TY - JOUR AU - Jarmuz, A. AU - Chester, A. AU - Bayliss, J. AU - Gisbourne, J. AU - Dunham, I. AU - Scott, J. PY - 2002 DA - 2002// TI - An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22 JO - Genomics VL - 79 UR - https://doi.org/10.1006/geno.2002.6718 DO - 10.1006/geno.2002.6718 ID - Jarmuz2002 ER - TY - JOUR AU - Rogozin, I. B. AU - Basu, M. K. AU - Jordan, I. K. AU - Pavlov, Y. I. AU - Koonin, E. V. PY - 2005 DA - 2005// TI - APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis JO - Cell Cycle VL - 4 UR - https://doi.org/10.4161/cc.4.9.1994 DO - 10.4161/cc.4.9.1994 ID - Rogozin2005 ER - TY - JOUR AU - Sato, Y. AU - Probst, H. C. AU - Tatsumi, R. AU - Ikeuchi, Y. AU - Neuberger, M. S. AU - Rada, C. PY - 2010 DA - 2010// TI - Deficiency in APOBEC2 leads to a shift in muscle fiber type, diminished body mass, and myopathy JO - J Biol Chem VL - 285 UR - https://doi.org/10.1074/jbc.M109.052977 DO - 10.1074/jbc.M109.052977 ID - Sato2010 ER - TY - JOUR AU - Muramatsu, M. AU - Sankaranand, V. S. AU - Anant, S. AU - Sugai, M. AU - Kinoshita, K. AU - Davidson, N. O. PY - 1999 DA - 1999// TI - Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells JO - J Biol Chem VL - 274 UR - https://doi.org/10.1074/jbc.274.26.18470 DO - 10.1074/jbc.274.26.18470 ID - Muramatsu1999 ER - TY - JOUR AU - Daniel, J. AU - Nussenzweig, A. PY - 2013 DA - 2013// TI - The AID-induced DNA damage response in chromatin JO - Mol Cell VL - 50 UR - https://doi.org/10.1016/j.molcel.2013.04.017 DO - 10.1016/j.molcel.2013.04.017 ID - Daniel2013 ER - TY - JOUR AU - Kinomoto, M. AU - Kanno, T. AU - Shimura, M. AU - Ishizaka, Y. AU - Kojima, A. AU - Kurata, T. PY - 2007 DA - 2007// TI - All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm181 DO - 10.1093/nar/gkm181 ID - Kinomoto2007 ER - TY - JOUR AU - Hultquist, J. F. AU - Lengyel, J. A. AU - Refsland, E. W. AU - LaRue, R. S. AU - Lackey, L. AU - Brown, W. L. PY - 2011 DA - 2011// TI - Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict vif-deficient HIV-1 JO - J Virol VL - 85 UR - https://doi.org/10.1128/JVI.05238-11 DO - 10.1128/JVI.05238-11 ID - Hultquist2011 ER - TY - JOUR AU - Langlois, M. A. AU - Beale, R. C. L. AU - Conticello, S. G. AU - Neuberger, M. S. PY - 2005 DA - 2005// TI - Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki343 DO - 10.1093/nar/gki343 ID - Langlois2005 ER - TY - JOUR AU - Burns, M. B. AU - Lackey, L. AU - Carpenter, M. A. AU - Rathore, A. AU - Land, A. M. AU - Leonard, B. PY - 2013 DA - 2013// TI - APOBEC3B is an enzymatic source of mutation in breast cancer JO - Nature VL - 494 UR - https://doi.org/10.1038/nature11881 DO - 10.1038/nature11881 ID - Burns2013 ER - TY - JOUR AU - Burns, M. B. AU - Temiz, N. A. AU - Harris, R. S. PY - 2013 DA - 2013// TI - Evidence for APOBEC3B mutagenesis in multiple human cancers JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2701 DO - 10.1038/ng.2701 ID - Burns2013 ER - TY - STD TI - Tsuboi M, Yamane A, Horiguchi J, Yokobori T, Kawabata-Iwakawa R, Yoshiyama S, et al. APOBEC3B high expression status is associated with aggressive phenotype in Japanese breast cancers. Breast Cancer. 2015:1–9. doi:10.1007/s12282-015-0641-8 ID - ref11 ER - TY - JOUR AU - Cescon, D. W. AU - Haibe-Kains, B. AU - Mak, T. W. PY - 2015 DA - 2015// TI - APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation JO - Proc Natl Acad Sci VL - 112 UR - https://doi.org/10.1073/pnas.1424869112 DO - 10.1073/pnas.1424869112 ID - Cescon2015 ER - TY - JOUR AU - Leonard, B. AU - Hart, S. N. AU - Burns, M. B. AU - Carpenter, M. A. AU - Temiz, N. A. AU - Rathore, A. PY - 2013 DA - 2013// TI - APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma JO - Cancer Res VL - 73 UR - https://doi.org/10.1158/0008-5472.CAN-13-1753 DO - 10.1158/0008-5472.CAN-13-1753 ID - Leonard2013 ER - TY - JOUR AU - Roberts, S. A. AU - Lawrence, M. S. AU - Klimczak, L. J. AU - Grimm, S. A. AU - Fargo, D. AU - Stojanov, P. PY - 2013 DA - 2013// TI - An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2702 DO - 10.1038/ng.2702 ID - Roberts2013 ER - TY - JOUR AU - Nik-Zainal, S. AU - Alexandrov, L. B. AU - Wedge, D. C. AU - Loo, P. AU - Greenman, C. D. AU - Raine, K. PY - 2012 DA - 2012// TI - Mutational processes molding the genomes of 21 breast cancers JO - Cell VL - 149 UR - https://doi.org/10.1016/j.cell.2012.04.024 DO - 10.1016/j.cell.2012.04.024 ID - Nik-Zainal2012 ER - TY - JOUR AU - Kan, Z. AU - Jaiswal, B. S. AU - Stinson, J. AU - Janakiraman, V. AU - Bhatt, D. AU - Stern, H. M. PY - 2010 DA - 2010// TI - Diverse somatic mutation patterns and pathway alterations in human cancers JO - Nature VL - 466 UR - https://doi.org/10.1038/nature09208 DO - 10.1038/nature09208 ID - Kan2010 ER - TY - JOUR AU - Network, T. C. G. A. PY - 2012 DA - 2012// TI - Comprehensive molecular portraits of human breast tumours JO - Nature VL - 490 UR - https://doi.org/10.1038/nature11412 DO - 10.1038/nature11412 ID - Network2012 ER - TY - JOUR AU - Stephens, P. J. AU - McBride, D. J. AU - Lin, M. L. AU - Varela, I. AU - Pleasance, E. D. AU - Simpson, J. T. PY - 2009 DA - 2009// TI - Complex landscapes of somatic rearrangement in human breast cancer genomes JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08645 DO - 10.1038/nature08645 ID - Stephens2009 ER - TY - JOUR AU - Consortium, T. E. P. PY - 2012 DA - 2012// TI - An integrated encyclopedia of DNA elements in the human genome JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11247 DO - 10.1038/nature11247 ID - Consortium2012 ER - TY - JOUR AU - Hon, G. C. AU - Hawkins, R. D. AU - Caballero, O. L. AU - Lo, C. AU - Lister, R. AU - Pelizzola, M. PY - 2012 DA - 2012// TI - Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.125872.111 DO - 10.1101/gr.125872.111 ID - Hon2012 ER - TY - JOUR AU - Sun, Z. AU - Asmann, Y. W. AU - Kalari, K. R. AU - Bot, B. AU - Eckel-Passow, J. E. AU - Baker, T. R. PY - 2011 DA - 2011// TI - Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing JO - PLoS ONE VL - 6 UR - https://doi.org/10.1371/journal.pone.0017490 DO - 10.1371/journal.pone.0017490 ID - Sun2011 ER - TY - JOUR AU - Frietze, S. AU - Wang, R. AU - Yao, L. AU - Tak, Y. AU - Ye, Z. AU - Gaddis, M. PY - 2012 DA - 2012// TI - Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-9-r52 DO - 10.1186/gb-2012-13-9-r52 ID - Frietze2012 ER - TY - JOUR AU - Kouzarides, T. PY - 2007 DA - 2007// TI - Chromatin modifications and their function JO - Cell VL - 128 UR - https://doi.org/10.1016/j.cell.2007.02.005 DO - 10.1016/j.cell.2007.02.005 ID - Kouzarides2007 ER - TY - JOUR AU - Mikkelsen, T. S. AU - Ku, M. AU - Jaffe, D. B. AU - Issac, B. AU - Lieberman, E. AU - Giannoukos, G. PY - 2007 DA - 2007// TI - Genome-wide maps of chromatin state in pluripotent and lineage-committed cells JO - Nature VL - 448 UR - https://doi.org/10.1038/nature06008 DO - 10.1038/nature06008 ID - Mikkelsen2007 ER - TY - JOUR AU - Wang, Z. AU - Zang, C. AU - Rosenfeld, J. A. AU - Schones, D. E. AU - Barski, A. AU - Cuddapah, S. PY - 2008 DA - 2008// TI - Combinatorial patterns of histone acetylations and methylations in the human genome JO - Nat Genet VL - 40 UR - https://doi.org/10.1038/ng.154 DO - 10.1038/ng.154 ID - Wang2008 ER - TY - JOUR AU - Heintzman, N. D. AU - Stuart, R. K. AU - Hon, G. AU - Fu, Y. AU - Ching, C. W. AU - Hawkins, R. D. PY - 2007 DA - 2007// TI - Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome JO - Nat Genet VL - 39 UR - https://doi.org/10.1038/ng1966 DO - 10.1038/ng1966 ID - Heintzman2007 ER - TY - JOUR AU - Zhao, X. D. AU - Han, X. AU - Chew, J. L. AU - Liu, J. AU - Chiu, K. P. AU - Choo, A. PY - 2007 DA - 2007// TI - Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells JO - Cell Stem Cell VL - 1 UR - https://doi.org/10.1016/j.stem.2007.08.004 DO - 10.1016/j.stem.2007.08.004 ID - Zhao2007 ER - TY - JOUR AU - Jones, P. A. PY - 2012 DA - 2012// TI - Functions of DNA methylation: islands, start sites, gene bodies and beyond JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3230 DO - 10.1038/nrg3230 ID - Jones2012 ER - TY - JOUR AU - Weisenberger, D. J. PY - 2014 DA - 2014// TI - Characterizing DNA, methylation alterations from The Cancer Genome Atlas JO - J Clin Invest VL - 124 UR - https://doi.org/10.1172/JCI69740 DO - 10.1172/JCI69740 ID - Weisenberger2014 ER - TY - JOUR AU - Kidd, J. M. AU - Newman, T. L. AU - Tuzun, E. AU - Kaul, R. AU - Eichler, E. E. PY - 2007 DA - 2007// TI - Population stratification of a common APOBEC gene deletion polymorphism JO - PLoS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030063 DO - 10.1371/journal.pgen.0030063 ID - Kidd2007 ER - TY - JOUR AU - Creyghton, M. P. AU - Cheng, A. W. AU - Welstead, G. G. AU - Kooistra, T. AU - Carey, B. W. AU - Steine, E. J. PY - 2010 DA - 2010// TI - Histone H3K27ac separates active from poised enhancers and predicts developmental state JO - Proc Natl Acad Sci VL - 107 UR - https://doi.org/10.1073/pnas.1016071107 DO - 10.1073/pnas.1016071107 ID - Creyghton2010 ER - TY - JOUR AU - Guttman, M. AU - Amit, I. AU - Garber, M. AU - French, C. AU - Lin, M. F. AU - Feldser, D. PY - 2009 DA - 2009// TI - Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals JO - Nature VL - 458 UR - https://doi.org/10.1038/nature07672 DO - 10.1038/nature07672 ID - Guttman2009 ER - TY - JOUR AU - Fujimura, S. AU - Matsui, T. AU - Kuwahara, K. AU - Maeda, K. AU - Sakaguchi, N. PY - 2008 DA - 2008// TI - Germinal center B-cell-associated DNA hypomethylation at transcriptional regions of the AID gene JO - Mol Immunol VL - 45 UR - https://doi.org/10.1016/j.molimm.2007.09.023 DO - 10.1016/j.molimm.2007.09.023 ID - Fujimura2008 ER - TY - JOUR AU - Isobe, T. AU - Song, S. N. AU - Tiwari, P. AU - Ito, H. AU - Yamaguchi, Y. AU - Yoshizaki, K. PY - 2013 DA - 2013// TI - Activation-induced cytidine deaminase auto-activates and triggers aberrant gene expression JO - FEBS Lett VL - 587 UR - https://doi.org/10.1016/j.febslet.2013.06.028 DO - 10.1016/j.febslet.2013.06.028 ID - Isobe2013 ER - TY - JOUR AU - Pauklin, S. AU - Sernandez, I. V. AU - Bachmann, G. AU - Ramiro, A. R. AU - Petersen-Mahrt, S. K. PY - 2009 DA - 2009// TI - Estrogen directly activates AID transcription and function JO - J Exp Med VL - 206 UR - https://doi.org/10.1084/jem.20080521 DO - 10.1084/jem.20080521 ID - Pauklin2009 ER - TY - JOUR AU - Gaughan, L. AU - Stockley, J. AU - Coffey, K. AU - ONeill, D. AU - Jones, D. L. AU - Wade, M. PY - 2013 DA - 2013// TI - KDM4B is a master regulator of the estrogen receptor signalling cascade JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt469 DO - 10.1093/nar/gkt469 ID - Gaughan2013 ER - TY - JOUR AU - Lackey, L. AU - Law, E. K. AU - Brown, W. L. AU - Harris, R. S. PY - 2013 DA - 2013// TI - Subcellular localization of the APOBEC3 proteins during mitosis and implications for genomic DNA deamination JO - Cell Cycle VL - 12 UR - https://doi.org/10.4161/cc.23713 DO - 10.4161/cc.23713 ID - Lackey2013 ER - TY - JOUR AU - Niewiadomska, A. M. AU - Tian, C. AU - Tan, L. AU - Wang, T. AU - Sarkis, P. T. N. AU - Yu, X. F. PY - 2007 DA - 2007// TI - Differential inhibition of long interspersed element 1 by APOBEC3 does not correlate with high-molecular-mass-complex formation or P-body association JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.02800-06 DO - 10.1128/JVI.02800-06 ID - Niewiadomska2007 ER - TY - JOUR AU - Muckenfuss, H. AU - Hamdorf, M. AU - Held, U. AU - Perkovic, M. AU - Lower, J. AU - Cichutek, K. PY - 2006 DA - 2006// TI - APOBEC3 proteins inhibit human LINE-1 retrotransposition JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M601716200 DO - 10.1074/jbc.M601716200 ID - Muckenfuss2006 ER - TY - JOUR AU - Fujino, T. AU - Navaratnam, N. AU - Scott, J. PY - 1998 DA - 1998// TI - Human apolipoprotein B RNA editing deaminase gene (APOBEC1) JO - Genomics VL - 47 UR - https://doi.org/10.1006/geno.1997.5110 DO - 10.1006/geno.1997.5110 ID - Fujino1998 ER - TY - JOUR AU - LaRue, R. S. AU - Andresdottir, V. AU - Blanchard, Y. AU - Conticello, S. G. AU - Derse, D. AU - Emerman, M. PY - 2009 DA - 2009// TI - Guidelines for naming nonprimate APOBEC3 genes and proteins JO - J Virol VL - 83 UR - https://doi.org/10.1128/JVI.01976-08 DO - 10.1128/JVI.01976-08 ID - LaRue2009 ER - TY - JOUR AU - Kitamura, S. AU - Ode, H. AU - Nakashima, M. AU - Imahashi, M. AU - Naganawa, Y. AU - Kurosawa, T. PY - 2012 DA - 2012// TI - The APOBEC3C crystal structure and the interface for HIV-1 Vif binding JO - Nat Struct Mol Biol VL - 19 UR - https://doi.org/10.1038/nsmb.2378 DO - 10.1038/nsmb.2378 ID - Kitamura2012 ER - TY - STD TI - Siu KK, Sultana A, Azimi FC, Lee JE. Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F. Nat Commun. 2013;4–2593. ID - ref43 ER - TY - STD TI - Mitra M, Hercik K, Byeon IJ, Ahn J, Hill S, Hinchee-Rodriguez K, et al. Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties. Nucleic Acids Research. 2014;42(2):1095-110. ID - ref44 ER - TY - JOUR AU - Horn, A. V. AU - Klawitter, S. AU - Held, U. AU - Berger, A. AU - Jaguva Vasudevan, A. A. AU - Bock, A. PY - 2014 DA - 2014// TI - Human LINE-1 restriction by APOBEC3C is deaminase independent and mediated by an ORF1p interaction that affects LINE reverse transcriptase activity JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt898 DO - 10.1093/nar/gkt898 ID - Horn2014 ER - TY - JOUR AU - Gary, L. B. AU - Robert, D. C. R. AU - Thomas, G. F. PY - 1994 DA - 1994// TI - Expression of LINE-1 retrotransposons in human breast cancer JO - Cancer VL - 73 UR - https://doi.org/3.0.CO;2-4 DO - 3.0.CO;2-4 ID - Gary1994 ER - TY - JOUR AU - Belgnaoui, S. M. AU - Gosden, R. AU - Semmes, O. J. AU - Haoudi, A. PY - 2006 DA - 2006// TI - Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells JO - Cancer Cell Int VL - 6 UR - https://doi.org/10.1186/1475-2867-6-13 DO - 10.1186/1475-2867-6-13 ID - Belgnaoui2006 ER - TY - JOUR AU - Gasior, S. L. AU - Wakeman, T. P. AU - Xu, B. AU - Deininger, P. L. PY - 2006 DA - 2006// TI - The human LINE-1 retrotransposon creates DNA double-strand breaks JO - J Mol Biol VL - 357 UR - https://doi.org/10.1016/j.jmb.2006.01.089 DO - 10.1016/j.jmb.2006.01.089 ID - Gasior2006 ER - TY - JOUR AU - Daskalos, A. AU - Nikolaidis, G. AU - Xinarianos, G. AU - Savvari, P. AU - Cassidy, A. AU - Zakopoulou, R. PY - 2009 DA - 2009// TI - Hypomethylation of retrotransposable elements correlates with genomic instability in non-small cell lung cancer JO - Int J Cancer VL - 124 UR - https://doi.org/10.1002/ijc.23849 DO - 10.1002/ijc.23849 ID - Daskalos2009 ER - TY - STD TI - Hancks DC, Kazazian J. Active human retrotransposons: variation and disease. Curr Opin Genet Dev. 6/20122012. 2012;22(3):191–203. ID - ref50 ER - TY - JOUR AU - Symer, D. E. AU - Connelly, C. AU - Szak, S. T. AU - Caputo, E. M. AU - Cost, G. J. AU - Parmigiani, G. PY - 2002 DA - 2002// TI - Human L1 retrotransposition is associated with genetic instability in vivo JO - Cell VL - 110 UR - https://doi.org/10.1016/S0092-8674(02)00839-5 DO - 10.1016/S0092-8674(02)00839-5 ID - Symer2002 ER - TY - JOUR AU - Barrett, T. AU - Troup, D. B. AU - Wilhite, S. E. AU - Ledoux, P. AU - Evangelista, C. AU - Kim, I. F. PY - 2011 DA - 2011// TI - NCBI GEO: archive for functional genomics data sets—10 years on JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1184 DO - 10.1093/nar/gkq1184 ID - Barrett2011 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Meth VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - STD TI - Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map (SAM) Format and SAMtools. Bioinformatics. 2009. ID - ref54 ER - TY - JOUR AU - Yan, G. AU - Zhang, G. AU - Fang, X. AU - Zhang, Y. AU - Li, C. AU - Ling, F. PY - 2011 DA - 2011// TI - Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques JO - Nat Biotech VL - 29 UR - https://doi.org/10.1038/nbt.1992 DO - 10.1038/nbt.1992 ID - Yan2011 ER - TY - JOUR AU - Zhang, Y. AU - Liu, T. AU - Meyer, C. AU - Eeckhoute, J. AU - Johnson, D. AU - Bernstein, B. PY - 2008 DA - 2008// TI - Model-based Analysis of ChIP-Seq (MACS) JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-9-r137 DO - 10.1186/gb-2008-9-9-r137 ID - Zhang2008 ER - TY - JOUR AU - Ernst, J. AU - Kellis, M. PY - 2012 DA - 2012// TI - ChromHMM: automating chromatin-state discovery and characterization JO - Nat Meth VL - 9 UR - https://doi.org/10.1038/nmeth.1906 DO - 10.1038/nmeth.1906 ID - Ernst2012 ER - TY - JOUR AU - Xi, Y. AU - Li, W. PY - 2009 DA - 2009// TI - BSMAP: whole genome bisulfite sequence MAPping program JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-232 DO - 10.1186/1471-2105-10-232 ID - Xi2009 ER - TY - JOUR AU - Korn, J. M. AU - Kuruvilla, F. G. AU - McCarroll, S. A. AU - Wysoker, A. AU - Nemesh, J. AU - Cawley, S. PY - 2008 DA - 2008// TI - Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs JO - Nat Genet VL - 40 UR - https://doi.org/10.1038/ng.237 DO - 10.1038/ng.237 ID - Korn2008 ER -