Journal Articles

Sharma, R., Smolkin, R. M., Chowdhury, P., Fernandez, K. C., Kim, Y., Cols, M., Alread, W., Yen, W.-F., Hu, W., Wang, Z.-M., Violante, S., Chaligné, R., Li, M. O., Cross, J. R., & Chaudhuri, J. (2023). Distinct metabolic requirements regulate B cell activation and germinal center responses. Nature Immunology, 24(8), 1358–1369. https://doi.org/10.1038/s41590-023-01540-y

Fernandez, K. C., Feeney, L., Smolkin, R. M., Yen, W.-F., Matthews, A. J., Alread, W., Petrini, J. H. J., & Chaudhuri, J. (2022). The structure-selective endonucleases GEN1 and MUS81 mediate complementary functions in safeguarding the genome of proliferating B lymphocytes. eLife, 11, e77073. https://doi.org/10.7554/eLife.77073

Maekawa, K., Yamada, S., Sharma, R., Chaudhuri, J., & Keeney, S. (2022). Triple-helix potential of the mouse genome. Proceedings of the National Academy of Sciences of the United States of America, 119(19), e2203967119. https://doi.org/10.1073/pnas.2203967119

Yewdell, W. T., Smolkin, R. M., Belcheva, K. T., Mendoza, A., Michaels, A. J., Cols, M., Angeletti, D., Yewdell, J. W., & Chaudhuri, J. (2021). Temporal dynamics of persistent germinal centers and memory B cell differentiation following respiratory virus infection. Cell Reports, 37(6), 109961. https://doi.org/10.1016/j.celrep.2021.109961

Mendoza, A., Yewdell, W. T., Hoyos, B., Schizas, M., Bou-Puerto, R., Michaels, A. J., Brown, C. C., Chaudhuri, J., & Rudensky, A. Y. (2021). Assembly of a spatial circuit of T-bet-expressing T and B lymphocytes is required for antiviral humoral immunity. Science Immunology, 6(60), eabi4710. https://doi.org/10.1126/sciimmunol.abi4710

Yewdell, W. T., Kim, Y., Chowdhury, P., Lau, C. M., Smolkin, R. M., Belcheva, K. T., Fernandez, K. C., Cols, M., Yen, W.-F., Vaidyanathan, B., Angeletti, D., McDermott, A. B., Yewdell, J. W., Sun, J. C., & Chaudhuri, J. (2020). A Hyper-IgM Syndrome Mutation in Activation-Induced Cytidine Deaminase Disrupts G-Quadruplex Binding and Genome-wide Chromatin Localization. Immunity, 53(5), 952-970.e11. https://doi.org/10.1016/j.immuni.2020.10.003

Angeletti, D., Kosik, I., Santos, J. J. S., Yewdell, W. T., Boudreau, C. M., Mallajosyula, V. V. A., Mankowski, M. C., Chambers, M., Prabhakaran, M., Hickman, H. D., McDermott, A. B., Alter, G., Chaudhuri, J., & Yewdell, J. W. (2019). Outflanking immunodominance to target subdominant broadly neutralizing epitopes. Proceedings of the National Academy of Sciences of the United States of America, 116(27), 13474–13479. https://doi.org/10.1073/pnas.1816300116

Nicolas, L., Cols, M., Smolkin, R., Fernandez, K. C., Yewdell, W. T., Yen, W.-F., Zha, S., Vuong, B. Q., & Chaudhuri, J. (2019). Cutting Edge: ATM Influences Germinal Center Integrity. Journal of Immunology, 202(11), 3137–3142. https://doi.org/10.4049/jimmunol.1801033

Yen, W.-F., Sharma, R., Cols, M., Lau, C. M., Chaudhry, A., Chowdhury, P., Yewdell, W. T., Vaidyanathan, B., Sun, A., Coffre, M., Pucella, J. N., Chen, C.-C., Jasin, M., Sun, J. C., Rudensky, A. Y., Koralov, S. B., & Chaudhuri, J. (2019). Distinct Requirements of CHD4 during B Cell Development and Antibody Response. Cell Reports, 27(5), 1472-1486.e5. https://doi.org/10.1016/j.celrep.2019.04.011

Pucella, J. N., Cols, M., Yen, W.-F., Xu, S., & Chaudhuri, J. (2019). The B Cell Activation-Induced miR-183 Cluster Plays a Minimal Role in Canonical Primary Humoral Responses. Journal of Immunology, 202(5), 1383–1396. https://doi.org/10.4049/jimmunol.1800071

Zheng, S., Kusnadi, A., Choi, J. E., Vuong, B. Q., Rhodes, D., & Chaudhuri, J. (2019). NME proteins regulate class switch recombination. FEBS Letters, 593(1), 80–87. https://doi.org/10.1002/1873-3468.13290

Yen, W.-F., Chaudhry, A., Vaidyanathan, B., Yewdell, W. T., Pucella, J. N., Sharma, R., Liang, Y., Li, K., Rudensky, A. Y., & Chaudhuri, J. (2017). BRCT-domain protein BRIT1 influences class switch recombination. Proceedings of the National Academy of Sciences of the United States of America, 114(31), 8354–8359. https://doi.org/10.1073/pnas.1708211114

Chen, C.-C., Kass, E. M., Yen, W.-F., Ludwig, T., Moynahan, M. E., Chaudhuri, J., & Jasin, M. (2017). ATM loss leads to synthetic lethality in BRCA1 BRCT mutant mice associated with exacerbated defects in homology-directed repair. Proceedings of the National Academy of Sciences of the United States of America, 114(29), 7665–7670. https://doi.org/10.1073/pnas.1706392114

Kunimoto, H., McKenney, A. S., Meydan, C., Shank, K., Nazir, A., Rapaport, F., Durham, B., Garrett-Bakelman, F. E., Pronier, E., Shih, A. H., Melnick, A., Chaudhuri, J., & Levine, R. L. (2017). Aid is a key regulator of myeloid/erythroid differentiation and DNA methylation in hematopoietic stem/progenitor cells. Blood, 129(13), 1779–1790. https://doi.org/10.1182/blood-2016-06-721977

DiMenna, L. J., Yen, W.-F., Nicolas, L., Sharma, R., Saldanha, Z. N., & Chaudhuri, J. (2017). Cutting Edge: The Transcription Factor Sox2 Regulates AID Expression in Class-Switched B Cells. Journal of Immunology, 198(6), 2244–2248. https://doi.org/10.4049/jimmunol.1502266

Vaidyanathan, B., Chaudhry, A., Yewdell, W. T., Angeletti, D., Yen, W.-F., Wheatley, A. K., Bradfield, C. A., McDermott, A. B., Yewdell, J. W., Rudensky, A. Y., & Chaudhuri, J. (2017). The aryl hydrocarbon receptor controls cell-fate decisions in B cells. The Journal of Experimental Medicine, 214(1), 197–208. https://doi.org/10.1084/jem.20160789

Balestrini, A., Nicolas, L., Yang-Lott, K., Guryanova, O. A., Levine, R. L., Bassing, C. H., Chaudhuri, J., & Petrini, J. H. J. (2016). Defining ATM-Independent Functions of the Mre11 Complex with a Novel Mouse Model. Molecular Cancer Research, 14(2), 185–195. https://doi.org/10.1158/1541-7786.MCR-15-0281

Zheng, S., Vuong, B. Q., Vaidyanathan, B., Lin, J.-Y., Huang, F.-T., & Chaudhuri, J. (2015). Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA. Cell, 161(4), 762–773. https://doi.org/10.1016/j.cell.2015.03.020

Pucella, J. N., Yen, W.-F., Kim, M. V., van der Veeken, J., Luo, C. T., Socci, N. D., Naito, Y., Li, M. O., Iwai, N., & Chaudhuri, J. (2015). miR-182 is largely dispensable for adaptive immunity: Lack of correlation between expression and function. Journal of Immunology, 194(6), 2635–2642. https://doi.org/10.4049/jimmunol.1402261

Matthews, A. J., Husain, S., & Chaudhuri, J. (2014). Binding of AID to DNA does not correlate with mutator activity. Journal of Immunology, 193(1), 252–257. https://doi.org/10.4049/jimmunol.1400433

Vuong, B. Q., Herrick-Reynolds, K., Vaidyanathan, B., Pucella, J. N., Ucher, A. J., Donghia, N. M., Gu, X., Nicolas, L., Nowak, U., Rahman, N., Strout, M. P., Mills, K. D., Stavnezer, J., & Chaudhuri, J. (2013). A DNA break- and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination. Nature Immunology, 14(11), 1183–1189. https://doi.org/10.1038/ni.2732

Kumar, R., DiMenna, L., Schrode, N., Liu, T.-C., Franck, P., Muñoz-Descalzo, S., Hadjantonakis, A.-K., Zarrin, A. A., Chaudhuri, J., Elemento, O., & Evans, T. (2013). AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes. Nature, 500(7460), 89–92. https://doi.org/10.1038/nature12299

Nowak, U., Matthews, A. J., Zheng, S., & Chaudhuri, J. (2011). The splicing regulator PTBP2 interacts with the cytidine deaminase AID and promotes binding of AID to switch-region DNA. Nature Immunology, 12(2), 160–166. https://doi.org/10.1038/ni.1977

Lee-Theilen, M., Matthews, A. J., Kelly, D., Zheng, S., & Chaudhuri, J. (2011). CtIP promotes microhomology-mediated alternative end joining during class-switch recombination. Nature Structural & Molecular Biology, 18(1), 75–79. https://doi.org/10.1038/nsmb.1942

Vuong, B. Q., Lee, M., Kabir, S., Irimia, C., Macchiarulo, S., McKnight, G. S., & Chaudhuri, J. (2009). Specific recruitment of protein kinase A to the immunoglobulin locus regulates class-switch recombination. Nature Immunology, 10(4), 420–426. https://doi.org/10.1038/ni.1708

Cheng, H.-L., Vuong, B. Q., Basu, U., Franklin, A., Schwer, B., Astarita, J., Phan, R. T., Datta, A., Manis, J., Alt, F. W., & Chaudhuri, J. (2009). Integrity of the AID serine-38 phosphorylation site is critical for class switch recombination and somatic hypermutation in mice. Proceedings of the National Academy of Sciences of the United States of America, 106(8), 2717–2722. https://doi.org/10.1073/pnas.0812304106

Basu, U., Chaudhuri, J., Alpert, C., Dutt, S., Ranganath, S., Li, G., Schrum, J. P., Manis, J. P., & Alt, F. W. (2005). The AID antibody diversification enzyme is regulated by protein kinase A phosphorylation. Nature, 438(7067), 508–511. https://doi.org/10.1038/nature04255

Zarrin, A. A., Alt, F. W., Chaudhuri, J., Stokes, N., Kaushal, D., Du Pasquier, L., & Tian, M. (2004). An evolutionarily conserved target motif for immunoglobulin class-switch recombination. Nature Immunology, 5(12), 1275–1281. https://doi.org/10.1038/ni1137

Chaudhuri, J., Khuong, C., & Alt, F. W. (2004). Replication protein A interacts with AID to promote deamination of somatic hypermutation targets. Nature, 430(7003), 992–998. https://doi.org/10.1038/nature02821

Chaudhuri, J., Tian, M., Khuong, C., Chua, K., Pinaud, E., & Alt, F. W. (2003). Transcription-targeted DNA deamination by the AID antibody diversification enzyme. Nature, 422(6933), 726–730. https://doi.org/10.1038/nature01574

Review Articles

Belcheva, K. T., & Chaudhuri, J. (2022). Maintenance of Lineage Identity: Lessons from a B Cell. Journal of Immunology, 209(11), 2073–2081. https://doi.org/10.4049/jimmunol.2200497

Lue, J. K., Downs-Canner, S., & Chaudhuri, J. (2022). The role of B cells in the development, progression, and treatment of lymphomas and solid tumors. Advances in Immunology, 154, 71–117. https://doi.org/10.1016/bs.ai.2022.07.002

Nicolas, L., Cols, M., Choi, J. E., Chaudhuri, J., & Vuong, B. (2018). Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination. F1000Research, 7, 458. https://doi.org/10.12688/f1000research.13247.1

Yewdell, W. T., & Chaudhuri, J. (2017). A transcriptional serenAID: The role of noncoding RNAs in class switch recombination. International Immunology, 29(4), 183–196. https://doi.org/10.1093/intimm/dxx027

DiMenna, L. J., & Chaudhuri, J. (2016). Regulating infidelity: RNA-mediated recruitment of AID to DNA during class switch recombination. European Journal of Immunology, 46(3), 523–530. https://doi.org/10.1002/eji.201545809

Casellas, R., Basu, U., Yewdell, W. T., Chaudhuri, J., Robbiani, D. F., & Di Noia, J. M. (2016). Mutations, kataegis and translocations in B cells: Understanding AID promiscuous activity. Nature Reviews Immunology, 16(3), 164–176. https://doi.org/10.1038/nri.2016.2

Vaidyanathan, B., & Chaudhuri, J. (2015). Epigenetic Codes Programing Class Switch Recombination. Frontiers in Immunology, 6, 405. https://doi.org/10.3389/fimmu.2015.00405

Vaidyanathan, B., Yen, W.-F., Pucella, J. N., & Chaudhuri, J. (2014). AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination. Frontiers in Immunology, 5, 120. https://doi.org/10.3389/fimmu.2014.00120

Matthews, A. J., Zheng, S., DiMenna, L. J., & Chaudhuri, J. (2014). Regulation of immunoglobulin class-switch recombination: Choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Advances in Immunology, 122, 1–57. https://doi.org/10.1016/B978-0-12-800267-4.00001-8

Kumar, R., DiMenna, L. J., Chaudhuri, J., & Evans, T. (2014). Biological function of activation-induced cytidine deaminase (AID). Biomedical Journal, 37(5), 269–283. https://doi.org/10.4103/2319-4170.128734

Vuong, B. Q., & Chaudhuri, J. (2012). Combinatorial mechanisms regulating AID-dependent DNA deamination: Interacting proteins and post-translational modifications. Seminars in Immunology, 24(4), 264–272. https://doi.org/10.1016/j.smim.2012.05.006

Basu, U., Franklin, A., Schwer, B., Cheng, H.-L., Chaudhuri, J., & Alt, F. W. (2009). Regulation of activation-induced cytidine deaminase DNA deamination activity in B-cells by Ser38 phosphorylation. Biochemical Society Transactions, 37(Pt 3), 561–568. https://doi.org/10.1042/BST0370561

Chaudhuri, J., Basu, U., Zarrin, A., Yan, C., Franco, S., Perlot, T., Vuong, B., Wang, J., Phan, R. T., Datta, A., Manis, J., & Alt, F. W. (2007). Evolution of the immunoglobulin heavy chain class switch recombination mechanism. Advances in Immunology, 94, 157–214. https://doi.org/10.1016/S0065-2776(06)94006-1

Basu, U., Chaudhuri, J., Phan, R. T., Datta, A., & Alt, F. W. (2007). Regulation of activation induced deaminase via phosphorylation. Advances in Experimental Medicine and Biology, 596, 129–137. https://doi.org/10.1007/0-387-46530-8_11

Dudley, D. D., Chaudhuri, J., Bassing, C. H., & Alt, F. W. (2005). Mechanism and control of V(D)J recombination versus class switch recombination: Similarities and differences. Advances in Immunology, 86, 43–112. https://doi.org/10.1016/S0065-2776(04)86002-4

Rooney, S., Chaudhuri, J., & Alt, F. W. (2004). The role of the non-homologous end-joining pathway in lymphocyte development. Immunological Reviews, 200, 115–131. https://doi.org/10.1111/j.0105-2896.2004.00165.x

Chaudhuri, J., & Alt, F. W. (2004). Class-switch recombination: Interplay of transcription, DNA deamination and DNA repair. Nature Reviews Immunology, 4(7), 541–552. https://doi.org/10.1038/nri1395

Perspectives

Fernandez, K. C., & Chaudhuri, J. (2019). Uncoupling the DSB End-Protecting and CSR-Promoting Functions of 53BP1. Cell Reports, 28(6), 1387–1388. https://doi.org/10.1016/j.celrep.2019.07.076

Pucella, J. N., & Chaudhuri, J. (2017). AID Invited to the G4 Summit. Molecular Cell, 67(3), 355–357. https://doi.org/10.1016/j.molcel.2017.07.020

Yewdell, W. T., & Chaudhuri, J. (2017). Molecular biology: RNA editing packs a one-two punch. Nature, 542(7642), 420–421. https://doi.org/10.1038/542420a

Nicolás, L., & Chaudhuri, J. (2013). 4C-ing the Igh Landscape. Immunity, 39(2), 199–201. https://doi.org/10.1016/j.immuni.2013.08.014

Lee-Theilen, M., & Chaudhuri, J. (2010). Walking the AID tightrope. Nature Immunology, 11(2), 107–109. https://doi.org/10.1038/ni0210-107

Chaudhuri, J., & Jasin, M. (2007). Immunology. Antibodies get a break. Science (New York, N.Y.), 315(5810), 335–336. https://doi.org/10.1126/science.1138091