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Prochazkova-Carlotti M, Gros A, Richard E, Cherrier F, Laharanne E, Idrissi Y, Baron C, Poglio S, Ducharme O, Menguy S, Pham-Ledard A, Beylot-Barry M, Merlio JP, Bresson-Bepoldin L. Patient-Derived Xenograft and Cell Line Models of Human Primary Cutaneous Diffuse Large B-Cell Lymphoma-Leg Type. J Invest Dermatol 2023; 143:340-344.e6. [PMID: 36084691 DOI: 10.1016/j.jid.2022.08.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 01/25/2023]
Affiliation(s)
| | - Audrey Gros
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France; Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Bordeaux, France
| | - Elodie Richard
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 11, University of Bordeaux, Bordeaux, France
| | - Floriane Cherrier
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France
| | - Elodie Laharanne
- Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Bordeaux, France
| | - Yamina Idrissi
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France
| | - Camille Baron
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France
| | - Sandrine Poglio
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France
| | - Océane Ducharme
- Dermatology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Sarah Menguy
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France; Pathology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Anne Pham-Ledard
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France; Dermatology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Marie Beylot-Barry
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France; Dermatology Department, University Hospital of Bordeaux, Bordeaux, France
| | - Jean-Philippe Merlio
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France; Tumor Bank and Tumor Biology Laboratory, University Hospital of Bordeaux, Bordeaux, France
| | - Laurence Bresson-Bepoldin
- BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, University of Bordeaux, Bordeaux, France; BRIC (BoRdeaux Institute of onCology), INSERM UMR1312, Team 5, CNRS, Université de Bordeaux, Bordeaux, France.
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Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions. Viruses 2021; 13:v13030497. [PMID: 33802945 PMCID: PMC8002816 DOI: 10.3390/v13030497] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) proteins belong to a family of deaminase proteins that can catalyze the deamination of cytosine to uracil on single-stranded DNA or/and RNA. APOBEC proteins are involved in diverse biological functions, including adaptive and innate immunity, which are critical for restricting viral infection and endogenous retroelements. Dysregulation of their functions can cause undesired genomic mutations and RNA modification, leading to various associated diseases, such as hyper-IgM syndrome and cancer. This review focuses on the structural and biochemical data on the multimerization status of individual APOBECs and the associated functional implications. Many APOBECs form various multimeric complexes, and multimerization is an important way to regulate functions for some of these proteins at several levels, such as deaminase activity, protein stability, subcellular localization, protein storage and activation, virion packaging, and antiviral activity. The multimerization of some APOBECs is more complicated than others, due to the associated complex RNA binding modes.
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Ducharme O, Beylot-Barry M, Pham-Ledard A, Bohers E, Viailly PJ, Bandres T, Faur N, Frison E, Vergier B, Jardin F, Merlio JP, Gros A. Mutations of the B-Cell Receptor Pathway Confer Chemoresistance in Primary Cutaneous Diffuse Large B-Cell Lymphoma Leg Type. J Invest Dermatol 2019; 139:2334-2342.e8. [PMID: 31150604 DOI: 10.1016/j.jid.2019.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/16/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
Abstract
Primary cutaneous diffuse large B-cell lymphoma, leg type (PCLBCL-LT) preferentially involves the lower limb in elderly subjects. A combination of polychemotherapy and rituximab has improved prognosis. However, about 50% of patients will experience progression or relapse without any predictive biologic marker of therapeutic response. The mutational profile of PCLBCL-LT has highlighted mutations contributing to constitutive NF-κB and B-cell receptor (BCR) signaling pathways but has not demonstrated clinical utility. Therefore, the mutational status of 32 patients with PCLBCL-LT (14 patients with complete durable response and 18 patients with relapsing or refractory disease) was determined with a dedicated lymphopanel. Tumor pairs at diagnosis and relapse or progression were analyzed in 14 relapsing or refractory patients. Patients with PCLBCL-LT harboring one mutation that targets one of the BCR signaling genes, CD79A/B or CARD11, displayed a reduced progression-free survival and specific survival (median 18 months, P = 0.002 and 51 months, P = 0.03, respectively, whereas median duration in the wild-type group was not reached) and were associated with therapeutic resistance (P = 0.0006). Longitudinal analyses revealed that MYD88 and CD79B were the earliest and among the most mutated genes. Our data suggest that evaluating BCR mutations in patients with PCLBCL-LT may help to predict first-line therapeutic response and to select targeted therapies.
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Affiliation(s)
- Océane Ducharme
- Service de Dermatologie, CHU de Bordeaux, Bordeaux, France; INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux
| | - Marie Beylot-Barry
- Service de Dermatologie, CHU de Bordeaux, Bordeaux, France; INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux
| | - Anne Pham-Ledard
- Service de Dermatologie, CHU de Bordeaux, Bordeaux, France; INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux
| | - Elodie Bohers
- INSERM U1245 and Centre Henri Becquerel, Rouen, France
| | | | - Thomas Bandres
- Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France
| | - Nicolas Faur
- Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France
| | - Eric Frison
- Service d'information médicale, CHU Bordeaux, Bordeaux, France
| | - Béatrice Vergier
- INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux; Service d'Anatomie pathologique, CHU de Bordeaux, Pessac, France
| | | | - Jean-Philippe Merlio
- INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux; Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France
| | - Audrey Gros
- INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux; Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France.
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Rogozin IB, Roche-Lima A, Lada AG, Belinky F, Sidorenko IA, Glazko GV, Babenko VN, Cooper DN, Pavlov YI. Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes. Cancers (Basel) 2019; 11:cancers11020211. [PMID: 30759888 PMCID: PMC6406962 DOI: 10.3390/cancers11020211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/08/2023] Open
Abstract
Cancer genomes accumulate nucleotide sequence variations that number in the tens of thousands per genome. A prominent fraction of these mutations is thought to arise as a consequence of the off-target activity of DNA/RNA editing cytosine deaminases. These enzymes, collectively called activation induced deaminase (AID)/APOBECs, deaminate cytosines located within defined DNA sequence contexts. The resulting changes of the original C:G pair in these contexts (mutational signatures) provide indirect evidence for the participation of specific cytosine deaminases in a given cancer type. The conventional method used for the analysis of mutable motifs is the consensus approach. Here, for the first time, we have adopted the frequently used weight matrix (sequence profile) approach for the analysis of mutagenesis and provide evidence for this method being a more precise descriptor of mutations than the sequence consensus approach. We confirm that while mutational footprints of APOBEC1, APOBEC3A, APOBEC3B, and APOBEC3G are prominent in many cancers, mutable motifs characteristic of the action of the humoral immune response somatic hypermutation enzyme, AID, are the most widespread feature of somatic mutation spectra attributable to deaminases in cancer genomes. Overall, the weight matrix approach reveals that somatic mutations are significantly associated with at least one AID/APOBEC mutable motif in all studied cancers.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894-6075, USA.
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities⁻RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico 00936-5067.
| | - Artem G Lada
- Department Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Frida Belinky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894-6075, USA.
| | | | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | | | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff CF14 4AY, UK.
| | - Youri I Pavlov
- Departments of Microbiology and Pathology; Biochemistry and Molecular Biology; Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.
- Eppley Institute for Research in Cancer and Allied Diseases, Omaha, NE 68198, USA.
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5
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Abdouni HS, King JJ, Ghorbani A, Fifield H, Berghuis L, Larijani M. DNA/RNA hybrid substrates modulate the catalytic activity of purified AID. Mol Immunol 2017; 93:94-106. [PMID: 29161581 DOI: 10.1016/j.molimm.2017.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 11/28/2022]
Abstract
Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID.
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Affiliation(s)
- Hala S Abdouni
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Justin J King
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Atefeh Ghorbani
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Heather Fifield
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Lesley Berghuis
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Mani Larijani
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada.
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Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Sci Rep 2016; 6:38133. [PMID: 27924834 PMCID: PMC5141443 DOI: 10.1038/srep38133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/07/2016] [Indexed: 01/12/2023] Open
Abstract
Follicular lymphoma (FL) is an uncurable cancer characterized by progressive severity of relapses. We analyzed sequence context specificity of mutations in the B cells from a large cohort of FL patients. We revealed substantial excess of mutations within a novel hybrid nucleotide motif: the signature of somatic hypermutation (SHM) enzyme, Activation Induced Deaminase (AID), which overlaps the CpG methylation site. This finding implies that in FL the SHM machinery acts at genomic sites containing methylated cytosine. We identified the prevalence of this hybrid mutational signature in many other types of human cancer, suggesting that AID-mediated, CpG-methylation dependent mutagenesis is a common feature of tumorigenesis.
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Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli. Proc Natl Acad Sci U S A 2016; 113:2176-81. [PMID: 26839411 DOI: 10.1073/pnas.1522325113] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The rate of cytosine deamination is much higher in single-stranded DNA (ssDNA) than in double-stranded DNA, and copying the resulting uracils causes C to T mutations. To study this phenomenon, the catalytic domain of APOBEC3G (A3G-CTD), an ssDNA-specific cytosine deaminase, was expressed in an Escherichia coli strain defective in uracil repair (ung mutant), and the mutations that accumulated over thousands of generations were determined by whole-genome sequencing. C:G to T:A transitions dominated, with significantly more cytosines mutated to thymine in the lagging-strand template (LGST) than in the leading-strand template (LDST). This strand bias was present in both repair-defective and repair-proficient cells and was strongest and highly significant in cells expressing A3G-CTD. These results show that the LGST is accessible to cellular cytosine deaminating agents, explains the well-known GC skew in microbial genomes, and suggests the APOBEC3 family of mutators may target the LGST in the human genome.
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Roberts SA, Gordenin DA. Clustered and genome-wide transient mutagenesis in human cancers: Hypermutation without permanent mutators or loss of fitness. Bioessays 2014; 36:382-393. [PMID: 24615916 DOI: 10.1002/bies.201300140] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The gain of a selective advantage in cancer as well as the establishment of complex traits during evolution require multiple genetic alterations, but how these mutations accumulate over time is currently unclear. There is increasing evidence that a mutator phenotype perpetuates the development of many human cancers. While in some cases the increased mutation rate is the result of a genetic disruption of DNA repair and replication or environmental exposures, other evidence suggests that endogenous DNA damage induced by AID/APOBEC cytidine deaminases can result in transient localized hypermutation generating simultaneous, closely spaced (i.e. "clustered") multiple mutations. Here, we discuss mechanisms that lead to mutation cluster formation, the biological consequences of their formation in cancer and evidence suggesting that APOBEC mutagenesis can also occur genome-wide. This raises the possibility that dysregulation of these enzymes may enable rapid malignant transformation by increasing mutation rates without the loss of fitness associated with permanent mutators.
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Affiliation(s)
- Steven A Roberts
- Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Durham, NC, USA
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Chahwan R, Wontakal SN, Roa S. Crosstalk between genetic and epigenetic information through cytosine deamination. Trends Genet 2010; 26:443-8. [DOI: 10.1016/j.tig.2010.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/16/2010] [Accepted: 07/19/2010] [Indexed: 01/25/2023]
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Alternative induction of meiotic recombination from single-base lesions of DNA deaminases. Genetics 2009; 182:41-54. [PMID: 19237686 DOI: 10.1534/genetics.109.101683] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination enhances genetic diversity as well as ensures proper segregation of homologous chromosomes, requiring Spo11-initiated double-strand breaks (DSBs). DNA deaminases act on regions of single-stranded DNA and deaminate cytosine to uracil (dU). In the immunoglobulin locus, this lesion will initiate point mutations, gene conversion, and DNA recombination. To begin to delineate the effect of induced base lesions on meiosis, we analyzed the effect of expressing DNA deaminases (activation-induced deaminase, AID, and APOBEC3C) in germ cells. We show that meiotic dU:dG lesions can partially rescue a spo11Delta phenotype in yeast and worm. In rec12 Schizosaccharomyces pombe, AID expression increased proper chromosome segregation, thereby enhancing spore viability, and induced low-frequency meiotic crossovers. Expression of AID in the germ cells of Caenorhabditis elegans spo-11 induced meiotic RAD-51 foci formation and chromosomal bivalency and segregation, as well as an increase in viability. RNAi experiments showed that this rescue was dependent on uracil DNA-glycosylase (Ung). Furthermore, unlike ionizing radiation-induced spo-11 rescue, AID expression did not induce large numbers of DSBs during the rescue. This suggests that the products of DNA deamination and base excision repair, such as uracil, an abasic site, or a single-stranded nick, are sufficient to initiate and alter meiotic recombination in uni- and multicellular organisms.
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Arudchandran A, Bernstein RM, Max EE. Single-strand DNA breaks in Ig class switch recombination that depend on UNG but not AID. Int Immunol 2008; 20:1381-93. [PMID: 18794203 DOI: 10.1093/intimm/dxn097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
B lymphocytes switch from secreting IgM to secreting IgG, IgA or IgE through a DNA recombination, class switch recombination (CSR), whose mechanism is incompletely understood. CSR is thought to be triggered by activation-induced deaminase (AID), which is believed to deaminate cytosines to uracil in single-strand regions of switch region DNA. Subsequent excision of uracils by uracil DNA glycosylase (UNG) (product of the UNG gene) generates abasic sites, which are targeted for DNA cleavage, producing DNA breaks that are critical intermediates in CSR. Consistent with this model, CSR-related double-strand breaks (DSBs)--detected by ligation-mediated PCR (LMPCR)--have been reported to be dramatically reduced in B cells from either AID(-/-) or UNG(-/-) mice. Here we examine single-strand breaks (SSBs) using LMPCR and report, surprisingly, that CSR-related anti-sense strand breaks in Sgamma regions are dependent only on UNG, and not AID, suggesting participation of a cytosine deaminase other than AID. This conclusion is supported by the sequences at these DNA breaks, which show a bias for a consensus sequence different from that reported for AID. The SSBs appear to be part of the normal CSR pathway since in B cells in which CSR is blocked by deletion of Smu, the content of Sgamma SSBs is elevated as though the breaks resolve inefficiently owing to the lack of a recombination partner for completing mu-to-gamma CSR. These results suggest a narrower role for AID in CSR than previously recognized and prompt a search for a putative alternative cytosine deaminase participating in CSR.
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Affiliation(s)
- Arulvathani Arudchandran
- Division of Therapeutic Proteins, Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
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12
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John Wiley & Sons, Ltd.. Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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