Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation
暂无分享,去创建一个
F. Alt | Yaofeng Zhao | Q. Pan-Hammarström | X. Ye | T. Gui | Jiaquan Liu | Chong Wang | Fei-Long Meng | Yanyan Wang | Xiaojing Liu | Joyce K. Hwang | Pengfei Dai | Lu Zhang | Jie Song | Leng-Siew Yeap | Xiaoqi Zheng | Xinrui Yang | Chong Han | Q. Hao | Zhiwei Cao | Lin-tai Da | Yanni Cai | Senxin Zhang | Xiaopeng Xie | Huizhi Zhang | Chaoyang Lian | Chuanzong Zhan | Ying Tian | Binbin Wang | Shaohui Huang
[1] Ryan D. Morin,et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma , 2022, Nature.
[2] Jonathan R. McDaniel,et al. THE MAJOR ROLE OF JUNCTIONAL DIVERSITY IN THE HORSE ANTIBODY REPERTOIRE , 2022, bioRxiv.
[3] F. Alt,et al. C‐terminal deletion‐induced condensation sequesters AID from IgH targets in immunodeficiency , 2022, The EMBO journal.
[4] Kui Wu,et al. Genome-wide mutational signatures revealed distinct developmental paths for human B cell lymphomas , 2020, The Journal of experimental medicine.
[5] T. Gui,et al. REV7 is required for processing AID initiated DNA lesions in activated B cells , 2020, Nature Communications.
[6] F. Alt,et al. BCR selection and affinity maturation in Peyer’s patch germinal centres , 2020, Nature.
[7] R. Roeder,et al. AID–RNA polymerase II transcription-dependent deamination of IgV DNA , 2019, Nucleic acids research.
[8] Peter D. Kwong,et al. cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence , 2019, bioRxiv.
[9] Michael S. Lawrence,et al. Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features , 2019, Science.
[10] J. Cyster,et al. B Cell Responses: Cell Interaction Dynamics and Decisions , 2019, Cell.
[11] Jia Gu,et al. fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.
[12] F. Alt,et al. AID Recognizes Structured DNA for Class Switch Recombination. , 2017, Molecular cell.
[13] Rommie E. Amaro,et al. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B , 2016, Nature Structural &Molecular Biology.
[14] L. Wysocki,et al. Functional Versatility of AGY Serine Codons in Immunoglobulin Variable Region Genes , 2016, Front. Immunol..
[15] C. Landes,et al. Measuring the Hydrodynamic Size of Nanoparticles Using Fluctuation Correlation Spectroscopy. , 2016, Annual review of physical chemistry.
[16] J. Chaudhuri,et al. Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity , 2016, Nature Reviews Immunology.
[17] Thomas B. Kepler,et al. Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes , 2015, Cell.
[18] J. Chaudhuri,et al. Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA , 2015, Cell.
[19] Aviv Bergman,et al. Overlapping hotspots in CDRs are critical sites for V region diversification , 2015, Proceedings of the National Academy of Sciences.
[20] D. Schatz,et al. Super-Enhancer Transcription Converges on AID , 2014, Cell.
[21] Yijun Ruan,et al. B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity , 2014, Cell.
[22] James E. Bradner,et al. Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability , 2014, Cell.
[23] R. Rabadán,et al. Noncoding RNA transcription targets AID to divergently transcribed loci in B cells , 2014, Nature.
[24] Fidel Ramírez,et al. deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..
[25] L. Macdonald,et al. Mice with megabase humanization of their immunoglobulin genes generate antibodies as efficiently as normal mice , 2014, Proceedings of the National Academy of Sciences.
[26] Anneliese O. Speak,et al. Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery , 2014, Nature Biotechnology.
[27] Ning Ma,et al. IgBLAST: an immunoglobulin variable domain sequence analysis tool , 2013, Nucleic Acids Res..
[28] Tongqing Zhou,et al. Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization , 2013, Cell.
[29] Yu Zhang,et al. Mechanisms of Programmed DNA Lesions and Genomic Instability in the Immune System , 2013, Cell.
[30] Erik Aronesty,et al. Comparison of Sequencing Utility Programs , 2013 .
[31] Kevin W Eliceiri,et al. NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.
[32] B. Helmink,et al. The response to and repair of RAG-mediated DNA double-strand breaks. , 2012, Annual review of immunology.
[33] J. Florián,et al. Intramolecular base stacking of dinucleoside monophosphate anions in aqueous solution. , 2012, The journal of physical chemistry. B.
[34] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[35] Alberto Martin,et al. Negative Supercoiling Creates Single-Stranded Patches of DNA That Are Substrates for AID–Mediated Mutagenesis , 2012, PLoS genetics.
[36] D. Schatz,et al. V(D)J recombination: mechanisms of initiation. , 2011, Annual review of genetics.
[37] Kefei Yu,et al. Overlapping activation-induced cytidine deaminase hotspot motifs in Ig class-switch recombination , 2011, Proceedings of the National Academy of Sciences.
[38] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[39] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer , 2011, Nature Biotechnology.
[40] Liming Ren,et al. A comprehensive analysis of germline and expressed immunoglobulin repertoire in the horse. , 2010, Developmental and comparative immunology.
[41] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[42] Sergio Roa,et al. The biochemistry of somatic hypermutation. , 2008, Annual review of immunology.
[43] D. Schatz,et al. Two levels of protection for the B cell genome during somatic hypermutation , 2008, Nature.
[44] M. Neuberger,et al. Molecular mechanisms of antibody somatic hypermutation. , 2007, Annual review of biochemistry.
[45] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[46] Patrice Duroux,et al. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences , 2005, Nucleic Acids Res..
[47] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[48] K. Rhee,et al. Intestinal bacteria and development of the B-lymphocyte repertoire. , 2005, Trends in immunology.
[49] Jérôme Lane,et al. IMGT®, the international ImMunoGeneTics information system® , 2004, Nucleic Acids Res..
[50] M. Neuberger,et al. Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation. , 2004, Molecular cell.
[51] Sachdev S Sidhu,et al. Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[52] T. Ha,et al. Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. , 2004, Biophysical journal.
[53] M. Lieber,et al. DNA Substrate Length and Surrounding Sequence Affect the Activation-induced Deaminase Activity at Cytidine* , 2004, Journal of Biological Chemistry.
[54] M. Lieber,et al. Nucleic acid structures and enzymes in the immunoglobulin class switch recombination mechanism. , 2003, DNA repair.
[55] M. Goodman,et al. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation , 2003, Nature.
[56] M. Lieber,et al. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells , 2003, Nature Immunology.
[57] F. Alt,et al. Transcription-targeted DNA deamination by the AID antibody diversification enzyme , 2003, Nature.
[58] Toshiro Matsuda,et al. Somatic mutation hotspots correlate with DNA polymerase η error spectrum , 2001, Nature Immunology.
[59] K. Rajewsky,et al. DNA double-strand breaks in immunoglobulin genes undergoing somatic hypermutation. , 2000, Immunity.
[60] A Libchaber,et al. Sequence dependent rigidity of single stranded DNA. , 2000, Physical review letters.
[61] T. Honjo,et al. Class Switch Recombination and Hypermutation Require Activation-Induced Cytidine Deaminase (AID), a Potential RNA Editing Enzyme , 2000, Cell.
[62] A. Fischer,et al. Activation-Induced Cytidine Deaminase (AID) Deficiency Causes the Autosomal Recessive Form of the Hyper-IgM Syndrome (HIGM2) , 2000, Cell.
[63] P. Hagerman,et al. Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). , 1999, Journal of molecular biology.
[64] C. Bustamante,et al. Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. , 1998, Journal of molecular biology.
[65] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..
[66] T. Kepler. Codon bias and plasticity in immunoglobulins. , 1997, Molecular biology and evolution.
[67] R. Brezinschek,et al. Analysis of the frequency and pattern of somatic mutations within nonproductively rearranged human variable heavy chain genes. , 1997, Journal of immunology.
[68] K. Rajewsky. Clonal selection and learning in the antibody system , 1996, Nature.
[69] C. Milstein,et al. The targeting of somatic hypermutation. , 1996, Seminars in immunology.
[70] T. Honjo,et al. High frequency class switching of an IgM+ B lymphoma clone CH12F3 to IgA+ cells. , 1996, International immunology.
[71] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[72] C. Milstein,et al. Codon bias targets mutation , 1995, Nature.
[73] J. Weill,et al. Hypermutation generating the sheep immunoglobulin repertoire is an antigen-independent process , 1995, Cell.
[74] R. Mage,et al. Rabbit IgH sequences in appendix germinal centers: VH diversification by gene conversion-like and hypermutation mechanisms. , 1994, Immunity.
[75] C. Milstein,et al. Passenger transgenes reveal intrinsic specificity of the antibody hypermutation mechanism: clustering, polarity, and specific hot spots. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[76] N A Kolchanov,et al. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis. , 1992, Biochimica et biophysica acta.
[77] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[78] D. Baltimore,et al. Somatic variants of murine immunoglobulin λ light chains , 1982, Nature.
[79] Leroy Hood,et al. A single VH gene segment encodes the immune response to phosphorylcholine: Somatic mutation is correlated with the class of the antibody , 1981, Cell.
[80] D. Baltimore,et al. Heavy chain variable region contribution to the NPb family of antibodies: somatic mutation evident in a γ2a variable region , 1981, Cell.
[81] E. Kabat,et al. ATTEMPTS TO LOCATE COMPLEMENTARITY‐DETERMINING RESIDUES IN THE VARIABLE POSITIONS OF LIGHT AND HEAVY CHAINS * , 1971, Annals of the New York Academy of Sciences.
[82] OUP accepted manuscript , 2022, Nucleic Acids Research.
[83] Zhang Huizhi,et al. Principles of fluorescence correlation spectroscopy applied to studies of biomolecular liquid–liquid phase separation , 2022, Biophysics reports.
[84] Fei-Long Meng,et al. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. , 2019, Advances in immunology.
[85] D. Calado,et al. Germinal Centers , 2017, Methods in Molecular Biology.
[86] P. Gearhart,et al. DNA polymerase η is an A-T mutator in somatic hypermutation of immunoglobulin variable genes , 2001, Nature Immunology.