Review
Oncology
Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Summary: RNA editing, induced by ADAR, plays a crucial regulatory role in metazoans, affecting multiple cellular processes and functions. Despite the development of bioinformatics tools for identifying editing sites, the lack of widely accepted standards and challenges in tumor sample analysis still exist. Numerous editing sites have been reported in non-coding regions, impacting the biosynthesis of ncRNAs.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biology
Yulan Wang, Jian Zhao, Jing Wu, Jingjing Liu, Yixuan Wang, Tianyi Xu, Meng Zhang, Minhui Zhuang, Lingxiao Zou, Wei Sun, Ping Han, Xiaofeng Song
Summary: This study identifies dysregulated RNA editing events in circRNAs in cervical cancer and reveals a decrease in A-to-I RNA editing levels compared to normal tissues. The findings suggest that editing may influence circRNA biogenesis and the back-splicing process through structural modifications of Alu elements. Furthermore, RNA editing is shown to modulate circRNA expression and coding potential, and three potential RNA editing sites are identified as biomarkers.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Oncology
Gioacchino P. Marceca, Luisa Tomasello, Rosario Distefano, Mario Acunzo, Carlo M. Croce, Giovanni Nigita
Summary: A-to-I editing in RNA plays a crucial role in cancer biology, affecting miRNA function with clinical significance. Challenges remain in identifying and characterizing miRNA editing events in tumors.
Article
Biochemistry & Molecular Biology
Ilana Buchumenski, Karoline Holler, Lior Appelbaum, Eli Eisenberg, Jan Philipp Junker, Erez Y. Levanon
Summary: A-to-I RNA editing, mediated by ADAR enzymes, increases transcript and protein diversity. Studying zebrafish editing sites revealed high editing levels in early embryos and reproductive organs, providing insights into editing roles during development and maturity.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Jizhe Liu, Fei Wang, Yindan Zhang, Jingfeng Liu, Bixing Zhao
Summary: RNA stability, RNA-protein interaction, and correct protein translation are significant forces in driving the transition from normal cell to malignant tumor. ADAR1 is an RNA editing enzyme that modifies the transcriptome by catalyzing the deamination of adenosine to inosine. Dysregulation of ADAR1 can lead to aberrant editing and affect phenotypic changes in cancer. ADAR1's overediting phenomenon is observed in many cancers and promotes tumor progression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Huimin Zhu, Lu Huang, Songbin Liu, Zhiming Dai, Zhou Songyang, Zhihui Weng, Yuanyan Xiong
Summary: This paper presents REIA, an interactive web server for analyzing and visualizing the association between human cancers and A-to-I RNA editing sites. REIA offers various options to browse annotation/editing levels and compare differences between editing and non-editing groups.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Oncology
Shu-Yang Wang, Ling-Jie Zhang, Guo-Jun Chen, Qi-Qi Ni, Yuan Huang, Dan Zhang, Fang-Yi Han, Wen-Feng He, Li-Ling He, Yan-Qing Ding, Hong-Li Jiao, Ya-Ping Ye
Summary: RNA editing, specifically the COPA A-to-I editing event, is significantly increased in metastatic CRC tissues and associated with aggressive tumors. The COPA I164V protein activates ER stress and promotes CRC cell invasion and metastasis. Additionally, the COPA A-to-I editing rate is correlated with immune infiltration score.
Article
Biochemistry & Molecular Biology
Yoav Shoshan, Noa Liscovitch-Brauer, Joshua J. C. Rosenthal, Eli Eisenberg
Summary: RNA editing by ADAR enzymes converts adenosines into inosines, altering protein-coding sequences and diversifying the proteome; recoding is abundant in neural tissues of coleoid cephalopods with over-representation of nonsynonymous edits; shared, strongly recoded sites in coleoids have been selected for proteome diversification, suggesting that an editable A is more beneficial than an uneditable A or a genomically encoded G.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Chia-Yu Shih, Yun-Chi Chen, Heng-Yi Lin, Chia-Ying Chu
Summary: The DEAD-box proteins, including DDX6, are RNA-binding proteins that play a role in post-transcriptional regulation of gene expression. DDX6 has functions in translational repression, miRNA-mediated gene silencing, and RNA decay in the cytoplasm. Its nuclear function was previously unknown until this study discovered its interaction with ADAR1, a protein involved in RNA editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yulong Song, Xiuju He, Wenbing Yang, Yaoxing Wu, Jun Cui, Tian Tang, Rui Zhang
Summary: This study developed an editing identification pipeline specifically for RNA viruses and constructed an atlas of A-to-I RNA editing sites in SARS-CoV-2 from diverse samples. The findings showed that A-to-I editing was dynamically regulated, varied between tissue and cell types, and correlated with the intensity of innate immune response. Additionally, editing hotspots were observed, including recoding sites in the spike gene that affect viral infectivity and antigenicity. The study also provided evidence that RNA editing accelerated SARS-CoV-2 evolution in humans during the epidemic.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Tram Anh Nguyen, Jia Wei Joel Heng, Yan Ting Ng, Rui Sun, Shira Fisher, Gokce Oguz, Pornchai Kaewsapsak, Shifeng Xue, Bruno Reversade, Adaikalavan Ramasamy, Eli Eisenberg, Meng How Tan
Summary: This study identified millions of editing events in Xenopus with high accuracy and systematically mapped the editome across developmental stages, adult organs, and species. The highest deamination activity was observed in early embryogenesis and in the ovary. Editing events showed poor conservation across different Xenopus species. The findings suggest that species-specific editing may play a role in the unique physiology or environmental adaptation of each animal.
Review
Biochemistry & Molecular Biology
Anton O. Goncharov, Victoria O. Shender, Ksenia G. Kuznetsova, Anna A. Kliuchnikova, Sergei A. Moshkovskii
Summary: Adenosine-to-inosine RNA editing is a widespread post-transcriptional modification system catalyzed by ADAR enzymes, which mainly occurs in dsRNA before splicing. This review focuses on the interconnections between RNA editing and splicing in human cancer. Dysregulated RNA splicing in cancer can lead to the release of excess dsRNA into the cytosol, triggering antiviral-like responses and potentially inhibiting tumor growth. Inhibiting ADAR may enhance the effects of spliceosome inhibitors and could be a promising approach in cancer therapies targeting RNA splicing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
David Rodriguez Morales, Mirolyuba Ilieva, Sarah Rennie, Shizuka Uchida
Summary: Adenosine to inosine (A-to-I) RNA editing is a common RNA modification in mammalian transcriptomes. Upregulated RNA editing enzymes, adenosine deaminase acting on RNAs (ADARs), suggest that monitoring RNA editing patterns could be useful as diagnostic biomarkers for diseases. This article provides an overview of epitranscriptomics and focuses on the detection and analysis of A-to-I RNA editing using bioinformatic tools in RNA-seq data sets, while briefly reviewing its involvement in disease progressions. The authors argue for routine detection of RNA editing patterns in RNA-based data sets to accelerate the identification of disease-related RNA editing targets.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Oncology
Yue Mei, Dong Liang, Bin Ai, Tengjiao Wang, Shiwei Guo, Gang Jin, Dong Yu
Summary: RNA editing is involved in the occurrence and development of pancreatic cancer, primarily regulated by ADAR1. Tumor samples have a higher editing level and more editing sites compared to normal samples. Certain genes show significantly different editing events and expression levels between tumor and normal samples, with enrichment in cancer-related pathways. Furthermore, RNA editing regulates alternative splicing and RNA secondary structure of important genes, and single cell sequencing results indicate the involvement of type2ductal cells in tumor RNA editing events.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemical Research Methods
Sijia Wu, Mengyuan Yang, Pora Kim, Xiaobo Zhou
Summary: A-to-I RNA editing plays a crucial role in the pathogenesis of Alzheimer's disease (AD) and the establishment of the ADeditome database provides valuable insights for identifying therapeutic target genes. Through functional annotation of 1676 363 editing sites in 1524 samples, key editing events influencing AD progression were identified.
BRIEFINGS IN BIOINFORMATICS
(2021)
