Detection technologies for RNA modifications

To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the ‘epitranscriptome’. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput...

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Published inExperimental & molecular medicine Vol. 54; no. 10; pp. 1601 - 1616
Main Authors Zhang, Yan, Lu, Liang, Li, Xiaoyu
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.10.2022
Springer Nature B.V
Subjects
38
38/91
631/1647
631/208/514
Biomedical and Life Sciences
Biomedicine
Epigenetics
Gene expression
Gene Expression Regulation
Gene regulation
High-Throughput Nucleotide Sequencing - methods
Medical Biochemistry
Molecular Medicine
Next-generation sequencing
Nucleotide sequence
Review
Review Article
RNA - genetics
RNA - metabolism
RNA modification
Sequence Analysis, RNA
Stem Cells
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Abstract To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the ‘epitranscriptome’. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome. RNA modifications: Comparing detection tools Improved methods for detecting chemical modifications of RNA will help to understand the epitranscriptome, the collection of RNA modifications in a cell. Chemical modifications to RNA molecules do not alter the sequence, but can nonetheless greatly affect RNA function. More than 170 RNA modifications have been discovered over the past 60 years and their effects are analogous to epigenetic modifications of DNA. Xiaoyu Li and co-workers at Zhejiang University School of Medicine in Hangzhou, China, reviewed existing tools for detecting RNA modifications. These tools, which are developed based on the inherent chemical properties of RNA modifications, vary in sensitivity, quantification, specificity and accuracy. The researchers also summarize the recent progress in nanopore direct RNA sequencing based detection technology and are optimistic that future advances will enable detection of different modifications simultaneously in the single molecules.
AbstractList To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the ‘epitranscriptome’. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.RNA modifications: Comparing detection toolsImproved methods for detecting chemical modifications of RNA will help to understand the epitranscriptome, the collection of RNA modifications in a cell. Chemical modifications to RNA molecules do not alter the sequence, but can nonetheless greatly affect RNA function. More than 170 RNA modifications have been discovered over the past 60 years and their effects are analogous to epigenetic modifications of DNA. Xiaoyu Li and co-workers at Zhejiang University School of Medicine in Hangzhou, China, reviewed existing tools for detecting RNA modifications. These tools, which are developed based on the inherent chemical properties of RNA modifications, vary in sensitivity, quantification, specificity and accuracy. The researchers also summarize the recent progress in nanopore direct RNA sequencing based detection technology and are optimistic that future advances will enable detection of different modifications simultaneously in the single molecules.
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the ‘epitranscriptome’. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome. RNA modifications: Comparing detection tools Improved methods for detecting chemical modifications of RNA will help to understand the epitranscriptome, the collection of RNA modifications in a cell. Chemical modifications to RNA molecules do not alter the sequence, but can nonetheless greatly affect RNA function. More than 170 RNA modifications have been discovered over the past 60 years and their effects are analogous to epigenetic modifications of DNA. Xiaoyu Li and co-workers at Zhejiang University School of Medicine in Hangzhou, China, reviewed existing tools for detecting RNA modifications. These tools, which are developed based on the inherent chemical properties of RNA modifications, vary in sensitivity, quantification, specificity and accuracy. The researchers also summarize the recent progress in nanopore direct RNA sequencing based detection technology and are optimistic that future advances will enable detection of different modifications simultaneously in the single molecules.
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the ‘epitranscriptome’. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome. Improved methods for detecting chemical modifications of RNA will help to understand the epitranscriptome, the collection of RNA modifications in a cell. Chemical modifications to RNA molecules do not alter the sequence, but can nonetheless greatly affect RNA function. More than 170 RNA modifications have been discovered over the past 60 years and their effects are analogous to epigenetic modifications of DNA. Xiaoyu Li and co-workers at Zhejiang University School of Medicine in Hangzhou, China, reviewed existing tools for detecting RNA modifications. These tools, which are developed based on the inherent chemical properties of RNA modifications, vary in sensitivity, quantification, specificity and accuracy. The researchers also summarize the recent progress in nanopore direct RNA sequencing based detection technology and are optimistic that future advances will enable detection of different modifications simultaneously in the single molecules.
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
Author Li, Xiaoyu
Lu, Liang
Zhang, Yan
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Biomedical and Life Sciences
Biomedicine
Epigenetics
Gene expression
Gene Expression Regulation
Gene regulation
High-Throughput Nucleotide Sequencing - methods
Medical Biochemistry
Molecular Medicine
Next-generation sequencing
Nucleotide sequence
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RNA - genetics
RNA - metabolism
RNA modification
Sequence Analysis, RNA
Stem Cells
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Title Detection technologies for RNA modifications
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