Chapter 5 DNA Targets of AID
Tài liệu tham khảo
Bachl, 1999, Hypermutation targets a green fluorescent protein-encoding transgene in the presence of immunoglobulin enhancers, Eur. J. Immunol., 29, 1383, 10.1002/(SICI)1521-4141(199904)29:04<1383::AID-IMMU1383>3.0.CO;2-X
Barreto, 2005, AID from bony fish catalyzes class switch recombination, J. Exp. Med., 202, 733, 10.1084/jem.20051378
Betz, 1994, Elements regulating somatic hypermutation of an immunoglobulin kappa gene: Critical role for the intron enhancer/matrix attachment region, Cell, 77, 239, 10.1016/0092-8674(94)90316-6
Bottaro, 1994, S region transcription per se promotes basal IgE class switch recombination but additional factors regulate the efficiency of the process, EMBO J., 13, 665, 10.1002/j.1460-2075.1994.tb06305.x
Bransteitter, 2004, Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase, J. Biol. Chem., 279, 51612, 10.1074/jbc.M408135200
Bransteitter, 2003, Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase, Proc. Natl. Acad. Sci. USA, 100, 4102, 10.1073/pnas.0730835100
Chaudhuri, 2007, Antibodies get a break, Science, 315, 335, 10.1126/science.1138091
Chaudhuri, 2004, Replication protein A interacts with AID to promote deamination of somatic hypermutation targets, Nature, 430, 992, 10.1038/nature02821
Chaudhuri, 2003, Transcription-targeted DNA deamination by the AID antibody diversification enzyme, Nature, 422, 726, 10.1038/nature01574
Chen, 1993, RAG-2-deficient blastocyst complementation: An assay of gene function in lymphocyte development, Proc. Natl. Acad. Sci. USA, 90, 4528, 10.1073/pnas.90.10.4528
Cogne, 1994, A class switch control region at the 3′ end of the immunoglobulin heavy chain locus, Cell, 77, 737, 10.1016/0092-8674(94)90057-4
Di Noia, 2002, Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase, Nature, 419, 43, 10.1038/nature00981
Di Noia, 2007, Molecular mechanisms of antibody somatic hypermutation, Annu. Rev. Biochem., 76, 1, 10.1146/annurev.biochem.76.061705.090740
Diaz, 1998, Evolution of somatic hypermutation and gene conversion in adaptive immunity, Immunol. Rev., 162, 13, 10.1111/j.1600-065X.1998.tb01425.x
Dorner, 1998, Somatic hypermutation of human immunoglobulin heavy chain genes: Targeting of RGYW motifs on both DNA strands, Eur. J. Immunol., 28, 3384, 10.1002/(SICI)1521-4141(199810)28:10<3384::AID-IMMU3384>3.0.CO;2-T
Dudley, 2005, Mechanism and control of V(D)J recombination versus class switch recombination: Similarities and differences, Adv. Immunol., 86, 43, 10.1016/S0065-2776(04)86002-4
Dudley, 2002, Internal IgH class switch region deletions are position-independent and enhanced by AID expression, Proc. Natl. Acad. Sci. USA, 99, 9984, 10.1073/pnas.152333499
Dunnick, 1993, DNA sequences at immunoglobulin switch region recombination sites, Nucleic Acids Res., 21, 365, 10.1093/nar/21.3.365
Dunnick, 2004, Germline transcription and switch recombination of a transgene containing the entire H chain constant region locus: Effect of a mutation in a STAT6 binding site in the gamma 1 promoter, J. Immunol., 173, 5531, 10.4049/jimmunol.173.9.5531
Duquette, 2007, G-rich proto-oncogenes are targeted for genomic instability in B-cell lymphomas, Cancer Res., 67, 2586, 10.1158/0008-5472.CAN-06-2419
Duquette, 2005, AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation, Oncogene, 24, 5791, 10.1038/sj.onc.1208746
Flajnik, 2002, Comparative analyses of immunoglobulin genes: Surprises and portents, Nat. Rev. Immunol., 2, 688, 10.1038/nri889
Franco, 2006, H2AX prevents DNA breaks from progressing to chromosome breaks and translocations, Mol. Cell, 21, 201, 10.1016/j.molcel.2006.01.005
Gu, 1993, Independent control of immunoglobulin switch recombination at individual switch regions evidenced through Cre-loxP-mediated gene targeting, Cell, 73, 1155, 10.1016/0092-8674(93)90644-6
Honjo, 2002, Molecular mechanism of class switch recombination: Linkage with somatic hypermutation, Annu. Rev. Immunol., 20, 165, 10.1146/annurev.immunol.20.090501.112049
Hsu, 2006, The plasticity of immunoglobulin gene systems in evolution, Immunol. Rev., 210, 8, 10.1111/j.0105-2896.2006.00366.x
Huang, 2007, Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region, Mol. Cell. Biol., 27, 5921, 10.1128/MCB.00702-07
Jacquier, 1985, An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene, Cell, 41, 383, 10.1016/S0092-8674(85)80011-8
Jiang, 2007, Abrogation of lupus nephritis in activation-induced deaminase-deficient MRL/lpr mice, J. Immunol., 178, 7422, 10.4049/jimmunol.178.11.7422
Jiang, 2008, Activation-induced deaminase heterozygous MRL/lpr mice are delayed in the production of high-affinity pathogenic antibodies and in the development of lupus nephritis, Immunology, 10, 1365
Jung, 1993, Shutdown of class switch recombination by deletion of a switch region control element, Science, 259, 984, 10.1126/science.8438159
Kenter, 2004, Mapping of a functional recombination motif that defines isotype specificity for mu-->gamma3 switch recombination implicates NF-kappaB p50 as the isotype-specific switching factor, J. Exp. Med., 199, 617, 10.1084/jem.20031935
Khamlichi, 2004, Immunoglobulin class-switch recombination in mice devoid of any S mu tandem repeat, Blood, 103, 3828, 10.1182/blood-2003-10-3470
Kinoshita, 1998, Target specificity of immunoglobulin class switch recombination is not determined by nucleotide sequences of S regions, Immunity, 9, 849, 10.1016/S1074-7613(00)80650-0
Klein, 2008, Germinal centres: Role in B-cell physiology and malignancy, Nat. Rev. Immunol., 8, 22, 10.1038/nri2217
Larijani, 2007, Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID, Mol. Cell. Biol., 27, 8038, 10.1128/MCB.01046-07
Larijani, 2007, AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner, Mol. Cell. Biol., 27, 20, 10.1128/MCB.00824-06
Liu, 2008, Two levels of protection for the B cell genome during somatic hypermutation, Nature, 451, 841, 10.1038/nature06547
Luby, 2001, The mu switch region tandem repeats are important, but not required, for antibody class switch recombination, J. Exp. Med., 193, 159, 10.1084/jem.193.2.159
Lundqvist, 2001, The immunoglobulin heavy chain locus of the duck. Genomic organization and expression of D, J, and C region genes, J. Biol. Chem., 276, 46729, 10.1074/jbc.M106221200
Lundqvist, 2006, Immunoglobulins of the non-galliform birds: Antibody expression and repertoire in the duck, Dev. Comp. Immunol., 30, 93, 10.1016/j.dci.2005.06.019
Maizels, 2005, Immunoglobulin gene diversification, Annu. Rev. Genet., 39, 23, 10.1146/annurev.genet.39.073003.110544
Manis, 2002, IgH class switch recombination to IgG1 in DNA-PKcs-deficient B cells, Immunity, 16, 607, 10.1016/S1074-7613(02)00306-0
Manis, 2004, 53BP1 links DNA damage-response pathways to immunoglobulin heavy chain class-switch recombination, Nat. Immunol., 5, 481, 10.1038/ni1067
Martin, 2002, AID and mismatch repair in antibody diversification, Nat. Rev. Immunol., 2, 605, 10.1038/nri858
Martomo, 2006, Somatic hypermutation: Subverted DNA repair, Curr. Opin. Immunol., 18, 243, 10.1016/j.coi.2006.03.007
Meffre, 2001, Somatic hypermutation shapes the antibody repertoire of memory B cells in humans, J. Exp. Med., 194, 375, 10.1084/jem.194.3.375
Mietzner, 2008, Autoreactive IgG memory antibodies in patients with systemic lupus erythematosus arise from nonreactive and polyreactive precursors, Proc. Natl. Acad. Sci. USA, 105, 9727, 10.1073/pnas.0803644105
Migliazza, 1995, Frequent somatic hypermutation of the 5′ noncoding region of the BCL6 gene in B-cell lymphoma, Proc. Natl. Acad. Sci. USA, 92, 12520, 10.1073/pnas.92.26.12520
Mowatt, 1985, Unique sequences are interspersed among tandemly repeated elements in the murine gamma 1 switch segment, Nucleic Acids Res., 13, 225, 10.1093/nar/13.1.225
Muramatsu, 2000, Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme, Cell, 102, 553, 10.1016/S0092-8674(00)00078-7
Mussmann, 1997, Microsites for immunoglobulin switch recombination breakpoints from Xenopus to mammals, Eur. J. Immunol., 27, 2610, 10.1002/eji.1830271021
Nambu, 2003, Transcription-coupled events associating with immunoglobulin switch region chromatin, Science, 302, 2137, 10.1126/science.1092481
Neuberger, 2008, Antibody diversification by somatic mutation: From Burnet onwards, Immunol. Cell. Biol., 86, 124, 10.1038/sj.icb.7100160
Ohta, 2006, IgD, like IgM, is a primordial immunoglobulin class perpetuated in most jawed vertebrates, Proc. Natl. Acad. Sci. USA, 103, 10723, 10.1073/pnas.0601407103
Pan, 1998, Characterization of human gamma 4 switch region polymorphisms suggests a meiotic recombinational hot spot within the Ig locus: influence of S region length on IgG4 production, J. Immunol., 161, 3520, 10.4049/jimmunol.161.7.3520
Pasqualucci, 2001, Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas, Nature, 412, 341, 10.1038/35085588
Perlot, 2005, Elucidation of IgH intronic enhancer functions via germ-line deletion, Proc. Natl. Acad. Sci. USA, 102, 14362, 10.1073/pnas.0507090102
Petersen, 2001, AID is required to initiate Nbs1/gamma-H2AX focus formation and mutations at sites of class switching, Nature, 414, 660, 10.1038/414660a
Petersen-Mahrt, 2002, AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification, Nature, 418, 99, 10.1038/nature00862
Pham, 2003, Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation, Nature, 424, 103, 10.1038/nature01760
Pham, 2008, Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase, J. Biol. Chem., 283, 17428, 10.1074/jbc.M802121200
Pinaud, 2001, Localization of the 3′ IgH locus elements that effect long-distance regulation of class switch recombination, Immunity, 15, 187, 10.1016/S1074-7613(01)00181-9
Rada, 2004, Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation, Mol. Cell., 16, 163, 10.1016/j.molcel.2004.10.011
Rada, 2002, Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice, Curr. Biol., 12, 1748, 10.1016/S0960-9822(02)01215-0
Ramiro, 2006, Role of genomic instability and p53 in AID-induced c-myc-Igh translocations, Nature, 440, 105, 10.1038/nature04495
Ramiro, 2004, AID is required for c-myc/IgH chromosome translocations in vivo, Cell, 118, 431, 10.1016/j.cell.2004.08.006
Ramiro, 2003, Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand, Nat. Immunol., 4, 452, 10.1038/ni920
Reina-San-Martin, 2003, H2AX is required for recombination between immunoglobulin switch regions but not for intra-switch region recombination or somatic hypermutation, J. Exp. Med., 197, 1767, 10.1084/jem.20030569
Revy, 2000, Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2), Cell, 102, 565, 10.1016/S0092-8674(00)00079-9
Rogozin, 2004, Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process, J. Immunol., 172, 3382, 10.4049/jimmunol.172.6.3382
Roy, 2007, The Mechanism of R-Loop Formation at Immunoglobulin Class Switch Sequences, Mol. Cell. Biol., 28, 50, 10.1128/MCB.01251-07
Rush, 2004, Staggered AID-dependent DNA double strand breaks are the predominant DNA lesions targeted to S mu in Ig class switch recombination, Int. Immunol., 16, 549, 10.1093/intimm/dxh057
Sakai, 1999, Recombination and transcription of the endogenous Ig heavy chain locus is effected by the Ig heavy chain intronic enhancer core region in the absence of the matrix attachment regions, Proc. Natl. Acad. Sci. USA, 96, 1526, 10.1073/pnas.96.4.1526
Schrader, 2003, Mutations occur in the Ig Smu region but rarely in Sgamma regions prior to class switch recombination, EMBO J., 22, 5893, 10.1093/emboj/cdg550
Schrader, 2007, Activation-induced cytidine deaminase-dependent DNA breaks in class switch recombination occur during G1 phase of the cell cycle and depend upon mismatch repair, J. Immunol., 179, 6064, 10.4049/jimmunol.179.9.6064
Schrader, 2005, Inducible DNA breaks in Ig S regions are dependent on AID and UNG, J. Exp. Med., 202, 561, 10.1084/jem.20050872
Seidl, 1998, An expressed neo(r) cassette provides required functions of the 1gamma2b exon for class switching, Int. Immunol., 10, 1683, 10.1093/intimm/10.11.1683
Seidl, 1999, Position-dependent inhibition of class-switch recombination by PGK-neor cassettes inserted into the immunoglobulin heavy chain constant region locus, Proc. Natl. Acad. Sci. USA, 96, 3000, 10.1073/pnas.96.6.3000
Shen, 1998, Mutation of BCL-6 gene in normal B cells by the process of somatic hypermutation of Ig genes, Science, 280, 1750, 10.1126/science.280.5370.1750
Shinkura, 2003, The influence of transcriptional orientation on endogenous switch region function, Nat. Immunol., 4, 435, 10.1038/ni918
Sohail, 2003, Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations, Nucleic Acids Res., 31, 2990, 10.1093/nar/gkg464
Stavnezer, 2004, Evolution of isotype switching, Semin. Immunol., 16, 257, 10.1016/j.smim.2004.08.005
Storb, 1999, Molecular aspects of somatic hypermutation of immunoglobulin genes, Cold Spring Harb Symp Quant Biol., 64, 227, 10.1101/sqb.1999.64.227
Storb, 2002, Immunoglobulin genes: generating diversity with AID and UNG, Curr. Biol., 12, R725, 10.1016/S0960-9822(02)01247-2
Szurek, 1985, Complete nucleotide sequence of the murine gamma 3 switch region and analysis of switch recombination sites in two gamma 3-expressing hybridomas, J. Immunol., 135, 620, 10.4049/jimmunol.135.1.620
Tian, 2000, Transcription-induced cleavage of immunoglobulin switch regions by nucleotide excision repair nucleases in vitro, J. Biol. Chem., 275, 24163, 10.1074/jbc.M003343200
Unniraman, 2007, Strand-biased spreading of mutations during somatic hypermutation, Science, 317, 1227, 10.1126/science.1145065
Vernersson, 2002, Evidence for an early appearance of modern post-switch immunoglobulin isotypes in mammalian evolution (II); cloning of IgE, IgG1 and IgG2 from a monotreme, the duck-billed platypus, Ornithorhynchus anatinus, Eur. J. Immunol., 32, 2145, 10.1002/1521-4141(200208)32:8<2145::AID-IMMU2145>3.0.CO;2-I
Wakae, 2006, Evolution of class switch recombination function in fish activation-induced cytidine deaminase, AID, Int. Immunol., 18, 41, 10.1093/intimm/dxh347
Wang, 2004, Genome-wide somatic hypermutation, Proc. Natl. Acad. Sci. USA, 101, 7352, 10.1073/pnas.0402009101
Ward, 2004, 53BP1 is required for class switch recombination, J. Cell. Biol., 165, 459, 10.1083/jcb.200403021
Wardemann, 2007, B-cell self-tolerance in humans, Adv. Immunol., 95, 83, 10.1016/S0065-2776(07)95003-8
Wardemann, 2003, Predominant autoantibody production by early human B cell precursors, Science, 301, 1374, 10.1126/science.1086907
Warren, 2008, Genome analysis of the platypus reveals unique signatures of evolution, Nature, 455, 256, 10.1038/nature07253
Wuerffel, 2007, S-S synapsis during class switch recombination is promoted by distantly located transcriptional elements and activation-induced deaminase, Immunity, 27, 711, 10.1016/j.immuni.2007.09.007
Wuerffel, 1997, Ig Sgamma3 DNA-specifc double strand breaks are induced in mitogen-activated B cells and are implicated in switch recombination, J. Immunol., 159, 4139, 10.4049/jimmunol.159.9.4139
Xue, 2006, The in vivo pattern of AID targeting to immunoglobulin switch regions deduced from mutation spectra in msh2-/- ung-/- mice, J. Exp. Med., 203, 2085, 10.1084/jem.20061067
Yan, 2007, IgH class switching and translocations use a robust non-classical end-joining pathway, Nature, 449, 478, 10.1038/nature06020
Yelamos, 1995, Targeting of non-Ig sequences in place of the V segment by somatic hypermutation, Nature, 376, 225, 10.1038/376225a0
Yoshikawa, 2002, AID enzyme-induced hypermutation in an actively transcribed gene in fibroblasts, Science, 296, 2033, 10.1126/science.1071556
Yu, 2003, R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells, Nat. Immunol., 4, 442, 10.1038/ni919
Yu, 2004, DNA substrate length and surrounding sequence affect the activation-induced deaminase activity at cytidine, J. Biol. Chem., 279, 6496, 10.1074/jbc.M311616200
Yurasov, 2007, Regulation of autoreactive antibodies, Curr. Opin. Rheumatol., 19, 421, 10.1097/BOR.0b013e328277ef3b
Yurasov, 2005, Defective B cell tolerance checkpoints in systemic lupus erythematosus, J. Exp. Med., 201, 703, 10.1084/jem.20042251
Zarrin, 2004, An evolutionarily conserved target motif for immunoglobulin class-switch recombination, Nat. Immunol., 5, 1275, 10.1038/ni1137
Zarrin, 2007, Antibody class switching mediated by yeast endonuclease-generated DNA breaks, Science, 315, 377, 10.1126/science.1136386
Zarrin, 2008, Sgamma3 switch sequences function in place of endogenous Sgamma1 to mediate antibody class switching, J. Exp. Med., 205, 1567, 10.1084/jem.20080451
Zarrin, 2005, Influence of switch region length on immunoglobulin class switch recombination, Proc. Natl. Acad. Sci. USA, 102, 2466, 10.1073/pnas.0409847102
Zhang, 1993, A selective defect in IgG2b switching as a result of targeted mutation of the I gamma 2b promoter and exon, EMBO J., 12, 3529, 10.1002/j.1460-2075.1993.tb06027.x
Zhao, 2006, Identification of IgF, a hinge-region-containing Ig class, and IgD in Xenopus tropicalis, Proc. Natl. Acad. Sci. USA, 103, 12087, 10.1073/pnas.0600291103
