Article
Biochemistry & Molecular Biology
Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignano, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi
Summary: RNA editing is a significant epitranscriptome phenomenon that enhances the diversity of eukaryotic organisms, particularly in humans. While playing crucial roles in gene expression regulation, innate immune response modulation, and neurotransmitter receptor functioning, there is still a need for further research to uncover unknown aspects of RNA editing biology.
NUCLEIC ACIDS RESEARCH
(2021)
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
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.
Article
Biochemistry & Molecular Biology
Kayla M. Shumate, Sadik T. Tas, Ege T. Kavalali, Ronald B. Emeson
Summary: Caps editing plays a crucial role in modulating neurotransmission and synaptic plasticity, particularly at inhibitory synapses. The edited Cadps transcripts increase the proportion of synapses containing CAPS1, and editing is regulated by neuronal activity.
JOURNAL OF NEUROCHEMISTRY
(2021)
Review
Genetics & Heredity
Cornelia Vesely, Michael F. Jantsch
Summary: ADARs convert adenosines to inosines in structured RNAs, marking endogenous RNAs and recoding coding RNAs. The functions of ADARs differ during development, in different tissues, upon altered physiological conditions or after exposure to pathogens.
Article
Biochemistry & Molecular Biology
Turnee N. Malik, Erin E. Doherty, Vandana M. Gaded, Theodore M. Hill, Peter A. Beal, Ronald B. Emeson
Summary: ADAR-mediated RNA editing modulates various cellular pathways such as innate immunity and protein recoding and is considered as a strategy for treating genetic disorders. Research has shown that intracellular acidification increases RNA editing, mainly due to enhanced ADAR base-flipping and deamination rate under acidic pH conditions.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Rohini Datta, Julia Z. Adamska, Amruta Bhate, Jin Billy Li
Summary: ADAR1 is a crucial enzyme that regulates the RNA sensing pathway by editing RNA substrates, maintaining a balance between innate antiviral responses and autoimmunity. Reduced editing by ADAR1 is associated with autoimmune and inflammatory diseases. In viral infections and cancer, ADAR1 exhibits both antiviral and proviral effects. Understanding ADAR1's role can lead to therapeutic advancements.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Genetics & Heredity
Ernesto Picardi, Luigi Mansi, Graziano Pesole
Summary: This study demonstrates that the A-to-G changes observed in the SARS-COV-2 genomes are genuine RNA editing events mediated by ADAR1, and these edits may have significant impact on the virus-host interactions.
Article
Genetics & Heredity
Dean Light, Roni Haas, Mahmoud Yazbak, Tal Elfand, Tal Blau, Ayelet T. Lamm
Summary: This study introduces an efficient pipeline RESIC for detecting and classifying RNA editing sites, applicable to all organisms and integrating multiple approaches. Results demonstrate changes in A-to-I RNA editing patterns and ADAR enzyme RNA abundance following SARS-CoV-2 infection, suggesting potential involvement in COVID-19 disease phenotype.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Cristian Riella, Michelle McNulty, Guilherme T. Ribas, Calum F. Tattersfield, Chandra Perez-Gill, Felix Eichinger, Jessica Kelly, Justin Chun, Balajikarthick Subramanian, Dieval Guizelini, Seth L. Alper, Martin R. Pollak, Matthew G. Sampson, David J. Friedman
Summary: APOL1 risk variants are associated with increased risk of kidney disease in individuals of African ancestry. The expression of APOL1 gene is closely related to the degree of kidney cell injury. Regulation of APOL1 expression through ADAR-mediated editing may play a critical role in determining the penetrance of risk alleles. This study provides evidence that ADAR down-regulates APOL1 by preventing MDA5 recognition of dsRNA, and ADAR-mediated editing is an important regulator of APOL1 expression and may impact the severity of APOL1-associated kidney disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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.
Review
Genetics & Heredity
Chao Li, Wen Chu, Rafaqat Ali Gill, Shifei Sang, Yuqin Shi, Xuezhi Hu, Yuting Yang, Qamar U. Zaman, Baohong Zhang
Summary: In the past decade, significant progress has been made in developing versatile CRISPR/Cas nucleases and precise genome editors. Computer-assisted tools have played a crucial role in designing sgRNA and analyzing CRISPR/Cas-induced mutations. This review provides insights into the different features of CRISPR/Cas tools, the usage of computer-assisted tools, and the limitations and suggestions for further optimization.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Lev I. Levitsky, Mark V. Ivanov, Anton O. Goncharov, Anna A. Kliuchnikova, Julia A. Bubis, Anna A. Lobas, Elizaveta M. Solovyeva, Mikhail A. Pyatnitskiy, Ruslan K. Ovchinnikov, Michail S. Kukharsky, Tatiana E. Farafonova, Svetlana E. Novikova, Victor G. Zgoda, Irina A. Tarasova, Mikhail V. Gorshkov, Sergei A. Moshkovskii
Summary: The proteogenomic search pipeline was used to reanalyze 40 publicly available shotgun proteomic datasets from various human tissues. A total of 5442 .raw data files were processed, identifying 33 recoded protein sites in 21 datasets. The study demonstrated that neural and cancer tissues were enriched with recoded proteins and the recoding rate was regulated by the interaction of enzymes with mRNA.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Johan Ringlander, Joshua Fingal, Hanna Kann, Kasthuri Prakash, Gustaf Rydell, Maria Andersson, Anna Martner, Magnus Lindh, Peter Horal, Kristoffer Hellstrand, Michael Kann
Summary: This study utilized deep sequencing to analyze RNA mutations in early-phase SARS-CoV-2 infected patients, and found that ADAR-induced RNA editing played an important role in these mutations. A->G mutations were abundant in minor viral populations and significantly associated with low viral load. Moreover, the frequency of these mutations increased in European consensus sequences and then decreased in autumn and early winter.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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)