Small Nuclear RNAs: RNA Sequences, Structure, and Modifications

Reddy, Ram; Busch, Harris

doi:10.1007/978-3-642-73020-7_1

Cited by 170 publications

(169 citation statements)

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“…These modifications are controlled by guide RNAs acting in concert with a corresponding methyltransferase (fibrillarin) and pseudouridylase (NAP57/dyskerin; reviewed in Reddy and Busch, 1988;Matera et al, 2007). It is generally believed that modification of rRNA takes place in the nucleolus.…”

Section: Discussionmentioning

confidence: 99%

“…Modifications in Drosophila U5 snRNA have been described in detail, but less is known about modifications in Drosophila U1, U2, and U4 snRNAs (Myslinski et al, 1984;Reddy and Busch, 1988;Szkukalek et al, 1995;Huang et al, 2005b). To obtain a more complete list of modifications, we carried out primer extension reactions with fluorescently labeled oligonucleotides, followed by separation on capillary columns.…”

Section: Posttranscriptional Nucleotide Modifications In Drosophila Smentioning

confidence: 99%

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Small Cajal Body–specific RNAs ofDrosophilaFunction in the Absence of Cajal Bodies

Deryusheva

Gall

2009

MBoC

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During their biogenesis small nuclear RNAs (snRNAs) undergo multiple covalent modifications that require guide RNAs to direct methylase and pseudouridylase enzymes to the appropriate nucleotides. Because of their localization in the nuclear Cajal body (CB), these guide RNAs are known as small CB-specific RNAs (scaRNAs). Using a fluorescent primer extension technique, we mapped the modified nucleotides in Drosophila U1, U2, U4, and U5 snRNAs. By fluorescent in situ hybridization (FISH) we showed that seven Drosophila scaRNAs are concentrated in easily detectable CBs. We used two assays based on Xenopus oocyte nuclei to demonstrate that three of these Drosophila scaRNAs do, in fact, function as guide RNAs. In flies null for the CB marker protein coilin, CBs are absent and there are no localized FISH signals for the scaRNAs. Nevertheless, biochemical experiments show that scaRNAs are present at normal levels and snRNAs are properly modified. Our experiments demonstrate that several scaRNAs are concentrated as expected in the CBs of wild-type Drosophila, but they function equally well in the nucleoplasm of mutant flies that lack CBs. We propose that the snRNA modification machinery is not limited to CBs, but is dispersed throughout the nucleoplasm of cells in general. INTRODUCTIONThe two major ribosomal RNAs (rRNAs) and the spliceosomal small nuclear RNAs (snRNAs) U1, U2, U4, U5, and U6 contain many posttranscriptionally modified nucleotides, which are crucial for RNA-RNA and RNA-protein interactions, as well as spliceosome function (Yu et al., 1998; Yu, 2004, 2007). The most abundant modifications in both rRNAs and snRNAs are 2Ј-O-methylation and pseudouridylation, which are directed by small box C/D and box H/ACA guide RNAs, respectively. Each guide RNA molecule is associated with a set of four core proteins: box C/D RNAs form RNP particles with fibrillarin (the methyltransferase), Nop56, Nop58, and a 15.5-kDa protein, whereas box H/ACA RNAs associate with NAP57/dyskerin (the pseudouridine synthase), GAR1, NHP2, and NOP10 proteins (reviewed in Yu et al., 2004;Matera et al., 2007). Most guide RNAs are concentrated in the nucleolus, where they are involved in posttranscriptional modifications of rRNA. Because of their localization, they are referred to as small nucleolar RNAs (snoRNAs). However, the guide RNAs that mediate modification of the snRNAs are preferentially found in another nuclear organelle, the Cajal body (CB). These guide RNAs are called small CB-specific RNAs (scaRNAs).The first scaRNA to be studied in detail was U85 scaRNA (Jády and Kiss, 2001;Darzacq et al., 2002). U85 is a remarkable double guide RNA that contains both box C/D and box H/ACA motifs. In a set of detailed experiments it was shown that human U85 scaRNA guides both 2Ј-O-methylation at C45 and pseudouridylation at U46 in U5 snRNA. Modification takes place in the nucleus after import of the U5 snRNA from the cytoplasm . CB localization of U85 scaRNA was originally demonstrated by fluorescent in situ hybridization (FISH) in mammalian and ...

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Section: Discussionmentioning

confidence: 99%

Section: Posttranscriptional Nucleotide Modifications In Drosophila Smentioning

confidence: 99%

Small Cajal Body–specific RNAs ofDrosophilaFunction in the Absence of Cajal Bodies

Deryusheva

Gall

2009

MBoC

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“…However, the mere presence of Cresidues in single-stranded regions of RNAs does not seem to be sufficient for cleavage, since the U2, U3, U4, U5, and U6 snRNAs are not cleaved despite the presence of numerous C-residues. 32,33 Also the presence of two consecutive C-residues, which occur at the cleavage sites of U1 snRNA, does not seem to constitute the cleavage determinant, because such a C-doublet also occurs in a single-stranded region near the 5'-end (nucleotides 7 and 8) of the U2 snRNA molecule, which apparently is not cleaved at this position. Taken together, while at least one pseudouridine (in a single-stranded region) might be required for recognition by the putative apoptotically activated RNase, other structural elements seem to be necessary for cleavage to occur.…”

Section: Discussionmentioning

confidence: 99%

The fate of U1 snRNP during anti-Fas induced apoptosis: specific cleavage of the U1 snRNA molecule

et al. 2000

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During apoptosis, the U1-70K protein, a component of the spliceosomal U1 snRNP complex, is specifically cleaved by the enzyme caspase-3, converting it into a C-terminally truncated 40-kDa fragment. In this study, we show that the 40-kDa U1-70K fragment is still associated with the complete U1 snRNP complex, and that no obvious modifications occur with the U1 snRNP associated proteins U1A, U1C and Sm-B/B'. Furthermore, it is described for the first time that the U1 snRNA molecule, which is the backbone of the U1 snRNP complex, is modified during apoptosis by the specific removal of the first 5 ± 6 nucleotides including the 2,2,7-trimethylguanosine (TMG) cap. The observations that U1 snRNA cleavage is very specific (no such modifications were detected for the other U snRNAs tested) and that U1 snRNA cleavage is markedly inhibited in the presence of caspase inhibitors, indicate that an apoptotically activated ribonuclease is responsible for the specific modification of U1 snRNA during apoptosis. Cell Death and Differentiation (2000) 7, 70 ± 79.

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“…2A). On the basis of the previously reported copy number of U4 snRNA in HeLa cells (200,000 copies per cell) (Reddy and Busch 1988), the cellular abundance of the novel ACA snoRNAs was estimated to be between 8000 (U70) and 12,000 {U65) copies per cell. In mammalian cells, many snoRNPs that participate in pre-rRNA processing have been shown to be associ ated with higher order nucleolar complexes that sedi ment at 40S-80S and probably represent ribosomal par ticles undergoing maturation in the nucleolus (Epstein et al 1984;Tyc and Steitz 1989;Kiss and Filipowicz 1993;.…”

Section: The Novel Snornas Are Associated With Higher Order Nucleolarmentioning

confidence: 98%

The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation.

Ganot¹,

Caizergues‐Ferrer²,

Kiss³

1997

Genes Dev.

313

387

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Eukaryotic cells contain a large number of small nucleolar RNAs (snoRNAs).A major family of snoRNAs features a consensus ACA motif positioned 3 nucleotides from the 3' end of the RNA. In this study we have characterized nine novel human ACA snoRNAs (U64-U72). Structural probing of U64 RNA followed by systematic computer modeling of all known box ACA snoRNAs revealed that this class of snoRNAs is defined by a phylogenetically conserved secondary structure. The ACA snoRNAs fold into two hairpin structures connected by a single-stranded hinge region and followed by a short 3' tail. In eukaryotic cells, maturation of rRNAs takes place in the nucleolus. The 18S, 5.8S, and 25/28S rRNAs are syn thesized as a large precursor RNA (pre-rRNA) that car ries long external and internal spacer sequences. Shortly after transcription, many nucleotides in the coding re gions of pre-rRNA are methylated at the 2'-0-hydroxyl position and numerous U residues are converted into pseudouridines (Maden 1990;Eichler and Craig 1995). The covalently modified pre-rRNA is than processed into mature rRNAs through a series of endo-and exonucleolytic cleavages (Eichler and Craig 1995; Venema and Tollervey 1995;Sollner-Webb et al. 1996).The nucleolus contains a large number of snoRNAs. More than 80 distinct small nucleolar RNA (snoRNA) sequences have been identified in vertebrate and yeast

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Small Nuclear RNAs: RNA Sequences, Structure, and Modifications

Cited by 170 publications

References 174 publications

Small Cajal Body–specific RNAs ofDrosophilaFunction in the Absence of Cajal Bodies

Small Cajal Body–specific RNAs ofDrosophilaFunction in the Absence of Cajal Bodies

The fate of U1 snRNP during anti-Fas induced apoptosis: specific cleavage of the U1 snRNA molecule

The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation.

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