Journal
BIOMOLECULES
Volume 12, Issue 5, Pages -Publisher
MDPI
DOI: 10.3390/biom12050611
Keywords
short non-coding RNA; RNA-seq; 2 ',3 '-cyclic phosphate; cP-RNA-seq; phospho-seq; 5 '-hydroxyl-seq
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Funding
- National Institutes of Health [GM106047, HL150560, AI151641, AI168975]
- American Cancer Society Research Scholar Grant [RSG-17-059-01-RMC]
- Japan Society for the Promotion of Science
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RNA-seq is a common tool for characterizing RNA expression profiles and regulations in physiological processes and diseases. Specific RNA-seq methods have been developed to characterize the expression profiles of sncRNAs with various terminal formations, shedding light on previously unrecognized sncRNAs.
Next generation sequencing of RNA molecules (RNA-seq) has become a common tool to characterize the expression profiles of RNAs and their regulations in normal physiological processes and diseases. Although increasingly accumulating RNA-seq data are widely available through publicly accessible sites, most of the data for short non-coding RNAs (sncRNAs) have been obtained for microRNA (miRNA) analyses by standard RNA-seq, which only capture the sncRNAs with 5'-phosphate (5-P) and 3'-hydroxyl (3'-OH) ends. The sncRNAs with other terminal formations such as those with a 5'-hydroxyl end (5'-OH), a 3'-phosphate (3-P) end, or a 2',3'-cyclic phosphate end (2',3'-cP) cannot be efficiently amplified and sequenced by standard RNA-seq. Due to the invisibility in standard RNA-seq data, these non-miRNA-sncRNAs have been a hidden component in the transcriptome. However, as the functional significances of these sncRNAs have become increasingly apparent, specific RNA-seq methods compatible with various terminal formations of sncRNAs have been developed and started shedding light on the previously unrecognized sncRNAs that lack 5'-P/3'-OH ends. In this review, we summarize the expanding world of sncRNAs with various terminal formations and the strategic approaches of specific RNA-seq methods to distinctively characterize their expression profiles.
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