A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects

Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V

(2020) Steve D. Knutson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

(2020) Claudio Lo Giudice et al.   Nature Protocols

Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development

(2020) Sze Jing Tang et al.   Nature Communications

Novel Engineered Programmable Systems for ADAR-Mediated RNA Editing

(2020) Guillermo Aquino-Jarquin   Molecular Therapy-Nucleic Acids

Chemical Profiling of A‐to‐I RNA Editing Using a Click‐Compatible Phenylacrylamide

(2020) Steve D Knutson et al.   CHEMISTRY-A EUROPEAN JOURNAL

The A-to-I RNA Editing Enzyme Adar1 Is Essential for Normal Embryonic Cardiac Growth and Development

(2020) Joseph B Moore et al.   CIRCULATION RESEARCH

ADAR1 Regulates Early T Cell Development via MDA5-Dependent and -Independent Pathways

(2020) Tuangtong Vongpipatana et al.   JOURNAL OF IMMUNOLOGY

Long non-coding RNAs regulate drug resistance in cancer

(2020) Kaisheng Liu et al.   Molecular Cancer

The cell line A-to-I RNA editing catalogue

(2020) Amos A Schaffer et al.   NUCLEIC ACIDS RESEARCH

ADAR1-mediated RNA editing is a novel oncogenic process in thyroid cancer and regulates miR-200 activity

(2020) Julia Ramírez-Moya et al.   ONCOGENE

RNA editing mediates the functional switch of COPA in a novel mechanism of hepatocarcinogenesis

(2020) Yangyang Song et al.   JOURNAL OF HEPATOLOGY

De Novo A-to-I RNA Editing Discovery in lncRNA

(2020) Domenico Alessandro Silvestris et al.   Cancers

A-to-I RNA editing as a tuner of noncoding RNAs in cancer

(2020) Yuanfan Liao et al.   CANCER LETTERS

EPAI-NC: Enhanced prediction of adenosine to inosine RNA editing sites using nucleotide compositions

(2019) Ahsan Ahmad et al.   ANALYTICAL BIOCHEMISTRY

Mapping the dsRNA World

(2019) Daniel P. Reich et al.   Cold Spring Harbor Perspectives in Biology

ADAR1: A New Target for Immuno-oncology Therapy

(2019) Amruta Bhate et al.   MOLECULAR CELL

The Landscape of Circular RNA in Cancer

(2019) Josh N. Vo et al.   CELL

Circular RNAs in Cancer: emerging functions in hallmarks, stemness, resistance and roles as potential biomarkers

(2019) Min Su et al.   Molecular Cancer

Identification of Adenosine-to-Inosine RNA Editing with Acrylonitrile Reagents

(2019) Ying Li et al.   ORGANIC LETTERS

The Role of Non-coding RNAs in Oncology

(2019) Frank J. Slack et al.   CELL

Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity

(2019) Shalom Hillel Roth et al.   NATURE METHODS

Ranking of non-coding pathogenic variants and putative essential regions of the human genome

(2019) Alex Wells et al.   Nature Communications

A-to-I RNA Editing: An Overlooked Source of Cancer Mutations

(2018) Shay Ben-Aroya et al.   CANCER CELL

A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer

(2018) Xinxin Peng et al.   CANCER CELL

The role of A-to-I RNA editing in cancer development

(2018) Xiaoyan Xu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

RNA editing in nascent RNA affects pre-mRNA splicing

(2018) Yun-Hua Esther Hsiao et al.   GENOME RESEARCH

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

A-to-I RNA editing — immune protector and transcriptome diversifier

(2018) Eli Eisenberg et al.   NATURE REVIEWS GENETICS

Base modifications affecting RNA polymerase and reverse transcriptase fidelity

(2018) Vladimir Potapov et al.   NUCLEIC ACIDS RESEARCH

ADARs and editing: The role of A-to-I RNA modification in cancer progression

(2018) Kajsa Fritzell et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Accurate identification of RNA editing sites from primitive sequence with deep neural networks

(2018) Zhangyi Ouyang et al.   Scientific Reports

Increased RNA Editing May Provide a Source for Autoantigens in Systemic Lupus Erythematosus

(2018) Shalom Hillel Roth et al.   Cell Reports

Chemical Labeling and Affinity Capture of Inosine-Containing RNAs Using Acrylamidofluorescein

(2018) Steve D. Knutson et al.   BIOCONJUGATE CHEMISTRY

Single-nucleotide variants in human RNA: RNA editing and beyond

(2018) Yan Guo et al.   Briefings in Functional Genomics

Computational approaches for detection and quantification of A-to-I RNA-editing

(2018) Yishay Pinto et al.   METHODS

Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade

(2018) Jeffrey J. Ishizuka et al.   NATURE

Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss

(2018) Huayang Liu et al.   NATURE MEDICINE

ADAR2-dependent A-to-I RNA editing in the extracellular linear and circular RNAs

(2018) Takashi Hosaka et al.   NEUROSCIENCE RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells

(2018) Hugh S. Gannon et al.   Nature Communications

The Role of RNA Editing in Cancer Development and Metabolic Disorders

(2018) Che-Pei Kung et al.   Frontiers in Endocrinology

Activation of AZIN1 RNA editing is a novel mechanism that promotes invasive potential of cancer-associated fibroblasts in colorectal cancer

(2018) Sho Takeda et al.   CANCER LETTERS

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

(2017) Yumeng Wang et al.   GENOME RESEARCH

Adenosine Deaminase That Acts on RNA 3 (ADAR3) Binding to Glutamate Receptor Subunit B Pre-mRNA Inhibits RNA Editing in Glioblastoma

(2017) Eimile Oakes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamic landscape and regulation of RNA editing in mammals

(2017) Meng How Tan et al.   NATURE

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins

(2017) Aparna Anantharaman et al.   NUCLEIC ACIDS RESEARCH

Single-cell transcriptomics reveals specific RNA editing signatures in the human brain

(2017) Ernesto Picardi et al.   RNA

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizingFAK

(2017) Elianna M. Amin et al.   Science Signaling

Circular RNA expression is suppressed by androgen receptor (AR)-regulated adenosine deaminase that acts on RNA (ADAR1) in human hepatocellular carcinoma

(2017) Liang Shi et al.   Cell Death & Disease

The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizingFAK

(2017) Elianna M. Amin et al.   Science Signaling

RED-ML: a novel, effective RNA editing detection method based on machine learning

(2017) Heng Xiong et al.   GigaScience

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data

(2016) Min-su Kim et al.   BMC GENOMICS

RNAEditor: easy detection of RNA editing events and the introduction of editing islands

(2016) David John et al.   BRIEFINGS IN BIOINFORMATICS

ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis

(2016) Maria Anna Zipeto et al.   Cell Stem Cell

Editing of Cellular Self-RNAs by Adenosine Deaminase ADAR1 Suppresses Innate Immune Stress Responses

(2016) Cyril X. George et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of human RNA editing sites: A historical perspective

(2016) Gokul Ramaswami et al.   METHODS

Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation

(2016) Konstantinos Stellos et al.   NATURE MEDICINE

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

LNCediting: a database for functional effects of RNA editing in lncRNAs

(2016) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters

(2016) Yongmei Sun et al.   PLoS One

Next-generation sequencing technologies for detection of modified nucleotides in RNAs

(2016) Schraga Schwartz et al.   RNA Biology

The mRNA-edited form of GABRA3 suppresses GABRA3-mediated Akt activation and breast cancer metastasis

(2016) Kiranmai Gumireddy et al.   Nature Communications

iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences

(2016) Wei Chen et al.   Oncotarget

RES-Scanner: a software package for genome-wide identification of RNA-editing sites

(2016) Zongji Wang et al.   GigaScience

PAI: Predicting adenosine to inosine editing sites by using pseudo nucleotide compositions

(2016) Wei Chen et al.   Scientific Reports

RASER: reads aligner for SNPs and editing sites of RNA

(2015) Jaegyoon Ahn et al.   BIOINFORMATICS

DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data

(2015) Shahar Alon et al.   BIOINFORMATICS

RCARE: RNA Sequence Comparison and Annotation for RNA Editing

(2015) Soo Youn Lee et al.   BMC Medical Genomics

The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers

(2015) Leng Han et al.   CANCER CELL

Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development

(2015) Kathleen Pestal et al.   IMMUNITY

An RNA editing fingerprint of cancer stem cell reprogramming

(2015) Leslie A Crews et al.   Journal of Translational Medicine

Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates

(2015) Xin-Zhuang Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

(2015) Agnieszka Rybak-Wolf et al.   MOLECULAR CELL

Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis

(2015) Einav Shoshan et al.   NATURE CELL BIOLOGY

Genome sequence–independent identification of RNA editing sites

(2015) Qing Zhang et al.   NATURE METHODS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The re-emergence of natural products for drug discovery in the genomics era

(2015) Alan L. Harvey et al.   NATURE REVIEWS DRUG DISCOVERY

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The reverse transcription signature ofN-1-methyladenosine in RNA-Seq is sequence dependent

(2015) Ralf Hauenschild et al.   NUCLEIC ACIDS RESEARCH

PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNAPCA3

(2015) Ahmad Salameh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease

(2015) Khen Khermesh et al.   RNA

RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself

(2015) B. J. Liddicoat et al.   SCIENCE

Profiling RNA editing in human tissues: towards the inosinome Atlas

(2015) Ernesto Picardi et al.   Scientific Reports

Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors

(2015) Nurit Paz-Yaacov et al.   Cell Reports

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

(2015) Andranik Ivanov et al.   Cell Reports

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

A genome-wide map of hyper-edited RNA reveals numerous new sites

(2014) Hagit T. Porath et al.   Nature Communications

The RNA-Editing Enzyme ADAR1 Controls Innate Immune Responses to RNA

(2014) Niamh M. Mannion et al.   Cell Reports

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

VIRGO: visualization of A-to-I RNA editing sites in genomic sequences

(2013) Rosario Distefano et al.   BMC BIOINFORMATICS

Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences

(2013) Shanshan Zhu et al.   BMC GENOMICS

A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma

(2013) Tim Hon Man Chan et al.   GUT

Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma

(2013) Leilei Chen et al.   NATURE MEDICINE

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing

(2013) Rui Zhang et al.   NATURE METHODS

Identifying RNA editing sites using RNA sequencing data alone

(2013) Gokul Ramaswami et al.   NATURE METHODS

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

ADAR1 is essential for intestinal homeostasis and stem cell maintenance

(2013) W Qiu et al.   Cell Death & Disease

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Attenuated adenosine-to-inosine editing of microRNA-376a* promotes invasiveness of glioblastoma cells

(2012) Yukti Choudhury et al.   JOURNAL OF CLINICAL INVESTIGATION

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Accurate identification of human Alu and non-Alu RNA editing sites

(2012) Gokul Ramaswami et al.   NATURE METHODS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Predicting sites of ADAR editing in double-stranded RNA

(2011) Julie M. Eggington et al.   Nature Communications

DARNED: a DAtabase of RNa EDiting in humans

(2010) A. Kiran et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Influence of an Adenosine Deaminase Inhibitor, Erythro-9-(2-hydroxy-3-nonyl) Adenine Hydrochloride, on 5-HT2CR mRNA Editing in Primary Cultured Cortical Cells

(2010) Pham Nguyet Thi Hang et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

ADAR1 is essential for the maintenance of hematopoiesis and suppression of interferon signaling

(2008) Jochen C Hartner et al.   NATURE IMMUNOLOGY