Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations
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,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/12/5/611 |
| _version_ | 1797501343398625280 |
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| author | Megumi Shigematsu Yohei Kirino |
| author_facet | Megumi Shigematsu Yohei Kirino |
| author_sort | Megumi Shigematsu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T03:17:02Z |
| format | Article |
| id | doaj.art-f3941d2cac584e45b945e5c3809fee0c |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T03:17:02Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-f3941d2cac584e45b945e5c3809fee0c2023-11-23T10:12:57ZengMDPI AGBiomolecules2218-273X2022-04-0112561110.3390/biom12050611Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal FormationsMegumi Shigematsu0Yohei Kirino1Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USAComputational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USANext 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.https://www.mdpi.com/2218-273X/12/5/611short non-coding RNARNA-seq2′,3′-cyclic phosphatecP-RNA-seqphospho-seq5’-hydroxyl-seq |
| spellingShingle | Megumi Shigematsu Yohei Kirino Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations Biomolecules short non-coding RNA RNA-seq 2′,3′-cyclic phosphate cP-RNA-seq phospho-seq 5’-hydroxyl-seq |
| title | Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations |
| title_full | Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations |
| title_fullStr | Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations |
| title_full_unstemmed | Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations |
| title_short | Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations |
| title_sort | making invisible rna visible discriminative sequencing methods for rna molecules with specific terminal formations |
| topic | short non-coding RNA RNA-seq 2′,3′-cyclic phosphate cP-RNA-seq phospho-seq 5’-hydroxyl-seq |
| url | https://www.mdpi.com/2218-273X/12/5/611 |
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