Technical challenges in defining RNA modifications

Gefei Huang, Qiutao Ding, Dongying Xie, Zongwei Cai*, Zhongying Zhao*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

8 Citations (Scopus)


It is well established that DNA base modifications play a key role in gene regulation during development and in response to environmental stress. This type of epigenetic control of development and environmental responses has been intensively studied over the past few decades. Similar to DNA, various RNA species also undergo modifications that play important roles in, for example, RNA splicing, protein translation, and the avoidance of immune surveillance by host. More than 160 different types of RNA modifications have been identified. In addition to base modifications, RNA modification also involves splicing of pre-mRNAs, leading to as many as tens of transcript isoforms from a single pre-RNA, especially in higher organisms. However, the function, prevalence and distribution of RNA modifications are poorly understood. The lack of a suitable method for the reliable identification of RNA modifications constitutes a significant challenge to studying their functions. This review focuses on the technologies that enable de novo identification of RNA base modifications and the alternatively spliced mRNA transcripts.

Original languageEnglish
Pages (from-to)155-165
Number of pages11
JournalSeminars in Cell and Developmental Biology
Early online date24 Nov 2021
Publication statusPublished - Jul 2022

Scopus Subject Areas

  • Developmental Biology
  • Cell Biology

User-Defined Keywords

  • Nanopore sequencing
  • RNA base modification
  • RNA splicing
  • Third-generation sequencing


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