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Non-Coding RNA, Volume 1, Issue 2 (September 2015) – 5 articles , Pages 94-169

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166 KiB  
Editorial
The Non-Coding RNA Journal Club: Highlights on Recent Papers—2
by Claire Francastel, Florent Hubé, Sendurai A. Mani, Gaetano Santulli, Joseph H. Taube and Zofia Szweykowska-Kulinska
Non-Coding RNA 2015, 1(2), 167-169; https://doi.org/10.3390/ncrna1020167 - 22 Sep 2015
Cited by 1 | Viewed by 4129
Abstract
We are glad to share with you our second Journal Club and to highlight some of the most interesting papers published recently. [...] Full article
(This article belongs to the Collection The Non-Coding RNA Journal Club: Highlights on Recent Papers)
981 KiB  
Article
Stabilization of Urinary MicroRNAs by Association with Exosomes and Argonaute 2 Protein
by Cristina Beltrami, Aled Clayton, Lucy J. Newbury, Peter Corish, Robert H. Jenkins, Aled O. Phillips, Donald J. Fraser and Timothy Bowen
Non-Coding RNA 2015, 1(2), 151-166; https://doi.org/10.3390/ncrna1020151 - 14 Sep 2015
Cited by 40 | Viewed by 6239
Abstract
A pressing need for new chronic kidney disease (CKD) biomarkers persists. MicroRNAs (miRNAs) are emerging as a novel class of disease biomarkers in body fluids, but mechanisms conferring their stability in urine have not been fully elucidated. Here we investigated stabilization in human [...] Read more.
A pressing need for new chronic kidney disease (CKD) biomarkers persists. MicroRNAs (miRNAs) are emerging as a novel class of disease biomarkers in body fluids, but mechanisms conferring their stability in urine have not been fully elucidated. Here we investigated stabilization in human urine of ubiquitously expressed miR-16, and miR-192, which we have shown previously to be downregulated in renal fibrosis, by association with extracellular vesicles and with argonaute protein (AGO) 2. Endogenous urinary miR-16 was significantly more resistant to RNase-mediated degradation than exogenous, spiked-in, Caenorhabditis elegans cel-miR-39. We used our previously optimized high-resolution exosome isolation protocol with sucrose gradient ultracentrifugation to sub-fractionate the primary extracellular vesicle-rich urinary pellet. MiR-16 and miR-192 were enriched in exosomal sucrose gradient fractions, but were also detected in all other fractions. This suggested association of urinary miRNAs with other urinary extracellular vesicles and/or pellet components, complicating previous estimates of miRNA:exosome stoichiometry. Proteinase K digestion destabilized urinary miR-16 and we showed, for the first time, RNA-immunoprecipitation of urinary miR-16:AGO2 and miR-192:AGO2 complexes. Association with exosomes and AGO2 stabilized urinary miR-16 and miR-192, suggesting quantitative urinary miRNA analysis has the potential to identify novel, non-invasive CKD biomarkers. Full article
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835 KiB  
Article
Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster
by Alberto Agrisani, Hakim Tafer, Peter F. Stadler and Maria Furia
Non-Coding RNA 2015, 1(2), 139-150; https://doi.org/10.3390/ncrna1020139 - 13 Jul 2015
Cited by 3 | Viewed by 5246
Abstract
A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors [...] Read more.
A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome. Full article
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659 KiB  
Article
“Pocket-sized RNA-Seq”: A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest
by Florent Hubé and Claire Francastel
Non-Coding RNA 2015, 1(2), 127-138; https://doi.org/10.3390/ncrna1020127 - 03 Jul 2015
Cited by 2 | Viewed by 5825
Abstract
Currently, the discovery of new small ncRNAs requires high throughput methods even in the case of focused research on the regulation of specific genes or set of genes. We propose herein a simple, rapid, efficient, and cost effective method to clone and sequence [...] Read more.
Currently, the discovery of new small ncRNAs requires high throughput methods even in the case of focused research on the regulation of specific genes or set of genes. We propose herein a simple, rapid, efficient, and cost effective method to clone and sequence single, yet unknown, small ncRNA. This technique that we called “Pocket-sized RNA-Seq” or psRNA-seq is based on in vitro transcription, RNA pull down and adapted RACE-PCR methods that allow its implementation using either available commercial kits or in-house reagents. Full article
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1699 KiB  
Article
Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to RNA Decay in S. cerevisiae
by Marta Kwapisz, Myriam Ruault, Erwin Van Dijk, Stephanie Gourvennec, Marc Descrimes, Angela Taddei and Antonin Morillon
Non-Coding RNA 2015, 1(2), 94-126; https://doi.org/10.3390/ncrna1020094 - 03 Jul 2015
Cited by 8 | Viewed by 7693
Abstract
Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomeric repeats containing long ncRNAs – TERRA in mammalian and yeast cells. However, their functions remain poorly [...] Read more.
Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomeric repeats containing long ncRNAs – TERRA in mammalian and yeast cells. However, their functions remain poorly characterized. Here, we report the existence in S. cerevisiae of several lncRNAs within Y′ subtelomeric regions. We have called them subTERRA. These belong to Cryptic Unstable Transcripts (CUTs) and Xrn1p-sensitive Unstable Transcripts (XUTs) family. subTERRA transcription, carried out mainly by RNAPII, is initiated within the subtelomeric Y’ element and occurs in both directions, towards telomeres as well as centromeres. We show that subTERRA are distinct from TERRA and are mainly degraded by the general cytoplasmic and nuclear 5′- and 3′- RNA decay pathways in a transcription-dependent manner. subTERRA accumulates preferentially during the G1/S transition and in C-terminal rap1 mutant but independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomeres, loss of telomeric clustering in mitotic cells and changes in silencing of subtelomeric regions. Our data suggest that subtelomeric RNAs expression links telomere maintenance to RNA degradation pathways. Full article
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