scholarly journals Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells

2019 ◽  
Vol 10 ◽  
Author(s):  
Julia A. Filippova ◽  
Anastasiya M. Matveeva ◽  
Evgenii S. Zhuravlev ◽  
Evgenia A. Balakhonova ◽  
Daria V. Prokhorova ◽  
...  
Keyword(s):  
Rna Editing ◽  
Human Cells ◽  
Small Nucleolar Rnas ◽  
Small Nucleolar Rna ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

scholarly journals ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs

2005 ◽  
Vol 169 (5) ◽  
pp. 745-753 ◽  
Author(s):  
Patrice Vitali ◽  
Eugenia Basyuk ◽  
Elodie Le Meur ◽  
Edouard Bertrand ◽  
Françoise Muscatelli ◽  
...  
Keyword(s):  
Rna Editing ◽  
Serotonin Receptor ◽  
Small Nucleolar Rnas ◽  
Ribonucleoprotein Particle ◽  
Subcellular Targeting ◽  
Adenosine Deaminases ◽  
Bona Fide ◽  
Cellular Compartments ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

Posttranscriptional, site-specific adenosine to inosine (A-to-I) base conversions, designated as RNA editing, play significant roles in generating diversity of gene expression. However, little is known about how and in which cellular compartments RNA editing is controlled. Interestingly, the two enzymes that catalyze RNA editing, adenosine deaminases that act on RNA (ADAR) 1 and 2, have recently been demonstrated to dynamically associate with the nucleolus. Moreover, we have identified a brain-specific small RNA, termed MBII-52, which was predicted to function as a nucleolar C/D RNA, thereby targeting an A-to-I editing site (C-site) within the 5-HT2C serotonin receptor pre-mRNA for 2′-O-methylation. Through the subcellular targeting of minigenes that contain natural editing sites, we show that ADAR2- but not ADAR1-mediated RNA editing occurs in the nucleolus. We also demonstrate that MBII-52 forms a bona fide small nucleolar ribonucleoprotein particle that specifically decreases the efficiency of RNA editing by ADAR2 at the targeted C-site. Our data are consistent with a model in which C/D small nucleolar RNA might play a role in the regulation of RNA editing.

scholarly journals Systematic mapping of small nucleolar RNA targets in human cells

2021 ◽  
Author(s):  
Hywel Dunn-Davies ◽  
Tatiana Dudnakova ◽  
Jean-Louis Langhendries ◽  
Nicholas Watkins ◽  
Denis LJ Lafontaine ◽  
...  
Keyword(s):  
Human Cells ◽  
Small Nucleolar Rnas ◽  
Systematic Mapping ◽  
Altered Expression ◽  
Proximity Ligation ◽  
Uv Crosslinking ◽  
Rna Targets ◽  
Folding Dynamics ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

Altered expression of box C/D small nucleolar RNAs (snoRNAs) is implicated in human diseases, including cancer. Box C/D snoRNAs canonically direct site-specific, 2′-O-methylation but the extent to which they participate in other functions remains unclear. To identify RNA targets of box C/D snoRNAs in human cells, we applied two techniques based on UV crosslinking, proximity ligation and sequencing of RNA hybrids (CLASH and FLASH). These identified hundreds of novel snoRNA interactions with rRNA, snoRNAs and mRNAs. We developed an informatic pipeline to rigorously call interactions predicted to direct methylation. Multiple snoRNA-rRNA interactions identified were not predicted to direct RNA methylation. These potentially modulate methylation efficiency and/or contribute to folding dynamics. snoRNA-mRNA hybrids included 1,300 interactions between 117 snoRNA families and 940 mRNAs. Human U3 is substantially more abundant than other snoRNAs and represented about 50% of snoRNA-mRNA hybrids. The distribution of U3 interactions across mRNAs also differed from other snoRNAs. Following U3 depletion, mRNAs showing altered abundance were strongly enriched for U3 CLASH targets. Most human snoRNAs are excised from pre-mRNA introns. Enrichment for snoRNA association with branch point regions of introns that contain snoRNA genes was common, suggesting widespread regulation of snoRNA maturation.

Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA

1993 ◽  
Vol 13 (7) ◽  
pp. 4382-4390
Author(s):  
O J Rimoldi ◽  
B Raghu ◽  
M K Nag ◽  
G L Eliceiri
Keyword(s):  
Small Rnas ◽  
18S Rrna ◽  
Rnase H ◽  
Antisense Oligodeoxynucleotide ◽  
28S Rrna ◽  
Small Nucleolar Rnas ◽  
Rrna Sequence ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.

scholarly journals Processing of the Precursors to Small Nucleolar RNAs and rRNAs Requires Common Components

1998 ◽  
Vol 18 (3) ◽  
pp. 1181-1189 ◽  
Author(s):  
Elisabeth Petfalski ◽  
Thomas Dandekar ◽  
Yves Henry ◽  
David Tollervey
Keyword(s):  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
5.8S Rrna ◽  
Genes Encoding ◽  
Sequences Analysis ◽  
Upstream Processing ◽  
Exonuclease Digestion ◽  
Nucleolar Rna ◽  
Nucleolar Rnas ◽  
Common Components

ABSTRACT The genes encoding the small nucleolar RNA (snoRNA) species snR190 and U14 are located close together in the genome of Saccharomyces cerevisiae. Here we report that these two snoRNAs are synthesized by processing of a larger common transcript. In strains mutant for two 5′→3′ exonucleases, Xrn1p and Rat1p, families of 5′-extended forms of snR190 and U14 accumulate; these have 5′ extensions of up to 42 and 55 nucleotides, respectively. We conclude that the 5′ ends of both snR190 and U14 are generated by exonuclease digestion from upstream processing sites. In contrast to snR190 and U14, the snoRNAs U18 and U24 are excised from the introns of pre-mRNAs which encode proteins in their exonic sequences. Analysis of RNA extracted from a dbr1-Δ strain, which lacks intron lariat-debranching activity, shows that U24 can be synthesized only from the debranched lariat. In contrast, a substantial level of U18 can be synthesized in the absence of debranching activity. The 5′ ends of these snoRNAs are also generated by Xrn1p and Rat1p. The same exonucleases are responsible for the degradation of several excised fragments of the pre-rRNA spacer regions, in addition to generating the 5′ end of the 5.8S rRNA. Processing of the pre-rRNA and both intronic and polycistronic snoRNAs therefore involves common components.

Small nucleolar RNA

1995 ◽  
Vol 73 (11-12) ◽  
pp. 845-858 ◽  
Author(s):  
Susan A. Gerbi
Keyword(s):  
Rna Polymerase Ii ◽  
Binding Sites ◽  
Ribosome Biogenesis ◽  
Internal Transcribed Spacers ◽  
28S Rrna ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
Conserved Sequence ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

A growing list of small nucleolar RNAs (snoRNAs) has been characterized in eukaryotes. They are transcribed by RNA polymerase II or III; some snoRNAs are encoded in the introns of other genes. The nonintronic polymerase II transcribed snoRNAs receive a trimethylguanosine cap, probably in the nucleus, and move to the nucleolus. snoRNAs are complexed with proteins, sometimes including fibrillarin. Localization and maintenance in the nucleolus of some snoRNAs requires the presence of initial precursor rRNA (pre-rRNA). Many snoRNAs have conserved sequence boxes C and D and a 3′ terminal stem; the roles of these features are discussed. Functional assays done for a few snoRNAs indicate their roles in rRNA processing for cleavage of the external and internal transcribed spacers (ETS and ITS). U3 is the most abundant snoRNA and is needed for cleavage of ETS1 and ITS1; experimental results on U3 binding sites in pre-rRNA are reviewed. 18S rRNA production also needs U14, U22, and snR30 snoRNAs, whereas U8 snoRNA is needed for 5.8S and 28S rRNA production. Other snoRNAs that are complementary to 18S or 28S rRNA might act as chaperones to mediate RNA folding. Whether snoRNAs join together in a large rRNA processing complex (the "processome") is not yet clear. It has been hypothesized that such complexes could anchor the ends of loops in pre-rRNA containing 18S or 28S rRNA, thereby replacing base-paired stems found in pre-rRNA of prokaryotes.Key words: RNA processing, small nucleolar RNAs, nucleolus, ribosome biogenesis, rRNA processing complex.

scholarly journals In Vivo Identification of Nuclear Factors Interacting with the Conserved Elements of Box C/D Small Nucleolar RNAs

1998 ◽  
Vol 18 (2) ◽  
pp. 1023-1028 ◽  
Author(s):  
Elisa Caffarelli ◽  
Massimo Losito ◽  
Corinna Giorgi ◽  
Alessandro Fatica ◽  
Irene Bozzoni
Keyword(s):  
Rna Binding ◽  
Protein Gene ◽  
Molecular Size ◽  
Ribosomal Protein Gene ◽  
The Novel ◽  
Small Nucleolar Rnas ◽  
Nuclear Factors ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

ABSTRACT The U16 small nucleolar RNA (snoRNA) is encoded by the third intron of the L1 (L4, according to the novel nomenclature) ribosomal protein gene of Xenopus laevis and originates from processing of the pre-mRNA in which it resides. The U16 snoRNA belongs to the box C/D snoRNA family, whose members are known to assemble in ribonucleoprotein particles (snoRNPs) containing the protein fibrillarin. We have utilized U16 snoRNA in order to characterize the factors that interact with the conserved elements common to the other members of the box C/D class. In this study, we have analyzed the in vivo assembly of U16 snoRNP particles in X. laevis oocytes and identified the proteins which interact with the RNA by label transfer after UV cross-linking. This analysis revealed two proteins, of 40- and 68-kDa apparent molecular size, which require intact boxes C and D together with the conserved 5′,3′-terminal stem for binding. Immunoprecipitation experiments showed that the p40 protein corresponds to fibrillarin, indicating that this protein is intimately associated with the RNA. We propose that fibrillarin and p68 represent the RNA-binding factors common to box C/D snoRNPs and that both proteins are essential for the assembly of snoRNP particles and the stabilization of the snoRNA.

scholarly journals Regulatory Role of Small Nucleolar RNAs in Human Diseases

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Grigory A. Stepanov ◽  
Julia A. Filippova ◽  
Andrey B. Komissarov ◽  
Elena V. Kuligina ◽  
Vladimir A. Richter ◽  
...  
Keyword(s):  
Gene Expression Regulation ◽  
Human Cells ◽  
Small Nucleolar Rnas ◽  
Posttranscriptional Modification ◽  
Cellular Processes ◽  
Promising Target ◽  
Regulatory Rnas ◽  
Nucleolar Rnas ◽  
Artificial Stress

Small nucleolar RNAs (snoRNAs) are appreciable players in gene expression regulation in human cells. The canonical function of box C/D and box H/ACA snoRNAs is posttranscriptional modification of ribosomal RNAs (rRNAs), namely, 2′-O-methylation and pseudouridylation, respectively. A series of independent studies demonstrated that snoRNAs, as well as other noncoding RNAs, serve as the source of various short regulatory RNAs. Some snoRNAs and their fragments can also participate in the regulation of alternative splicing and posttranscriptional modification of mRNA. Alterations in snoRNA expression in human cells can affect numerous vital cellular processes. SnoRNA level in human cells, blood serum, and plasma presents a promising target for diagnostics and treatment of human pathologies. Here we discuss the relation between snoRNAs and oncological, neurodegenerative, and viral diseases and also describe changes in snoRNA level in response to artificial stress and some drugs.

scholarly journals Analogues of Artificial Human Box C/D Small Nucleolar RNA As Regulators of Alternative Splicing of a pre-mRNA Target

Acta Naturae ◽  
2012 ◽  
Vol 4 (1) ◽  
pp. 32-41 ◽  
Author(s):  
G. A. Stepanov ◽  
D. V. Semenov ◽  
E. V. Kuligina ◽  
O. A. Koval ◽  
I. V. Rabinov ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Human Cells ◽  
28S Rrna ◽  
Small Nuclear Rnas ◽  
Cultured Human Cells ◽  
Heat Shock Cognate Protein ◽  
Nucleolar Rna ◽  
Nucleolar Rnas ◽  
Mature Mrnas ◽  
Mcf 7

Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA (rRNA) biogenesis. Box C/D snoRNAs guide the site-specific 2-O-ribose methylation of nucleotides in rRNAs and small nuclear RNAs (snRNAs). A number of box C/D snoRNAs and their fragments have recently been reported to regulate post-transcriptional modifications and the alternative splicing of pre-mRNA. Artificial analogues of U24 snoRNAs directed to nucleotides in 28S and 18S rRNAs, as well as pre-mRNAs and mature mRNAs of human heat shock cognate protein (hsc70), were designed and synthesized in this study. It was found that after the transfection of MCF-7 human cells with artificial box C/D RNAs in complex with lipofectamine, snoRNA analogues penetrated into cells and accumulated in the cytoplasm and nucleus. It was demonstrated that the transfection of cultured human cells with artificial box C/D snoRNA targeted to pre-mRNAs induce partial splicing impairments. It was found that transfection with artificial snoRNAs directed to 18S and 28S rRNA nucleotides, significant for ribosome functioning, induce a decrease in MCF-7 cell viability.

scholarly journals Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA.

1993 ◽  
Vol 13 (7) ◽  
pp. 4382-4390 ◽  
Author(s):  
O J Rimoldi ◽  
B Raghu ◽  
M K Nag ◽  
G L Eliceiri
Keyword(s):  
Small Rnas ◽  
18S Rrna ◽  
Rnase H ◽  
Antisense Oligodeoxynucleotide ◽  
28S Rrna ◽  
Small Nucleolar Rnas ◽  
Rrna Sequence ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.

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