Animal snoRNAs and scaRNAs with exceptional structures

Marz, Manja; Gruber, Andreas; Siederdissen, Christian Hoener zu; Amman, Fabian; Badelt, Stefan; Bartschat, Sebastian; Bernhart, Stephan H.; Beyer, Wolfgang; Kehr, Stephanie; Lorenz, Ronny; Tanzer, Andrea; Yusuf, Dilmurat; Tafer, Hakim; Hofacker, Ivo L.; Stadler, Peter F.

doi:10.4161/rna.8.6.16603

Cited by 34 publications

(27 citation statements)

References 59 publications

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“…Without the specific modifications controlled by the scaRNAs, the spliceosome fails to function properly [59]. Dysregulation of alternative splicing has been associated with the regulation of heart development and cardiovascular diseases [49].…”

Section: Noncoding Rnasmentioning

confidence: 99%

MicroRNA: A new therapeutic strategy for cardiovascular diseases

Samanta

Balasubramanian

Rajasingh

et al. 2016

Trends in Cardiovascular Medicine

110

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Myocardial infarction, atherosclerosis and hypertension are the most common heart-related diseases that affect both the heart and the blood vessels. Multiple independent risk factors have been shown to be responsible for cardiovascular diseases. The combination of a healthy diet, exercise and smoking cessation keeps these risk factors in check and helps maintain homeostasis. The dynamic monolayer endothelial cell integrity and cell-cell communication are the fundamental mechanisms in maintaining homeostasis. Recently, it has been revealed that small non-coding RNAs (ncRNAs) play a critical role in regulation of genes involved in either posttranscriptional or pretranslational modifications. They also control diverse biological functions like development, differentiation, growth, and metabolism. Among ncRNAs, the short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been extensively studied, but their specific functions remain largely unknown. In recent years, miRNAs are efficiently studied as one of the important candidates for involvement in most biological processes and have been implicated in many human diseases. Thus, the identification and the respective targets of miRNAs may provide novel molecular insight and new therapeutic strategies to treat diseases. This review summarizes the recent developments and insight on the role of miRNAs in cardiovascular disease prognosis, diagnostic and clinical applications.

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Section: Noncoding Rnasmentioning

confidence: 99%

MicroRNA: A new therapeutic strategy for cardiovascular diseases

Samanta

Balasubramanian

Rajasingh

et al. 2016

Trends in Cardiovascular Medicine

110

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“…However, more and more snoRNAs are discovered that don't follow this classification. For example, there are snoRNAs that have both C/D box and H/ACA box (24,25), or C/D snoRNAs that are not involved in 2’- O-methylation, like snoRNA U3 and U8, which instead are essential in the processing of 18S and 28S, 5.8S rRNAs, respectively (26–28).…”

Section: Introductionmentioning

confidence: 99%

Maternal- and somatic-type snoRNA expression and processing in zebrafish development

Pagano¹,

Locati²,

Ensink³

et al. 2019

Preprint

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Maternal-and somatic-type snoRNAs in zebrafishU3 U8 snoRNA, maternal expression, RNA processing, embryogenesis 1 ABSTRACT 2 Small nucleolar RNAs (snoRNAs) are non-coding RNAs that play an important role in the 3 complex maturation process of ribosomal RNAs (rRNAs). SnoRNAs are categorized in classes, 4 with each class member having several variants present in a genome. Similar to our finding 5 of specific rRNA expression types in zebrafish embryogenesis, we discovered preferential 6 maternal-and somatic-expression for snoRNAs. Most snoRNAs and their variants have 7 higher expression levels in somatic tissues than in eggs, yet we identified three snoRNAs; 8 U3, U8 and snoZ30 of which specific variants show maternal-or somatic-type expression.9 For U3 and U8 we also found small-derived snoRNAs that lack their 5' rRNA recognition part 10 and are essentially Domain II hairpin structures (U-DII). These U-DII snoRNAs from variants 11 showed similar preferential expression, in which maternal-type variants are prominently 12 expressed in eggs and subsequently replaced by a somatic-type variants during 13 embryogenesis. This differential expression is related to the organization in tandem repeats 14 (maternal type) or solitary (somatic-type) genes of the involved U snoRNA loci. The 15 collective data showed convincingly that the preferential expression of snoRNAs is achieved 16 by transcription regulation, as well as through RNA processing. Finally, we observed small-17 RNAs derived from internal transcribed spacers (ITSs) of a U3 snoRNA loci that via 18 complementarity binding, may be involved in the biosynthesis of U3-DII snoRNAs.19 Altogether, the here described maternal-and somatic-type snoRNAs are the latest addition 20 to the developing story about the dual ribosome system in zebrafish development. 22 INTRODUCTION23 Small nucleolar RNAs (snoRNAs) are a class of non-coding RNA molecules of variable length 24 (the majority being 60-200 nucleotides long), found in archaea and eukaryotes (1). SnoRNAs 3 25 are thought to mainly be involved in post-transcriptional modifications and maturation of 26 ribosomal RNAs (rRNAs) (2,3). However, recently additional functions have been ascribed to 27 specific snoRNAs, from regulation of mRNA editing and splicing (4) to post-transcriptional 28 gene silencing (5,6). SnoRNAs do not possess any intrinsic catalytic or modification activity, 29 but act both as a scaffold for partner proteins, forming small nucleolar ribonucleoproteins 30 (snoRNPs) and as guide for target specificity (7). Based on base-pairing interactions with 31 their target RNA, snoRNAs can thus direct the associated catalytic protein subunits to 32 accurately modify a specific RNA site (8).33 In general, eukaryotic genomes can contain up to 200+ unique snoRNA genes (9). Based on 34 the presence of conserved sequence motifs, the majority of snoRNAs are classified into two 35 distinct classes: box C/D snoRNAs, which guide 2'-O-methylation of ribose, and box H/ACA 36 snoRNAs, which are involved in the isomerization of sp...

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“…Two hundred seventy-one transcripts (including 14 microRNA, 10 snoRNA) are conserved in at least one of the Sauropsida. The deep conservation of host genes does not come as a surprise since in many cases their payload is conserved at least throughout the vertebrates (Hertel et al 2006;Lestrade and Weber 2006;Sempere et al 2006;Marz et al 2011).…”

Section: Hundreds Of Lncrnas Are Conserved Throughout the Vertebratesmentioning

confidence: 99%

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

Nitsche¹,

Rose²,

Fasold³

et al. 2015

RNA

Self Cite

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Large-scale RNA sequencing has revealed a large number of long mRNA-like transcripts (lncRNAs) that do not code for proteins. The evolutionary history of these lncRNAs has been notoriously hard to study systematically due to their low level of sequence conservation that precludes comprehensive homology-based surveys and makes them nearly impossible to align. An increasing number of special cases, however, has been shown to be at least as old as the vertebrate lineage. Here we use the conservation of splice sites to trace the evolution of lncRNAs. We show that >85% of the human GENCODE lncRNAs were already present at the divergence of placental mammals and many hundreds of these RNAs date back even further. Nevertheless, we observe a fast turnover of intron/exon structures. We conclude that lncRNA genes are evolutionary ancient components of vertebrate genomes that show an unexpected and unprecedented evolutionary plasticity. We offer a public web service (http://splicemap.bioinf.unileipzig.de) that allows to retrieve sets of orthologous splice sites and to produce overview maps of evolutionarily conserved splice sites for visualization and further analysis. An electronic supplement containing the ncRNA data sets used in this study is available at

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Animal snoRNAs and scaRNAs with exceptional structures

Cited by 34 publications

References 59 publications

MicroRNA: A new therapeutic strategy for cardiovascular diseases

MicroRNA: A new therapeutic strategy for cardiovascular diseases

Maternal- and somatic-type snoRNA expression and processing in zebrafish development

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

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