An Overview of Current Detection Methods for RNA Methylation

An Overview of Current Detection Methods for RNA Methylation

7 March 2024 | Buket Sağlam and Bünyamin Akgül
This review provides an overview of current detection methods for RNA methylation, highlighting their advantages and disadvantages, as well as the challenges in the field. RNA methylation, a key epitranscriptomic modification, plays vital roles in various cellular processes, including translation, splicing, and stability. Common RNA methylation marks include m6A, m1A, m7G, and m5C, each with distinct biochemical properties and functions. The detection of these modifications is crucial for understanding their impact on cellular processes under both health and disease conditions. RNA methylation detection methods can be classified into five categories: antibody-based, digestion-based, ligation-based, hybridization-based, and direct RNA-based methods. Each method has its own advantages and limitations in terms of resolution, cost, and technical requirements. For instance, antibody-based methods such as MeRIP-seq and miCLIP are widely used for global and site-specific detection of m6A, while digestion-based methods like MazF RNAse are used for site-specific detection. Ligation-based methods such as SELECT are also employed for site-specific detection of methylation marks. Recent advances in detection technologies, including DART-Seq and nanopore sequencing, have improved the accuracy and resolution of RNA methylation analysis. These methods allow for the quantification of methylation marks at the single-nucleotide level, providing insights into the dynamic nature of RNA modifications. However, challenges remain in terms of cost, technical complexity, and the need for specialized infrastructure. In conclusion, RNA methylation detection methods are essential for understanding the role of these modifications in health and disease. While various techniques are available, each has its own strengths and limitations, and the choice of method depends on the specific research question and available resources. Continued development of more efficient and cost-effective methods is needed to fully explore the functional implications of RNA methylation in biological systems.This review provides an overview of current detection methods for RNA methylation, highlighting their advantages and disadvantages, as well as the challenges in the field. RNA methylation, a key epitranscriptomic modification, plays vital roles in various cellular processes, including translation, splicing, and stability. Common RNA methylation marks include m6A, m1A, m7G, and m5C, each with distinct biochemical properties and functions. The detection of these modifications is crucial for understanding their impact on cellular processes under both health and disease conditions. RNA methylation detection methods can be classified into five categories: antibody-based, digestion-based, ligation-based, hybridization-based, and direct RNA-based methods. Each method has its own advantages and limitations in terms of resolution, cost, and technical requirements. For instance, antibody-based methods such as MeRIP-seq and miCLIP are widely used for global and site-specific detection of m6A, while digestion-based methods like MazF RNAse are used for site-specific detection. Ligation-based methods such as SELECT are also employed for site-specific detection of methylation marks. Recent advances in detection technologies, including DART-Seq and nanopore sequencing, have improved the accuracy and resolution of RNA methylation analysis. These methods allow for the quantification of methylation marks at the single-nucleotide level, providing insights into the dynamic nature of RNA modifications. However, challenges remain in terms of cost, technical complexity, and the need for specialized infrastructure. In conclusion, RNA methylation detection methods are essential for understanding the role of these modifications in health and disease. While various techniques are available, each has its own strengths and limitations, and the choice of method depends on the specific research question and available resources. Continued development of more efficient and cost-effective methods is needed to fully explore the functional implications of RNA methylation in biological systems.
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