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405 results on '"Chaudhuri, Jayanta"'

3. Contributors

Author

Alt, Frederick W., primary, Atisha-Fregoso, Yemil, additional, Barbulescu, Philip, additional, Basu, Uttiya, additional, Begum, Nasim A., additional, Boehm, Thomas, additional, Bournazos, Stylianos, additional, Carsetti, Rita, additional, Casanova, Jean-Laurent, additional, Chaudhuri, Jayanta, additional, Cooper, Max D., additional, Dalla-Favera, Riccardo, additional, Das, Sabyasachi, additional, De Simone, Pantaleo, additional, Diamond, Betty, additional, Di Noia, Javier M., additional, Dörner, Thomas, additional, Drutskaya, Marina S., additional, Fagarasan, Sidonia, additional, Feeney, Ann J., additional, Fernandez, Keith C., additional, Gold, Michael R., additional, Gommerman, Jennifer L., additional, Haque, Shabirul, additional, Hirano, Masayuki, additional, Honjo, Tasuku, additional, Hsu, Ellen, additional, Jani, Peter K., additional, Jellusova, Julia, additional, Kato, Lucia M., additional, Kläsener, Kathrin, additional, Kobayashi, Maki, additional, Kruglov, Andrey A., additional, Lefranc, Marie-Paule, additional, Lewis, Susanna M., additional, Lino, Andreia C., additional, Lucas, Joseph S., additional, Ma, Cindy S., additional, Mackay, Fabienne, additional, Macpherson, Andrew J., additional, Martin, Alberto, additional, Mashreghi, Mir-Farzin, additional, McGrath, Mairi Anne, additional, Melchers, Fritz, additional, Meng, Fei-Long, additional, Morimoto, Ryo, additional, Morris, Rhiannon, additional, Murre, Cornelis, additional, Nagaoka, Hitoshi, additional, Nair, Lekha, additional, Nedospasov, Sergei A., additional, Ng, Ashley P., additional, Nitschke, Lars, additional, Nutt, Stephen L., additional, Pasqualucci, Laura, additional, Piano Mortari, Eva, additional, Pozovskiy, Rita, additional, Radbruch, Andreas, additional, Rast, Jonathan P., additional, Ravetch, Jeffrey V., additional, Reth, Michael, additional, Riblet, Roy, additional, Ridani, Jana, additional, Rollenkse, Tim, additional, Schatz, David G., additional, Shlomchik, Mark, additional, Tangye, Stuart G., additional, Watanabe, Manami, additional, Weisel, Florian, additional, Xiao, Jianxiong, additional, Zha, Shan, additional, Zhang, Yiwen, additional, Zhang, Yu, additional, and Zou, Yong-Rui, additional

Published
2024
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9. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate

Author

Venturutti, Leandro, Teater, Matt, Zhai, Andrew, Chadburn, Amy, Babiker, Leena, Kim, Daleum, Béguelin, Wendy, Lee, Tak C., Kim, Youngjun, Chin, Christopher R., Yewdell, William T., Raught, Brian, Phillip, Jude M., Jiang, Yanwen, Staudt, Louis M., Green, Michael R., Chaudhuri, Jayanta, Elemento, Olivier, Farinha, Pedro, Weng, Andrew P., Nissen, Michael D., Steidl, Christian, Morin, Ryan D., Scott, David W., Privé, Gilbert G., and Melnick, Ari M.

Published
2020
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11. Outflanking immunodominance to target subdominant broadly neutralizing epitopes

Author

Angeletti, Davide, Kosik, Ivan, Santos, Jefferson J. S., Yewdell, William T., Boudreau, Carolyn M., Mallajosyula, Vamsee V. A., Mankowski, Madeleine C., Chambers, Michael, Prabhakaran, Madhu, Hickman, Heather D., McDermott, Adrian B., Alter, Galit, Chaudhuri, Jayanta, and Yewdell, Jonathan W.

Published
2019

13. MRI Is a DNA Damage Response Adaptor during Classical Non-homologous End Joining

Author

Hung, Putzer J., Johnson, Britney, Chen, Bo-Ruei, Byrum, Andrea K., Bredemeyer, Andrea L., Yewdell, William T., Johnson, Tanya E., Lee, Brian J., Deivasigamani, Shruthi, Hindi, Issa, Amatya, Parmeshwar, Gross, Michael L., Paull, Tanya T., Pisapia, David J., Chaudhuri, Jayanta, Petrini, John J.H., Mosammaparast, Nima, Amarasinghe, Gaya K., Zha, Shan, Tyler, Jessica K., and Sleckman, Barry P.

Published
2018
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19. Data from Androgen Receptor Signaling Regulates DNA Repair in Prostate Cancers

Author

Polkinghorn, William R., primary, Parker, Joel S., primary, Lee, Man X., primary, Kass, Elizabeth M., primary, Spratt, Daniel E., primary, Iaquinta, Phillip J., primary, Arora, Vivek K., primary, Yen, Wei-Feng, primary, Cai, Ling, primary, Zheng, Deyou, primary, Carver, Brett S., primary, Chen, Yu, primary, Watson, Philip A., primary, Shah, Neel P., primary, Fujisawa, Sho, primary, Goglia, Alexander G., primary, Gopalan, Anuradha, primary, Hieronymus, Haley, primary, Wongvipat, John, primary, Scardino, Peter T., primary, Zelefsky, Michael J., primary, Jasin, Maria, primary, Chaudhuri, Jayanta, primary, Powell, Simon N., primary, and Sawyers, Charles L., primary

Published
2023
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20. Supplementary Table S1 from Androgen Receptor Signaling Regulates DNA Repair in Prostate Cancers

Author

Polkinghorn, William R., primary, Parker, Joel S., primary, Lee, Man X., primary, Kass, Elizabeth M., primary, Spratt, Daniel E., primary, Iaquinta, Phillip J., primary, Arora, Vivek K., primary, Yen, Wei-Feng, primary, Cai, Ling, primary, Zheng, Deyou, primary, Carver, Brett S., primary, Chen, Yu, primary, Watson, Philip A., primary, Shah, Neel P., primary, Fujisawa, Sho, primary, Goglia, Alexander G., primary, Gopalan, Anuradha, primary, Hieronymus, Haley, primary, Wongvipat, John, primary, Scardino, Peter T., primary, Zelefsky, Michael J., primary, Jasin, Maria, primary, Chaudhuri, Jayanta, primary, Powell, Simon N., primary, and Sawyers, Charles L., primary

Published
2023
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25. Supplementary Figure S3 from Androgen Receptor Signaling Regulates DNA Repair in Prostate Cancers

Author

Polkinghorn, William R., primary, Parker, Joel S., primary, Lee, Man X., primary, Kass, Elizabeth M., primary, Spratt, Daniel E., primary, Iaquinta, Phillip J., primary, Arora, Vivek K., primary, Yen, Wei-Feng, primary, Cai, Ling, primary, Zheng, Deyou, primary, Carver, Brett S., primary, Chen, Yu, primary, Watson, Philip A., primary, Shah, Neel P., primary, Fujisawa, Sho, primary, Goglia, Alexander G., primary, Gopalan, Anuradha, primary, Hieronymus, Haley, primary, Wongvipat, John, primary, Scardino, Peter T., primary, Zelefsky, Michael J., primary, Jasin, Maria, primary, Chaudhuri, Jayanta, primary, Powell, Simon N., primary, and Sawyers, Charles L., primary

Published
2023
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32. Regulation of Activation Induced Deaminase via Phosphorylation

Author

Basu, Uttiya, Chaudhuri, Jayanta, Phan, Ryan T., Datta, Abhishek, Alt, Frederick W., Back, Nathan, editor, Cohen, Irun R., editor, Kritchevsky, David, editor, Lajtha, Abel, editor, Paoletti, Rodolfo, editor, Gupta, Sudhir, editor, Alt, Frederick, editor, Cooper, Max, editor, Melchers, Fritz, editor, and Rajewsky, Klaus, editor

Published
2007
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37. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function

Author

Drané, Pascal, Brault, Marie-Eve, Cui, Gaofeng, Meghani, Khyati, Chaubey, Shweta, Detappe, Alexandre, Parnandi, Nishita, He, Yizhou, Zheng, Xiao-Feng, Botuyan, Maria Victoria, Kalousi, Alkmini, Yewdell, William T., Münch, Christian, Harper, Wade J., Chaudhuri, Jayanta, Soutoglou, Evi, Mer, Georges, and Chowdhury, Dipanjan

Published
2017
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42. Triple-helix potential of the mouse genome

Author

20837869, Maekawa, Kaku, Yamada, Shintaro, Sharma, Rahul, Chaudhuri, Jayanta, Keeney, Scott, 20837869, Maekawa, Kaku, Yamada, Shintaro, Sharma, Rahul, Chaudhuri, Jayanta, and Keeney, Scott

Abstract

Certain DNA sequences, including mirror-symmetric polypyrimidine•polypurine runs, are capable of folding into a triple-helix–containing non–B-form DNA structure called H-DNA. Such H-DNA–forming sequences occur frequently in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)–specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides an approach for studying DNA secondary structure genome-wide at high spatial resolution.

Published
2022

48. AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes

Author

Kumar, Ritu, DiMenna, Lauren, Schrode, Nadine, Liu, Ting-Chun, Franck, Philipp, Munoz-Descalzo, Silvia, Hadjantonakis, Anna-Katerina, Zarrin, Ali A., Chaudhuri, Jayanta, Elemento, Olivier, and Evans, Todd

Subjects
Research, Properties, Epigenetic inheritance -- Research, Immunoglobulin genes -- Properties, Phenotypes -- Properties, Stem cells -- Properties, Phenotype -- Properties
Abstract

The path to pluripotency involves multiple steps that can be more or less efficient, and this can be modelled in transcription-factor-induced reprogramming (9). Reprogrammed induced pluripotent stem cell (iPSC) clones [...], The activation-induced cytidine deaminase (AID; also known as AICDA) enzyme is required for somatic hypermutation and class switch recombination at the immunoglobulin locus (1). In germinal-centre B cells, AID is highly expressed, and has an inherent mutator activity that helps generate antibody diversity (2). However, AID may also regulate gene expression epigenetically by directly deaminating 5-methylcytosine in concert with base-excision repair to exchange cytosine (3). This pathway promotes gene demethylation, thereby removing epigenetic memory. For example, AID promotes active demethylation of the genome in primordial germ cells (4). However, different studies have suggested either a requirement (5) or a lack of function (6) for AID in promoting pluripotency in somatic nuclei after fusion with embryonic stem cells. Here we tested directly whether AID regulates epigenetic memory by comparing the relative ability of cells lacking AID to reprogram from a differentiated murine cell type to an induced pluripotent stem cell. We show that Aid-null cells are transiently hyper-responsive to the reprogramming process. Although they initiate expression of pluripotency genes, they fail to stabilize in the pluripotent state. The genome of Aid-null cells remains hypermethylated in reprogramming cells, and hypermethylated genes associated with pluripotency fail to be stably upregulated, including many MYC target genes. Recent studies identified a late step of reprogramming associated with methylation status (7), and implicated a secondary set of pluripotency network components (8). AID regulates this late step, removing epigenetic memory to stabilize the pluripotent state.

Published
2013

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