scholarly journals Role of the Box C/D Motif in Localization of Small Nucleolar RNAs to Coiled Bodies and Nucleoli

1999 ◽  
Vol 10 (7) ◽  
pp. 2131-2147 ◽  
Author(s):  
Aarthi Narayanan ◽  
Wayne Speckmann ◽  
Rebecca Terns ◽  
Michael P. Terns
Keyword(s):  
Large Family ◽  
Nucleolar Localization ◽  
Small Nucleolar Rnas ◽  
Cis Acting ◽  
Coiled Bodies ◽  
Sequence Elements ◽  
Intranuclear Transport ◽  
Necessary And Sufficient ◽  
Nucleolar Rnas

Small nucleolar RNAs (snoRNAs) are a large family of eukaryotic RNAs that function within the nucleolus in the biogenesis of ribosomes. One major class of snoRNAs is the box C/D snoRNAs named for their conserved box C and box D sequence elements. We have investigated the involvement of cis-acting sequences and intranuclear structures in the localization of box C/D snoRNAs to the nucleolus by assaying the intranuclear distribution of fluorescently labeled U3, U8, and U14 snoRNAs injected into Xenopus oocyte nuclei. Analysis of an extensive panel of U3 RNA variants showed that the box C/D motif, comprised of box C′, box D, and the 3′ terminal stem of U3, is necessary and sufficient for the nucleolar localization of U3 snoRNA. Disruption of the elements of the box C/D motif of U8 and U14 snoRNAs also prevented nucleolar localization, indicating that all box C/D snoRNAs use a common nucleolar-targeting mechanism. Finally, we found that wild-type box C/D snoRNAs transiently associate with coiled bodies before they localize to nucleoli and that variant RNAs that lack an intact box C/D motif are detained within coiled bodies. These results suggest that coiled bodies play a role in the biogenesis and/or intranuclear transport of box C/D snoRNAs.

scholarly journals Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ami Shah ◽  
Madison Ratkowski ◽  
Alessandro Rosa ◽  
Paul Feinstein ◽  
Thomas Bozza
Keyword(s):  
Gene Expression ◽  
Large Family ◽  
Sequence Motifs ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Trace Amine ◽  
Sequence Elements ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

scholarly journals Evidence for the Role of PWCR1/HBII-85 C/D Box Small Nucleolar RNAs in Prader-Willi Syndrome

2002 ◽  
Vol 71 (3) ◽  
pp. 669-678 ◽  
Author(s):  
Renata C. Gallagher ◽  
Birgit Pils ◽  
Mohammed Albalwi ◽  
Uta Francke
Keyword(s):  
Prader Willi Syndrome ◽  
Small Nucleolar Rnas ◽  
Nucleolar Rnas

scholarly journals Internal Modification of U2 Small Nuclear (Snrna) Occurs in Nucleoli of Xenopus Oocytes

2001 ◽  
Vol 152 (6) ◽  
pp. 1279-1288 ◽  
Author(s):  
Yi-Tao Yu ◽  
Mei-Di Shu ◽  
Aarthi Narayanan ◽  
Rebecca M. Terns ◽  
Michael P. Terns ◽  
...  
Keyword(s):  
Binding Site ◽  
Xenopus Oocytes ◽  
Cajal Bodies ◽  
Nucleolar Localization ◽  
Small Nucleolar Rnas ◽  
Modified Nucleotides ◽  
Nucleolar Localization Signal ◽  
Localization Analysis ◽  
Localization Signal ◽  
Nucleolar Rnas

U2 small nuclear (sn)RNA contains a large number of posttranscriptionally modified nucleotides, including a 5′ trimethylated guanosine cap, 13 pseudouridines, and 10 2′-O-methylated residues. Using Xenopus oocytes, we demonstrated previously that at least some of these modified nucleotides are essential for biogenesis of a functional snRNP. Here we address the subcellular site of U2 internal modification. Upon injection into the cytoplasm of oocytes, G-capped U2 that is transported to the nucleus becomes modified, whereas A-capped U2 that remains in the cytoplasm is not modified. Furthermore, by injecting U2 RNA into isolated nuclei or enucleated oocytes, we observe that U2 internal modifications occur exclusively in the nucleus. Analysis of the intranuclear localization of fluorescently labeled RNAs shows that injected wild-type U2 becomes localized to nucleoli and Cajal bodies. Both internal modification and nucleolar localization of U2 are dependent on the Sm binding site. An Sm-mutant U2 is targeted only to Cajal bodies. The Sm binding site can be replaced by a nucleolar localization signal derived from small nucleolar RNAs (the box C/D motif), resulting in rescue of internal modification as well as nucleolar localization. Analysis of additional chimeric U2 RNAs reveals a correlation between internal modification and nucleolar localization. Together, our results suggest that U2 internal modification occurs within the nucleolus.

scholarly journals jouvence, a new human H/ACA snoRNA involves in the control of cell proliferation and differentiation

2020 ◽  
Author(s):  
Flaria El-Khoury ◽  
Jérôme Bignon ◽  
Jean-René Martin
Keyword(s):  
Cell Proliferation ◽  
Small Nucleolar Rnas ◽  
Primary Cells ◽  
Cell Proliferation And Differentiation ◽  
Cancerous Cell ◽  
Proliferation And Differentiation ◽  
Non Coding Rnas ◽  
Nucleolar Rnas

AbstractSmall nucleolar RNAs (snoRNAs) are non-coding RNAs conserved from archeobacteria to mammals. In humans, various snoRNAs have been associated with pathologies as well as with cancer. Recently in Drosophila, a new snoRNA named jouvence has been involved in lifespan. Since snoRNAs are well conserved through evolution, both structurally and functionally, jouvence orthologue has been identified in human, allowing hypothesizing that jouvence could display a similar function (increasing healthy lifespan) in human. Here, we report the characterization of the human snoRNA-jouvence, which was not yet annotated in the genome. We show, both in stably cancerous cell lines and in primary cells, that its overexpression stimulates the cell proliferation. In contrast, its knockdown, by siRNA leads to an opposite phenotype, a decrease in cell proliferation. Transcriptomic analysis reveals that overexpression of jouvence leads to a dedifferentiation signature of the cells, a cellular effect comparable to rejuvenation. Inversely, the knockdown of jouvence leads to a decrease of genes involved in ribosomes biogenesis and spliceosome in agreement with the canonical role of a H/ACA box snoRNA. In this context, jouvence could represent a now tool to fight against the deleterious effect of aging, as well as a new target in cancer therapy.

scholarly journals Immunopurified Small Nucleolar Ribonucleoprotein Particles Pseudouridylate rRNA Independently of Their Association with Phosphorylated Nopp140

2002 ◽  
Vol 22 (24) ◽  
pp. 8457-8466 ◽  
Author(s):  
Chen Wang ◽  
Charles C. Query ◽  
U. Thomas Meier
Keyword(s):  
Cajal Body ◽  
Small Nucleolar Rnas ◽  
Ribonucleoprotein Particle ◽  
Vitro Assay ◽  
Body Protein ◽  
Core Proteins ◽  
Layer Chromatography ◽  
Nucleolar Rnas

ABSTRACT The isomerization of up to 100 uridines to pseudouridines (Ψs) in eukaryotic rRNA is guided by a similar number of box H/ACA small nucleolar RNAs (snoRNAs), each forming a unique small nucleolar ribonucleoprotein particle (snoRNP) with the same four core proteins, NAP57 (also known as dyskerin or Cbf5p), GAR1, NHP2, and NOP10. Additionally, the nucleolar and Cajal body protein Nopp140 (Srp40p) associates with the snoRNPs. To understand the role of these factors in pseudouridylation, we established an in vitro assay system. Short site-specifically 32P-labeled rRNA substrates were incubated with subcellular fractions, and the conversion of uridine to Ψ was monitored by thin-layer chromatography after digestion to single nucleotides. Immunopurified box H/ACA core particles were sufficient for the reaction. SnoRNPs associated quantitatively and reversibly with Nopp140. However, pseudouridylation activity was independent of Nopp140, consistent with a chaperoning role for this highly phosphorylated protein. Although up to 14 bp between the snoRNA and rRNA were required for the in vitro reaction, rRNA pseudouridylation and release occurred in the absence of ATP and magnesium. These data suggest that substrate release takes place without RNA helicase activity but may be aided by the snoRNP core proteins.

scholarly journals The 216-nucleotide intron of the E1A pre-mRNA contains a hairpin structure that permits utilization of unusually distant branch acceptors.

1989 ◽  
Vol 9 (11) ◽  
pp. 4852-4861 ◽  
Author(s):  
K Chebli ◽  
R Gattoni ◽  
P Schmitt ◽  
G Hildwein ◽  
J Stevenin
Keyword(s):  
Splice Site ◽  
Site Directed Mutagenesis ◽  
Hairpin Structure ◽  
Cis Acting ◽  
Adenovirus E1a ◽  
Sequence Elements ◽  
In Vitro Splicing ◽  
Hairpin Formation

A recently characterized 216-nucleotide intron-splicing reaction occurs within the adenovirus E1A pre-mRNA through the use of three branch acceptor sites, located at 59, 55, and 51 nucleotides from the 3' splice site. To investigate the role of the cis-acting sequence elements in the selection of such unusually distant branch sites, transcripts differing in sequence downstream of the branch sites were analyzed for in vitro splicing. Initial results suggested that secondary structure could be involved in the use of distant branch sites. The involvement of a hairpin structure, including a nine-G C-base-pair stem, was supported by the results of site-directed mutagenesis analyses. Mutations that destroyed or weakened this hairpin resulted in an inefficient splicing reaction. In contrast, complementary mutation or deletion of two bulges, which involved a restoration or reinforcement of the hairpin, resulted in a reactivation or improvement of the splicing efficiency, respectively. Therefore, we conclude that the hairpin structure shortens the operational distance between the 3' splice site and the branch acceptors and brings the branch sites into the branch-permissive window, 18 to 40 nucleotides upstream of the 3' splice site. Our results confirm the importance of the constraint of distance for the splicing reaction and show that this constraint may be overcome by means of a stable hairpin formation.

scholarly journals Identification of a Novel Element Required for Processing of Intron-Encoded Box C/D Small Nucleolar RNAs inSaccharomyces cerevisiae

2000 ◽  
Vol 20 (4) ◽  
pp. 1311-1320 ◽  
Author(s):  
Tommaso Villa ◽  
Francesca Ceradini ◽  
Irene Bozzoni
Keyword(s):  
Comparative Analysis ◽  
Early Recognition ◽  
Small Nucleolar Rnas ◽  
Core Motif ◽  
Complementary Sequences ◽  
Transcriptional Units ◽  
Specific Factors ◽  
Conserved Core ◽  
Nucleolar Rnas

ABSTRACT Processing of intron-encoded box C/D small nucleolar RNAs (snoRNAs) in metazoans through both the splicing-dependent and -independent pathways requires the conserved core motif formed by boxes C and D and the adjoining 5′-3′-terminal stem. By comparative analysis, we found that five out of six intron-encoded box C/D snoRNAs in yeast do not possess a canonical terminal stem. Instead, complementary regions within the flanking host intron sequences have been identified in all these cases. Here we show that these sequences are essential for processing of U18 and snR38 snoRNAs and that they compensate for the lack of a canonical terminal stem. We also show that the Rnt1p endonuclease, previously shown to be required for the processing of many snoRNAs encoded by monocistronic or polycistronic transcriptional units, is not required for U18 processing. Our results suggest a role of the complementary sequences in the early recognition of intronic snoRNA substrates and point out the importance of base pairing in favoring the communication between boxes C and D at the level of pre-snoRNA molecules for efficient assembly with snoRNP-specific factors.

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