TY - JOUR
T1 - Technical challenges in defining RNA modifications
AU - Huang, Gefei
AU - Ding, Qiutao
AU - Xie, Dongying
AU - Cai, Zongwei
AU - Zhao, Zhongying
N1 - Funding Information:
We thank Dr. Cindy Tan for logistic support and members of Zhao’s lab for helpful comments. This work was supported by General Research Funds ( HKBU12100917 , HKBU12123716 , N_HKBU201/18 , HKBU12100118 ) from Hong Kong Research Grant Council and Interdisciplinary Research Clusters Matching Scheme ( RC-IRCs-17-18-06 ) from HKBU Research Committee to ZZ.
Publisher Copyright:
© 2022 Elsevier Ltd
PY - 2022/7
Y1 - 2022/7
N2 - 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.
AB - 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.
KW - HPLC-MS/MS
KW - Nanopore sequencing
KW - RNA base modification
KW - RNA splicing
KW - Third-generation sequencing
UR - http://www.scopus.com/inward/record.url?scp=85119901633&partnerID=8YFLogxK
U2 - 10.1016/j.semcdb.2021.11.009
DO - 10.1016/j.semcdb.2021.11.009
M3 - Journal article
AN - SCOPUS:85119901633
SN - 1084-9521
VL - 127
SP - 155
EP - 165
JO - Seminars in Cell and Developmental Biology
JF - Seminars in Cell and Developmental Biology
ER -