Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination

Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution

(2021) Jeremy Ratcliff et al.   VIROLOGY

Lung expression of genes putatively involved in SARS-CoV-2 infection is modulated in cis by germline variants

(2021) Chiara E. Cotroneo et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

(2021) Alex Graudenzi et al.   iScience

Programmable C‐to‐U RNA editing using the human APOBEC3A deaminase

(2021) Xinxin Huang et al.   EMBO JOURNAL

Induction of APOBEC3 exacerbates DNA replication stress and chromosomal instability in early breast and lung cancer evolution

(2021) Subramanian Venkatesan et al.   Cancer Discovery

Creating RNA Specific C-to-U Editase from APOBEC3A by Separation of Its Activities on DNA and RNA Substrates

(2021) Guiyue Tang et al.   ACS Synthetic Biology

Harnessing self-labeling enzymes for selective and concurrent A-to-I and C-to-U RNA base editing

(2021) Anna S Stroppel et al.   NUCLEIC ACIDS RESEARCH

APOBEC1 mediated C-to-U RNA editing: target sequence and trans-acting factor contribution to 177 RNA editing events in 119 murine transcripts in vivo

(2021) Saeed Soleymanjahi et al.   RNA

Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA

(2021) Peter Simmonds et al.   PLoS Pathogens

Site-directed RNA editing: recent advances and open challenges

(2021) Hamid Mansouri Khosravi et al.   RNA Biology

Detection of A-to-I RNA Editing in SARS-COV-2

(2021) Ernesto Picardi et al.   Genes

Step aside CRISPR, RNA editing is taking off

(2020) Sara Reardon   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

APOBEC3B-mediated corruption of the tumor cell immunopeptidome induces heteroclitic neoepitopes for cancer immunotherapy

(2020) Christopher B. Driscoll et al.   Nature Communications

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

(2020) Daniel Blanco-Melo et al.   CELL

Characterization and functional analysis of chicken APOBEC4

(2020) Mengyu Shi et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

(2020) Mingfeng Liao et al.   NATURE MEDICINE

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

(2020) Julia Ramírez-Moya et al.   ONCOGENE

Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2

(2020) Salvatore Di Giorgio et al.   Science Advances

Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots

(2020) Pégah Jalili et al.   Nature Communications

Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

(2020) Roman Matyášek et al.   Genes

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

(2020) Lucy van Dorp et al.   INFECTION GENETICS AND EVOLUTION

Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic

(2020) Leszek J. Klimczak et al.   PLoS One

Host Immune Response Driving SARS-CoV-2 Evolution

(2020) Rui Wang et al.   Viruses-Basel

Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding

(2019) Hande Boyaci et al.   NATURE

Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes

(2019) Igor Rogozin et al.   Cancers

Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides

(2019) Tobias Merkle et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

(2019) Changyang Zhou et al.   NATURE

Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs

(2019) Liang Qu et al.   NATURE BIOTECHNOLOGY

A cytosine deaminase for programmable single-base RNA editing

(2019) Omar O. Abudayyeh et al.   SCIENCE

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features

(2019) Rémi Buisson et al.   SCIENCE

Off-Target Editing by CRISPR-Guided DNA Base Editors

(2019) SeHee Park et al.   BIOCHEMISTRY

RNA editing in the forefront of epitranscriptomics and human health

(2019) Theodoulakis Christofi et al.   Journal of Translational Medicine

APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival

(2019) Mariko Asaoka et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The deaminase APOBEC3B triggers the death of cells lacking uracil DNA glycosylase

(2019) Artur A. Serebrenik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution

(2018) S Venkatesan et al.   ANNALS OF ONCOLOGY

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

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

Pancancer analysis identifies prognostic high-APOBEC1 expression level implicated in cancer in-frame insertions and deletions

(2018) Ahmadreza Niavarani et al.   CARCINOGENESIS

Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity

(2018) Joshua A Hayward et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism

(2018) Nadine M. Shaban et al.   MOLECULAR CELL

DNA/RNA hybrid substrates modulate the catalytic activity of purified AID

(2018) Hala S. Abdouni et al.   MOLECULAR IMMUNOLOGY

Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs

(2018) Paul Vogel et al.   NATURE METHODS

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

(2018) Eli Eisenberg et al.   NATURE REVIEWS GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands

(2018) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA

(2018) Atanu Maiti et al.   Nature Communications

APOBEC3-mediated restriction of RNA virus replication

(2018) Aleksandra Milewska et al.   Scientific Reports

APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction

(2018) Daniel J. Salamango et al.   MOLECULAR AND CELLULAR BIOLOGY

Current strategies for Site-Directed RNA Editing using ADARs

(2018) Maria Fernanda Montiel-Gonzalez et al.   METHODS

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

Apobec1 complementation factor (A1CF) and RBM47 interact in tissue-specific regulation of C to U RNA editing in mouse intestine and liver

(2018) Valerie Blanc et al.   RNA

RNA Editors, Cofactors, and mRNA Targets: An Overview of the C-to-U RNA Editing Machinery and Its Implication in Human Disease

(2018) Taga Lerner et al.   Genes

Critical review on engineering deaminases for site-directed RNA editing

(2018) Paul Vogel et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315

(2017) Bogdan Polevoda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

AID Recognizes Structured DNA for Class Switch Recombination

(2017) Qi Qiao et al.   MOLECULAR CELL

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

Loss of APOBEC1 RNA-editing function in microglia exacerbates age-related CNS pathophysiology

(2017) Daniel C. Cole et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epitranscriptomic profiling across cell types reveals associations between APOBEC1-mediated RNA editing, gene expression outcomes, and cellular function

(2017) Violeta Rayon-Estrada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

APOBEC1 complementation factor (A1CF) is dispensable for C-to-U RNA editing in vivo

(2017) Elizabeth M. Snyder et al.   RNA

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

(2017) Takahide Kouno et al.   Nature Communications

Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G

(2017) Shraddha Sharma et al.   PeerJ

A Novel Regulator of Activation-Induced Cytidine Deaminase/APOBECs in Immunity and Cancer: Schrödinger’s CATalytic Pocket

(2017) Justin J. King et al.   Frontiers in Immunology

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

APOBEC4 Enhances the Replication of HIV-1

(2016) Daniela Marino et al.   PLoS One

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

(2016) F. Jiang et al.   SCIENCE

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Clusters of Multiple Mutations: Incidence and Molecular Mechanisms

(2015) Kin Chan et al.   Annual Review of Genetics

Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA

(2015) Simin Zheng et al.   CELL

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

APOBECs and virus restriction

(2015) Reuben S. Harris et al.   VIROLOGY

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

(2015) C. Swanton et al.   Cancer Discovery

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

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

C to U RNA editing mediated by APOBEC1 requires RNA-binding protein RBM47

(2014) N. Fossat et al.   EMBO REPORTS

Zinc-binding Domain-dependent, Deaminase-independent Actions of Apolipoprotein B mRNA-editing Enzyme, Catalytic Polypeptide 2 (Apobec2), Mediate Its Effect on Zebrafish Retina Regeneration

(2014) Curtis Powell et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

APOBEC3A Functions as a Restriction Factor of Human Papillomavirus

(2014) Cody J. Warren et al.   JOURNAL OF VIROLOGY

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

(2014) Valerie Blanc et al.   GENOME BIOLOGY

Subcellular localization of the APOBEC3 proteins during mitosis and implications for genomic DNA deamination

(2013) Lela Lackey et al.   CELL CYCLE

The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5′-CC to 5′-TC by a Single Amino Acid Substitution

(2013) Anurag Rathore et al.   JOURNAL OF MOLECULAR BIOLOGY

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells

(2013) Eric L Fritz et al.   NATURE IMMUNOLOGY

Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties

(2013) M. Mitra et al.   NUCLEIC ACIDS RESEARCH

APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure

(2013) Colleen M. Holtz et al.   NUCLEIC ACIDS RESEARCH

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin et al.   RNA

APOBEC2 Is a Monomer in Solution: Implications for APOBEC3G Models

(2012) Troy C. Krzysiak et al.   BIOCHEMISTRY

An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals

(2012) Carsten Münk et al.   BMC EVOLUTIONARY BIOLOGY

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Viral Quasispecies Evolution

(2012) E. Domingo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions

(2012) Steven A. Roberts et al.   MOLECULAR CELL

AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

(2012) Christopher S Nabel et al.   Nature Chemical Biology

Transgenerational epigenetic effects of the Apobec1 cytidine deaminase deficiency on testicular germ cell tumor susceptibility and embryonic viability

(2012) V. R. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ADAR protein family

(2012) Yiannis A Savva et al.   GENOME BIOLOGY

APOBEC3A can activate the DNA damage response and cause cell-cycle arrest

(2011) Sébastien Landry et al.   EMBO REPORTS

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

(2011) Brad R Rosenberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Lack of Apobec2-related proteins causes a dystrophic muscle phenotype in zebrafish embryos

(2010) Christelle Etard et al.   JOURNAL OF CELL BIOLOGY

Structure-Function Analyses Point to a Polynucleotide-Accommodating Groove Essential for APOBEC3A Restriction Activities

(2010) Y. Bulliard et al.   JOURNAL OF VIROLOGY

Human APOBEC3G-Mediated Editing Can Promote HIV-1 Sequence Diversification and Accelerate Adaptation to Selective Pressure

(2010) E.-Y. Kim et al.   JOURNAL OF VIROLOGY

The B Cell Mutator AID Promotes B Lymphoid Blast Crisis and Drug Resistance in Chronic Myeloid Leukemia

(2009) Lars Klemm et al.   CANCER CELL

Deficiency in APOBEC2 Leads to a Shift in Muscle Fiber Type, Diminished Body Mass, and Myopathy

(2009) Yusuke Sato et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Specific recruitment of protein kinase A to the immunoglobulin locus regulates class-switch recombination

(2009) Bao Q Vuong et al.   NATURE IMMUNOLOGY

Active nuclear import and cytoplasmic retention of activation-induced deaminase

(2009) Anne-Marie Patenaude et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

(2009) Natasha Wood et al.   PLoS Pathogens

Zinc Coordination Geometry and Ligand Binding Affinity: The Structural and Kinetic Analysis of the Second-Shell Serine 228 Residue and the Methionine 180 Residue of the Aminopeptidase fromVibrio proteolyticus†

(2008) Niloufar J. Ataie et al.   BIOCHEMISTRY

Human Cytidine Deaminase APOBEC3H Restricts HIV-1 Replication

(2008) Ying Dang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Guidelines for Naming Nonprimate APOBEC3 Genes and Proteins

(2008) R. S. LaRue et al.   JOURNAL OF VIROLOGY

Interaction between Antibody-Diversification Enzyme AID and Spliceosome-Associated Factor CTNNBL1

(2008) Silvestro G. Conticello et al.   MOLECULAR CELL

The AID/APOBEC family of nucleic acid mutators

(2008) Silvestro G Conticello   GENOME BIOLOGY