and their spacers present in any eukaryote. Few comprehensive attempts have been made to directly measure the identity between the rDNA units. We used the original sequencing reads (trace archives) available through the whole-genome shotgun sequencing projects of 12 Drosophila species to locate the sequence variants within the 7.8-8.2 kb transcribed portions of the rDNA units. Three to 18 variants were identified in >3% of the total rDNA units from 11 species. Species where the rDNA units are present on multiple chromosomes exhibited only minor increases in sequence variation. Variants were 10-20 times more abundant in the noncoding compared with the coding regions of the rDNA unit. Within the coding regions, variants were three to eight times more abundant in the expansion compared with the conserved core regions. The distribution of variants was largely consistent with models of concerted evolution in which there is uniform recombination across the transcribed portion of the unit with the frequency of standing variants dependent upon the selection pressure to preserve that sequence. However, the 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster. We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.

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Transcription of the ‘non-transcribed’ spacer ofDrosophila melanogasterrDNA

Cited by 80 publications

References 17 publications

Additional RNA polymerase I initiation site within the nontranscribed spacer region of the rat rRNA gene.

Additional RNA polymerase I initiation site within the nontranscribed spacer region of the rat rRNA gene.

The origin of the rRNA precursor fromXenopus borealis, analysedin vivoandin vitro

Sequence variation within the rRNA gene loci of 12 Drosophila species

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