scholarly journals Base Pairing between U3 Small Nucleolar RNA and the 5′ End of 18S rRNA Is Required for Pre-rRNA Processing

1999 ◽  
Vol 19 (9) ◽  
pp. 6012-6019 ◽  
Author(s):  
Kishor Sharma ◽  
David Tollervey
Keyword(s):  
18S Rrna ◽  
Homologous Region ◽  
Compensatory Mutation ◽  
Loop Structure ◽  
Rrna Processing ◽  
Base Pairing ◽  
Small Nucleolar Rna ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
Nucleolar Rna

ABSTRACT The loop of a stem structure close to the 5′ end of the 18S rRNA is complementary to the box A region of the U3 small nucleolar RNA (snoRNA). Substitution of the 18S loop nucleotides inhibited pre-rRNA cleavage at site A1, the 5′ end of the 18S rRNA, and at site A2, located 1.9 kb away in internal transcribed spacer 1. This inhibition was largely suppressed by a compensatory mutation in U3, demonstrating functional base pairing. The U3–pre-rRNA base pairing is incompatible with the structure that forms in the mature 18S rRNA and may prevent premature folding of the pre-rRNA. In theEscherichia coli pre-rRNA the homologous region of the 16S rRNA is also sequestered, in that case by base pairing to the 5′ external transcribed spacer (5′ ETS). Cleavage at site A0in the yeast 5′ ETS strictly requires base pairing between U3 and a sequence within the 5′ ETS. In contrast, the U3-18S interaction is not required for A0 cleavage. U3 therefore carries out at least two functionally distinct base pair interactions with the pre-rRNA. The nucleotide at the site of A1 cleavage was shown to be specified by two distinct signals; one of these is the stem-loop structure within the 18S rRNA. However, in contrast to the efficiency of cleavage, the position of A1 cleavage is not dependent on the U3-loop interaction. We conclude that the 18S stem-loop structure is recognized at least twice during pre-rRNA processing.

scholarly journals The rRNA-processing function of the yeast U14 small nucleolar RNA can be rescued by a conserved RNA helicase-like protein.

1997 ◽  
Vol 17 (7) ◽  
pp. 4124-4132 ◽  
Author(s):  
W Q Liang ◽  
J A Clark ◽  
M J Fournier
Keyword(s):  
Mutational Analysis ◽  
Rna Helicase ◽  
Suppressor Gene ◽  
Rrna Processing ◽  
Base Pairing ◽  
Small Nucleolar Rna ◽  
Stem Loop ◽  
Dead Box ◽  
Extragenic Suppressor ◽  
Nucleolar Rna

The phylogenetically conserved U14 small nucleolar RNA is required for processing of rRNA, and this function involves base pairing with conserved complementary sequences in 18S RNA. With a view to identifying other important U14 interactions, a stem-loop domain required for activity of Saccharomyces cerevisiae U14 RNAs (the Y domain) was first subjected to detailed mutational analysis. The mapping results showed that most nucleotides of the Y domain can be replaced without affecting function, except for loop nucleotides conserved among five different yeast species. Defective variants were then used to identify both intragenic and extragenic suppressor mutations. All of the intragenic mutations mapped within six nucleotides of the primary mutation, suggesting that suppression involves a change in conformation and that the loop element is involved in an essential intermolecular interaction rather than intramolecular base pairing. A high-copy extragenic suppressor gene, designated DBP4 (DEAD box protein 4), encodes an essential, putative RNA helicase of the DEAD-DEXH box family. Suppression by DBP4 (initially CA4 [T.-H. Chang, J. Arenas, and J. Abelson, Proc. Natl. Acad. Sci. USA 87:1571-1575, 1990]) restores the level of 18S rRNA and is specific for the Y domain but is not allele specific. DBP4 is predicted to function either in assembly of the U14 small nucleolar RNP or, more likely, in its interaction with other components of the rRNA processing apparatus. Mediating the interaction of U14 with precursor 18S RNA is an especially attractive possibility.

A small predicted stem-loop structure mediates oocyte localization of Drosophila K10 mRNA

Development ◽  
1995 ◽  
Vol 121 (11) ◽  
pp. 3809-3818 ◽  
Author(s):  
T.L. Serano ◽  
R.S. Cohen
Keyword(s):  
Late Stage ◽  
Untranslated Region ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Loop Structure ◽  
Base Pairing ◽  
Mrna Transport ◽  
Nucleotide Substitutions ◽  
Stem Loop ◽  
Stem Loop Structure

The establishment of dorsoventral polarity in the Drosophila oocyte and future embryo is dependent on the efficient transport of K10 mRNA from nurse cells into the oocyte. To investigate the cis-requirements of K10 mRNA transport, we used a transgenic fly assay to analyze the expression patterns of a series of K10 deletion variants. Such studies identify a 44 nucleotide sequence within the K10 3′ untranslated region that is required and sufficient for K10 mRNA transport and subsequent localization to the oocyte's anterior cortex. An inspection of the 44 nucleotide transport/localization sequence (TLS) reveals a strong potential for the formation of a stem-loop secondary structure. Nucleotide substitutions that interfere with the predicted base-pairing of the TLS block mRNA transport and anterior localization. Conversely, mutations that alter the base composition of the TLS while maintaining predicted base-pairing do not block mRNA transport or anterior localization. We conclude that K10 mRNA transport and anterior localization is mediated by a 44 nucleotide stem-loop structure. A similar putative stem-loop structure is found in the 3′ untranslated region of the Drosophila orb mRNA, suggesting that the same factors mediate the transport and anterior localization of both K10 and orb mRNAs. Apart from orb, the K10 TLS is not found in any other localized mRNA, raising the possibility that the transport and localization of other mRNAs, e.g., bicoid, oskar and gurken, are mediated by novel sets of cis- and trans-acting factors. Moreover, we find that the K10 TLS overrides the activity of oskar cis-regulatory elements that mediate the late stage movement of the mRNA to the posterior pole. We propose the existence of a family of cis-regulatory elements that mediate mRNA transport into the oocyte, only some of which are compatible with the elements that mediate late stage movements.

scholarly journals Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis.

1993 ◽  
Vol 13 (4) ◽  
pp. 2469-2477 ◽  
Author(s):  
J P Morrissey ◽  
D Tollervey
Keyword(s):  
18S Rrna ◽  
Progressive Increase ◽  
Rrna Synthesis ◽  
Rrna Processing ◽  
Small Nucleolar Rna ◽  
Conditional Allele ◽  
Cell Doubling Time ◽  
Associated Proteins ◽  
Nucleolar Rna

Subnuclear fractionation and coprecipitation by antibodies against the nucleolar protein NOP1 demonstrate that the essential Saccharomyces cerevisiae RNA snR30 is localized to the nucleolus. By using aminomethyl trimethyl-psoralen, snR30 can be cross-linked in vivo to 35S pre-rRNA. To determine whether snR30 has a role in rRNA processing, a conditional allele was constructed by replacing the authentic SNR30 promoter with the GAL10 promoter. Repression of snR30 synthesis results in a rapid depletion of snR30 and a progressive increase in cell doubling time. rRNA processing is disrupted during the depletion of snR30; mature 18S rRNA and its 20S precursor underaccumulate, and an aberrant 23S pre-rRNA intermediate can be detected. Initial results indicate that this 23S pre-rRNA is the same as the species detected on depletion of the small nucleolar RNA-associated proteins NOP1 and GAR1 and in an snr10 mutant strain. It was found that the 3' end of 23S pre-rRNA is located in the 3' region of ITS1 between cleavage sites A2 and B1 and not, as previously suggested, at the B1 site, snR30 is the fourth small nucleolar RNA shown to play a role in rRNA processing.

Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis

1993 ◽  
Vol 13 (4) ◽  
pp. 2469-2477
Author(s):  
J P Morrissey ◽  
D Tollervey
Keyword(s):  
18S Rrna ◽  
Progressive Increase ◽  
Rrna Synthesis ◽  
Rrna Processing ◽  
Small Nucleolar Rna ◽  
Conditional Allele ◽  
Cell Doubling Time ◽  
Associated Proteins ◽  
Nucleolar Rna

Subnuclear fractionation and coprecipitation by antibodies against the nucleolar protein NOP1 demonstrate that the essential Saccharomyces cerevisiae RNA snR30 is localized to the nucleolus. By using aminomethyl trimethyl-psoralen, snR30 can be cross-linked in vivo to 35S pre-rRNA. To determine whether snR30 has a role in rRNA processing, a conditional allele was constructed by replacing the authentic SNR30 promoter with the GAL10 promoter. Repression of snR30 synthesis results in a rapid depletion of snR30 and a progressive increase in cell doubling time. rRNA processing is disrupted during the depletion of snR30; mature 18S rRNA and its 20S precursor underaccumulate, and an aberrant 23S pre-rRNA intermediate can be detected. Initial results indicate that this 23S pre-rRNA is the same as the species detected on depletion of the small nucleolar RNA-associated proteins NOP1 and GAR1 and in an snr10 mutant strain. It was found that the 3' end of 23S pre-rRNA is located in the 3' region of ITS1 between cleavage sites A2 and B1 and not, as previously suggested, at the B1 site, snR30 is the fourth small nucleolar RNA shown to play a role in rRNA processing.

scholarly journals Box H and Box ACA Are Nucleolar Localization Elements of U17 Small Nucleolar RNA

1999 ◽  
Vol 10 (11) ◽  
pp. 3877-3890 ◽  
Author(s):  
Thilo Sascha Lange ◽  
Michael Ezrokhi ◽  
Francesco Amaldi ◽  
Susan A. Gerbi
Keyword(s):  
Adverse Effect ◽  
Fluorescence Microscopy ◽  
Nucleolar Localization ◽  
Rrna Processing ◽  
Base Pairing ◽  
Small Nucleolar Rna ◽  
Family Function ◽  
Tail Structure ◽  
Localization Elements ◽  
Nucleolar Rna

The nucleolar localization elements (NoLEs) of U17 small nucleolar RNA (snoRNA), which is essential for rRNA processing and belongs to the box H/ACA snoRNA family, were analyzed by fluorescence microscopy. Injection of mutant U17 transcripts into Xenopus laevisoocyte nuclei revealed that deletion of stems 1, 2, and 4 of U17 snoRNA reduced but did not prevent nucleolar localization. The deletion of stem 3 had no adverse effect. Therefore, the hairpins of the hairpin–hinge–hairpin–tail structure formed by these stems are not absolutely critical for nucleolar localization of U17, nor are sequences within stems 1, 3, and 4, which may tether U17 to the rRNA precursor by base pairing. In contrast, box H and box ACA are major NoLEs; their combined substitution or deletion abolished nucleolar localization of U17 snoRNA. Mutation of just box H or just the box ACA region alone did not fully abolish the nucleolar localization of U17. This indicates that the NoLEs of the box H/ACA snoRNA family function differently from the bipartite NoLEs (conserved boxes C and D) of box C/D snoRNAs, where mutation of either box alone prevents nucleolar localization.

968: Gelsolin Gene Silencing Involving Unusual Chromatin Structures and a Novel Stem Loop Structure of the Promoter Region in Human Bladder Cancer

2004 ◽  
Vol 171 (4S) ◽  
pp. 256-257
Author(s):  
Kazunori Haga ◽  
Ataru Sazawa ◽  
Toru Harabayashi ◽  
Nobuo Shinohara ◽  
Minoru Nomoto ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Gene Silencing ◽  
Promoter Region ◽  
Loop Structure ◽  
Human Bladder Cancer ◽  
Human Bladder ◽  
Stem Loop ◽  
Stem Loop Structure

Detection and sequence analysis of an imperfect stem-loop structure in cis activating gene element from SV40PolyA

2011 ◽  
Vol 33 (4) ◽  
pp. 337-346
Author(s):  
Hong-Gang WANG ◽  
Huan MA ◽  
Zhu LI ◽  
Bin ZHANG ◽  
Xiang-Yang JING ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
In Cis ◽  
Gene Element

scholarly journals Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

2021 ◽  
Vol 14 (2) ◽  
pp. 121
Author(s):  
André Miranda ◽  
Tiago Santos ◽  
Eric Largy ◽  
Carla Cruz
Keyword(s):  
Loop Structure ◽  
Binding Properties ◽  
Stem Loop ◽  
Affinity Ligand ◽  
Stem Loop Structure ◽  
Topology Maintenance ◽  
G Quadruplex ◽  
Dimeric Form ◽  
Biophysical Techniques ◽  
Melting Experiments

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.

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