Tandemly arranged variant 5S ribosomal RNA genes In the yeast<i>Saccharomyces cerevisiae</i>

McMahon, Michael E.; Stamenkovich, Dorothy; Petes, Thomas D.

doi:10.1093/nar/12.21.8001

Cited by 28 publications

(16 citation statements)

References 22 publications

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“…The bent character of the 5S rDNA that rotationally phases NCPs (ref. 22 and this work) has been described (23). In conclusion, sequenceintrinsic and supercoil-induced curvatures attract and helically orient NCPs.…”

supporting

confidence: 52%

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Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo.

Buttinelli¹,

Mauro²,

Negri³

1993

Proc. Natl. Acad. Sci. U.S.A.

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A simple no-background assay was developed for high-resolution in vivo analysis of yeast chromatin. When applied to Saccharomyces cerevisiae SS rRNA genes (SS rDNA), this analysis shows that nucleosomes completely cover this chromosomal region, occupying alternative positions characterized by a unique helical phase. This supports the notion that sequence-intrinsic rotational signals are the major determinant of nucleosome localization. Nucleosomal core particles reconstituted in vito occupy the same positions and have the same helically phased distribution observed in vivo, as determined by mapping of exonuclease rn-resistant borders, mapping by restriction cleavages, and by DNase I and hydroxyl-radical digestion patterns.Nucleosomes have long been considered as general repressors of chromatin function. Their active role in transcription is now emerging (1), possibly related to functions of topological organization of chromatin in promoter regions (2). Therefore, understanding the rules that govern localization and stability of nucleosomes is of major relevance.The specific location of a nucleosomal core particle (NCP) on DNA is attained through the interaction of the histone proteins with an ensemble of rotational and translational signals intrinsic to the DNA sequence (3, 4). The relative contribution of these parameters and the function of other factors (boundary or domain effects, ancillary proteins, cooperativity, etc.; refs. 5 and 6) are open problems.Rotational phases on DNA are determined by a repetition of bendability signals due to particular combinations of base pairs (7,8). These sequence elements repeat themselves with the same periodicity as the DNA helical repeat, define a permissive rotational phase, and favor the deposition of a NCP onto a defined side of the double strand. DNA sequences with strong rotational signals are expected to favor occupancy by multiple, helically phased NCPs. In contrast, translational signals would favor unique occupancies. Examples of specific nucleosome positioning sequences are known, both in vitro (9-11) and in vivo (refs. 12-14; reviewed in ref. 15). The nature of the translational signals for nucleosome positioning remains elusive.We report that on Saccharomyces cerevisiae 5S repeat genes in vivo, nucleosomes occupy multiple, helically phased positions. This finding supports the notion that at least for these genes the rotational information is the major determinant for NCP localization, both in vitro and in vivo. It also implies that each individual NCP can choose among several quasi-isoenergetic positions (a phenomenon that may have important biological implications). The fact that the same multiplicity of positions, coupled with uniqueness of rotational phase, can be detected in vivo implies that genes exist on which nucleosomes form on multiple positions and/or enjoy facilitated rotational displacements.The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in a...

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supporting

confidence: 52%

“…Four evenly distributed cleavage sites map on the 5S fragment ( Fig. 1D) (22). Uniformly labeled DNA c was reconstituted and the monomeric complex was digested with MN.…”

mentioning

confidence: 99%

Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo.

Buttinelli¹,

Mauro²,

Negri³

1993

Proc. Natl. Acad. Sci. U.S.A.

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“…Sequence analysis determined a match with the EcoRI B fragment of the rDNA repeat that includes the 5 S rRNA gene and the nontranscribed spacer region ( JEMTLAND et al 1986). Our restriction map of pFS22 is identical to published maps of the yeast ribosomal RNA gene (MCMAHON et al 1984;JEMTLAND et al 1986) (Figure 2). Analysis of rDNA: :LEU2 and rDNA::URA3 integrative recombinant mutants Complementation of m j 9 -l by the 5 S rRNA gene suggested that mop-1 might be a mutation of the rDNA.…”

Section: Methodssupporting

confidence: 84%

5S rRNA is involved in fidelity of translational reading frame

1996

Trends in Genetics

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Chromosomal mutants (maintenance of frame = mof) in which the efficiency of -1 ribosomal frameshifting is increased can be isolated using constructs in which lacZ expression is dependent upon a -1 shift of reading frame. We isolate a new mof mutation, mop, in Saccharomyces cereuisiae and show that it is complemented by both single and multi-copy 5 S rDNA clones. Two independent insertion mutations in the rDNA locus (rDNA::LEUZ and rDNA::URA3) also display the Mof-phenotype and are also complemented by single and multicopy 5 S rDNA clones. Mutant 5 S rRNAs expressed from a plasmid as 20-50% of total 5 S rRNA in a wild-type host also induced the Mof-phenotype. The increase in frameshifting is greatest when the lac2 reporter gene is expressed on a high copy, episomal vector. No differences were found in 5 S rRNA copy number or electrophoretic mobilities in mopstrains. Both m o p and rDNA::LEUZincrease the efficiency of +1 frameshifting as well but have no effect on readthrough of UAG or UAA termination codons, indicating that not all translational specificity is affected. These data suggest a role for 5 S rRNA in the maintenance of frame in translation.A LTHOUGH correct maintenance of frame is critical to ribosome function, a growing number of cases of directed alterations in translational reading frame have been identified, mostly in viruses (e.g., retroviruses, coronaviruses BAUGH 1993). The study of these ribosomal frameshifts is important both because of their critical role in animal and plant pathogens and because of the information they provide about the mechanisms by which reading frame is normally maintained.Ribosomal frameshifting in the -1 direction in retroviruses, (+) sRNA viruses and dsRNA viruses generally requires a special sequence, X XXY W Z (the 0-frame is indicated by spaces) called the "slippery site" (JACKS et al. 1988). Here the simultaneous slippage of ribosome-bound A-and P-site tRNAs by one base in the 5' direction still leaves their nonwobble bases correctly paired in the new reading frame. A second promoting element (JACKS et al. 1988), usually an RNA pseudoknot, is located immediately 3' to the slippery site (BRIERLEY et , TEN DAM et al. 1992. The RNA pseudoknot makes the ribosome pause over the slippery site (TU et al. 1992, SOMOCYI et al. 1993, increasing the probability of 5' ribosomal movement. The efficiency of -1 ribosomal frameshifting can be affected by the ability of the ribosome-bound tRNAs (especially the Asite tRNA) to un-pair from the 0-frame (DINMAN et al. , BRIERLEY et al. 1992, the ability of these tRNAs to re-pair to the -1 frame (JACKS et al. 1988), and the relative position of the RNA pseudoknot from the slippery site and its thermodynamic stability (BRIERLEY et al. 1989,1991; DINMAN and WICKNER 1992). The efficiency of -1 ribosomal frameshifting can also be affected by mutations in cellular gene products that presumably interact with these tRNA and mRNA factors WICKNER 1992, 1994). Changes in any of these components can be observed as changes in the effici...

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“…shown), indicating the PSE-like sequence and at least one _-U6 RNA repeat are dispensable. The last 6 bp of the third direct repeat are also found immediately upstream of the initiation site of both the repeated and variant yeast 5S rRNA genes (45,53), but substitution of this hexamer (In-sub, Fig. 6A) also had no effect on transcription in vitro or in vivo (data PS wnot shown).…”

Section: Resultsmentioning

confidence: 97%

Architecture of a yeast U6 RNA gene promoter.

Eschenlauer¹,

Kaiser²,

Gerlach³

et al. 1993

Mol. Cell. Biol.

131

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actions responsible for the presumptive positioning of TF-IIIB upstream of vertebrate U6 RNA genes are unknown. The absence of A-and B-block promoter elements argues against the involvement of TFIIIC. The surprising discovery that in vitro transcription of vertebrate U6 genes requires the TATA-binding protein (TBP) subunit of RNAPII initiation factor TFIID (38, 51) and an RNAPII factor that stabilizes TBP binding to the TATA box, TFIIA (55), raises the possibility that TFIIIB is positioned by TBP and associated proteins bound to the vertebrate U6 gene TATA box.We have previously isolated the U6 RNA gene, SNR6, from the yeast Saccharomyces cerevisiae and found that unlike vertebrate U6 genes, it contains an essential B-block promoter element (7). The SNR6 B block is in a unique position, downstream of the coding region (see Fig. 1). A candidate A-block element in the conventional intragenic position was also identified, and it was suggested that the yeast U6 RNA gene binds TFIIIB by the same TFIIICdependent mechanism used by tRNA genes (7). However, the yeast U6 gene has upstream sequences similar to the vertebrate U6 gene TATA box and PSE (6)

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Tandemly arranged variant 5S ribosomal RNA genes In the yeastSaccharomyces cerevisiae

Abstract: Most of the ribosomal R-NA genes of the yeast Saccharomyces cerevisiae are about 9 kilobases (kb) in size and encode both the 35S rRNA (processed to produce the 25S, 18S, and 5.8S species) and 5S rRNA. These genes are arranged in a single tandem

Cited by 28 publications

References 22 publications

Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo.

Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo.

5S rRNA is involved in fidelity of translational reading frame

Architecture of a yeast U6 RNA gene promoter.

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