An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms.
RNA sequencing
non-coding RNA
small RNA
unusually short RNA
Journal
Non-coding RNA
ISSN: 2311-553X
Titre abrégé: Noncoding RNA
Pays: Switzerland
ID NLM: 101652294
Informations de publication
Date de publication:
19 May 2022
19 May 2022
Historique:
received:
22
02
2022
revised:
09
05
2022
accepted:
16
05
2022
entrez:
1
6
2022
pubmed:
2
6
2022
medline:
2
6
2022
Statut:
epublish
Résumé
Small RNA sequencing (sRNA-Seq) approaches unveiled sequences derived from longer non-coding RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA) fragments, known as tRFs and rRFs, respectively. However, rRNAs and RNAs shorter than 16 nt are often depleted from library preparations/sequencing analyses, although they may be functional. Here, we sought to obtain a complete repertoire of small RNAs by sequencing the total RNA from 11 samples of 6 different eukaryotic organisms, from yeasts to human, in an extended 8- to 30-nt window of RNA length. The 8- to 15-nt window essentially contained fragments of longer non-coding RNAs, such as microRNAs, PIWI-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs), tRNAs and rRNAs. Notably, unusually short RNAs < 16 nt were more abundant than those >16 nt in bilaterian organisms. A new RT-qPCR method confirmed that two unusually short rRFs of 12 and 13 nt were more overly abundant (~3-log difference) than two microRNAs. We propose to not deplete rRNA and to reduce the lower threshold of RNA length to include unusually short RNAs in sRNA-Seq analyses and datasets, as their abundance and diversity support their potential role and importance as biomarkers of disease and/or mediators of cellular function.
Identifiants
pubmed: 35645341
pii: ncrna8030034
doi: 10.3390/ncrna8030034
pmc: PMC9149858
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : Natural Sciences and Engineering Research Council
ID : RGPIN-2019-06502
Organisme : Fonds de Recherche du Québec - Nature et Technologies
ID : 289637
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