Functional Base-pairing Interaction Between Highly Conserved Elements of U3 Small Nucleolar RNA and the Small Ribosomal Subunit RNA

We have found that intron 11 of the nucleolin gene in humans and rodents encodes a previously unidentified small nucleolar RNA, termed U20. The single-copy U20 sequence is located on the same DNA strand as the nucleolin mRNA. U20 RNA, which does not possess a trimethyl cap, appears to result from intronic RNA processing and not from transcription of an independent gene. In mammals, U20 RNA is an 80-nucleotide-long, metabolically stable species, present at about 7 x 10(3) molecules per exponentially growing HeLa cell. It has a nucleolar localization, as indicated by fluorescence microscopy following in situ hybridization with digoxigenin-labeled oligonucleotides. U20 RNA contains the box C and box D sequence motifs, hallmarks of most small nucleolar RNAs reported to date, and is immunoprecipitated by antifibrillarin antibodies. It also exhibits a 5'-3' terminal stem bracketing the box C-box D motifs like U14, U15, U16, or Y RNA. A U20 homolog of similar size has been detected in all vertebrate classes by Northern (RNA) hybridization with mammalian oligonucleotide probes. U20 RNA contains an extended region (21 nucleotides) of perfect complementarity with a phylogenetically conserved sequence in 18S rRNA. This complementarity is strongly preserved among distant vertebrates, suggesting that U20 RNA may be involved in the formation of the small ribosomal subunit like nucleolin, the product of its host gene.

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

Molecular and Cellular Biology ◽

10.1128/mcb.17.7.4124 ◽

1997 ◽

Vol 17 (7) ◽

pp. 4124-4132 ◽

Cited By ~ 44

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.

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Evidence That Base-pairing Interaction between Intron and mRNA Leader Sequences Inhibits Initiation ofHAC1mRNA Translation in Yeast

Journal of Biological Chemistry ◽

10.1074/jbc.m115.649335 ◽

2015 ◽

Vol 290 (36) ◽

pp. 21821-21832 ◽

Cited By ~ 15

Author(s):

Leena Sathe ◽

Cheryl Bolinger ◽

M. Amin-ul Mannan ◽

Thomas E. Dever ◽

Madhusudan Dey

Keyword(s):

Base Pairing ◽

Pairing Interaction ◽

Base Pairing Interaction

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In vitro characterization of a base pairing interaction between the primer binding site and the minimal packaging signal of avian leukosis virus genomic RNA

Nucleic Acids Research ◽

10.1093/nar/gkg942 ◽

2003 ◽

Vol 31 (24) ◽

pp. 7070-7082 ◽

Cited By ~ 5

Author(s):

I. Kanevsky

Keyword(s):

Binding Site ◽

Primer Binding Site ◽

Genomic Rna ◽

Base Pairing ◽

Pairing Interaction ◽

Packaging Signal ◽

In Vitro Characterization ◽

Base Pairing Interaction

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U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin gene in mammals

Molecular and Cellular Biology ◽

10.1128/mcb.14.9.5766-5776.1994 ◽

1994 ◽

Vol 14 (9) ◽

pp. 5766-5776

Author(s):

M Nicoloso ◽

M Caizergues-Ferrer ◽

B Michot ◽

M C Azum ◽

J P Bachellerie

Keyword(s):

Ribosomal Subunit ◽

Single Copy ◽

Sequence Motifs ◽

Small Nucleolar Rna ◽

Conserved Sequence ◽

Stable Species ◽

Perfect Complementarity ◽

Dna Strand ◽

Nucleolar Rna

We have found that intron 11 of the nucleolin gene in humans and rodents encodes a previously unidentified small nucleolar RNA, termed U20. The single-copy U20 sequence is located on the same DNA strand as the nucleolin mRNA. U20 RNA, which does not possess a trimethyl cap, appears to result from intronic RNA processing and not from transcription of an independent gene. In mammals, U20 RNA is an 80-nucleotide-long, metabolically stable species, present at about 7 x 10(3) molecules per exponentially growing HeLa cell. It has a nucleolar localization, as indicated by fluorescence microscopy following in situ hybridization with digoxigenin-labeled oligonucleotides. U20 RNA contains the box C and box D sequence motifs, hallmarks of most small nucleolar RNAs reported to date, and is immunoprecipitated by antifibrillarin antibodies. It also exhibits a 5'-3' terminal stem bracketing the box C-box D motifs like U14, U15, U16, or Y RNA. A U20 homolog of similar size has been detected in all vertebrate classes by Northern (RNA) hybridization with mammalian oligonucleotide probes. U20 RNA contains an extended region (21 nucleotides) of perfect complementarity with a phylogenetically conserved sequence in 18S rRNA. This complementarity is strongly preserved among distant vertebrates, suggesting that U20 RNA may be involved in the formation of the small ribosomal subunit like nucleolin, the product of its host gene.

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