Conserved 5′ flank homologies in dipteran 5S RNA genes that would function on ‘A’ form DNA

Rubacha, Alice; Sumner, Walton; Richter, Lizabeth J.; Beckingham, Kathy

doi:10.1093/nar/12.21.8193

Cited by 23 publications

(14 citation statements)

References 47 publications

(17 reference statements)

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“…The present results reveal that the functional sequence determinants in the 5'-flanking sequence are within the TMR. The effect of TMR mutations on the position of the transcription initiation site suggests a direct interaction between the TMR and RNA polymerase III, consistent with the suggestion that the structural conformation of the 5'-flanking region may be important to correctly orient RNA polymerase III to the initiation site (33,44). The lack of strict sequence similarity in the tDNA TMR, however, combined with the mechanism of tRNA gene transcription, in which specific transcription by RNA polymerase III is dependent upon the prior binding of transcription factors, suggests that RNA polymerase III does not require specific recognition sequences for binding as, for example, is the case for procaryotic RNA polymerases.…”

Section: Tm9supporting

confidence: 79%

“…Interaction of trans-acting transcription factors with the 5'-flanking region of some tRNA genes may serve special regulatory functions. Limited sets of 5'-flanking sequence similarities (28,33) and two specific negative controlling sequence elements have been identified in some tRNA gene families (12,21). In general, however, the 5'-flanking sequences of tRNA genes show little similarity or homology between members of the same or different tRNA gene families (40).…”

Section: Tm9mentioning

confidence: 99%

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A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes.

1988

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We have studied the mechanism by which 5'-flanking sequences modulate the in vitro transcription of eucaryotic tRNA genes. Using deletion and linker substitution mutagenesis, we have found that the 5'-flanking sequences responsible for the different in vitro transcription levels of three Drosophila tRNA5.' genes are contained within a discrete region centered 22 nucleotides upstream from the transcription initiation site. In conjunction with the A-box intragenic control region, this upstream transcription-modulatory region functions in the selection mechanism for the site of transcription initiation. Since the transcription-modulatory region directs the position of the start site and the actual sequence of the transcription-modulatory region determines the level of tRNAAsn gene transcription, the possibility is raised that the transcription-modulatory region directs a transcription initiation event similar to open complex formation at procaryotic promoters.In procaryotic organisms, initiation of RNA synthesis is controlled by small, conserved DNA sequences located 10 and 35 nucleotides upstream of the transcription initiation site. RNA polymerase holoenzyme recognizes and binds these regions in this first step of the pathway that leads to open-complex formation and transcriptional activation (5, 42). The three nuclear RNA polymerases of eucaryotes do not recognize promoters efficiently and, as a result, are unable to independently initiate gene-specific transcription (for a review, see reference 38). Instead, eucaryotic transcription is dependent upon promoter-specific transcription factors that recognize and bind discrete sequence elements. Current models suggest that the binding of these protein factors activates transcription by allowing each gene to be recognized by the appropriate polymerase. For RNA polymerases I and II, the known sites of transcription factor interaction are 5' of the site of transcription initiation (9,15,45). For RNA polymerase III-directed transcription of eucaryotic 5S RNA, tRNA and adenovirus VA RNA genes, the sites of transcription factor interaction are 3' of the transcription initiation site, within the sequences encoding the RNA (6,16,17,48,50). RNA polymerase III-directed transcription of 7SL RNA, 7SK RNA, and U6 RNA genes requires enhancerlike sequence elements for transcription factor interaction 5' of the transcription initiation site, similar to RNA polymerase II promoters (3,7,30,47).The intragenic control regions (ICRs) in tRNA genes, the A-and B-box ICRs, contain the DNA sequence determinants that direct transcription factor activities (reviewed in reference 40). For tRNA genes, the transcription factors bind to the gene to form a complex that is stable throughout multiple rounds of transcription initiation (4,23,36). This stable complex, comprised of tRNA gene and transcription factors, is considered to form the recognition substrate for RNA polymerase III.Transcriptional activity of tRNA genes is particularly sensitive to mutations in the A-and B-box ICRs. All of the po...

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Section: Tm9supporting

confidence: 79%

Section: Tm9mentioning

confidence: 99%

A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes.

1988

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“…For this reason, we began a study of the 5S genes from several of the species most closely related to D. melanogaster. Sequences of several 5S gene units from D. melanogaster, D. simulans, and D. teissieri are already known (Tschudi and Pirrotta 1980;Samson and Wegnez 1984;Sharp et al 1984;Samson and Wegnez 1988), as is the sequence of one 5S unit of Calliphora erythrocephala, another dipteran species (Rubacha et al 1984). We report in this paper the sequence of eleven 5S genes from D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii. Comparison of all Drosophila 5S gene sequences reveals some features of their mode of evolution.…”

Section: Introductionmentioning

confidence: 99%

Structural evolution of the Drosophila 5S ribosomal genes

Pâques

Jordan

et al. 1995

J Mol Evol

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We compare the 5S gene structure from nine Drosophila species. New sequence data (5S genes of D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii) and already-published data (5S genes of D. melanogaster, D. simulans, and D. teissieri) are used in these comparisons. We show that four regions within the Drosophila 5S genes display distinct rates of evolution: the coding region (120 bp), the 5'-flanking region (54-55 bp), the 3'-flanking region (21-22 bp), and the internal spacer (149-206 bp). Intra- and interspecific heterogeneity is due mainly to insertions and deletions of 6-17-bp oligomers. These small rearrangements could be generated by fork slippages during replication and could produce rapid sequence divergence in a limited number of steps.

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“…The -30 region sequence motif is conserved in sequence and position in four dipteran 5S RNA genes (16). A similar six-of-eight sequence is present in a transcriptionally active mouse 5S RNA gene at position -42, but not in an inactive human 5S RNA gene (4).…”

mentioning

confidence: 99%

Formation of an active transcription complex in the Drosophila melanogaster 5S RNA gene is dependent on an upstream region.

García¹,

O'Connell²,

Sharp³

1987

Mol. Cell. Biol.

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We constructed deletion-substitution and linker-scanning mutations in the 5'-flanking region of the Drosophila melanogaster 5S RNA gene. In vitro transcription of these templates in Drosophila and HeLa cell extracts revealed the presence of an essential control region (-30 region) located between nucleotides -39 and -26 upstream of the transcription initiation site: deletion of sequences upstream of nucleotide position -39 had no detectable effect on the wild-type level of in vitro transcription, whereas mutations extending between positions -39 and 1 resulted in templates with decreased transcriptional levels; specifically, deletion and linker-scanning mutations in the -34 to -26 region (-30 region) resulted in loss of transcription. The -30 region is essential for transcription and therefore forms part of the Drosophila 5S RNA gene transcription promoter. Compared with the activity of the wild-type gene, mutant 5S DNAs exhibited no impairment in the ability to sequester limiting transcription factors in a template exclusion competition assay. While we do not know which transcription factor(s) interacts with the -30 region, the possible involvement of RNA polymerase Ill at this region is discussed.Transcription of genes by RNA polymerase III is controlled by sequences within the region encoding the RNA. As first proposed by Sakonju et al. (17), these regions were defined as "control regions" rather than as "promoters," because evidence was not available that RNA polymerase III recognizes and binds to these sequences. Xenopus laevis 5S RNA gene transcription requires three transcription factor activities (TFIIIA, TFIIIB, and TFIIIC) as well as RNA polymerase III (19). TFIIIA is a positive transcription factor that binds to the defined internal control region (5, 23). The interaction of TFIIIC, TFIIIA, and SS DNA forms a stable complex, referred to as stable complex I, directed by the internal control region which is sequestered into the stable transcription complex by interaction with TFIIIB (1). The current model for class III gene transcription is that RNA polymerase III recognizes this stable complex and initiates transcription (1,3,20). Since the recognition sequences for transcription factors are downstream from the site of initiation, it is conceivable that RNA polymerase III itself interacts in the 5'-flanking region of 5S DNA.Transposon-directed (Tn9) deletion mutants of X. laevis 5S DNA failed to reveal essential control sequences upstream of the 49-nucleotide nonrepetitive sequence immediately adjacent to the 5' terminus of the gene (6). Furthermore, extensive computer analysis of sequences preceding several 5S RNA genes revealed several common features (9) the deletion of which, while reducing transcription, did not result in loss of transcription (17). The transcription efficiency of Bombyx mori 5S DNA was, however, reduced to 5% of the level of wild-type transcription upon deletion of the sequence upstream to coordinate -17 (14). This critical region was shown to have a sequence similar to the 5'-fl...

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Conserved 5′ flank homologies in dipteran 5S RNA genes that would function on ‘A’ form DNA

Cited by 23 publications

References 47 publications

A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes.

A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes.

Structural evolution of the Drosophila 5S ribosomal genes

Formation of an active transcription complex in the Drosophila melanogaster 5S RNA gene is dependent on an upstream region.

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