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Rushad Pavri

In our lab, we study the phenomenon of antibody gene diversification in B lymphocytes – the process by which the immune system generates a vast repertoire of high-affinity antibodies essential to combat pathogenic challenges. We focus on the transcriptional and co-transcriptional mechanisms underlying these events using a combination of RNAi screening, genetic models, and genomic analysis.

Publications

2023

Costea, J., Schoeberl, UE., Malzl, D., von der Linde, M., Fitz, J., Gupta, A., Makharova, M., Goloborodko, A., Pavri, R. (2023)

A de novo transcription-dependent TAD boundary underpins critical multiway interactions during antibody class switch recombination.

Corresponding preprint Mol Cell. 83(5):681-697.e7

2022

Peycheva, M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, UE., Pavri, R. (2022)

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations.

 Science. 377(6612):eabj5502
Pre-printSchoeberl, U. E., Fitz, J., Froussios, K., Valieris, R., Makharova, M., Ourailidis, I., Bauer, B., Neumann, T., Wiedemann, E., Steininger, M., Garcia, A. C., Mastrovito, M., Mouquet, H., Tojal Da Silva, I., Pavri, R. (2022)

Somatic hypermutation spectra are independent of the local transcriptional and epigenetic landscape

 bioRxiv . 2022.05.21.492925

2021

Appel, LM., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., Schoeberl, UE., Puchinger, MG., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K., Lin, G., Vlasova, A., Leeb, M., Pavri, R., Stark, A., Akalin, A., Stefl, R., Bernecky, C., Djinovic-Carugo, K., Slade, D. (2021)

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.

 Nat Commun. 12(1):6078
Pre-printPeycheva,M., Neumann, T., Malzl, D., Nazarova, M., Schoeberl, U., and Pavri, R. (2021)

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations

 bioRxiv . 2021.05.29.446276

2020

Fitz, J., Neumann, T., Steininger, M., Wiedemann, EM., Garcia, AC., Athanasiadis, A., Schoeberl, UE., Pavri, R. (2020)

Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction.

 Nat Genet. 52(5):505-515

2018

Fitz, J., Neumann, T., Pavri, R. (2018)

Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.

 EMBO J. 37(8)

2017

Pavri, R. (2017)

R Loops in the Regulation of Antibody Gene Diversification.

 Genes (Basel). 8(6)

2016

Wiedemann, EM., Peycheva, M., Pavri, R. (2016)

DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.

 Cell Rep. 17(11):2927-2942

2014

Qian, J., Wang, Q., Dose, M., Pruett, N., Kieffer-Kwon, KR., Resch, W., Liang, G., Tang, Z., Mathé, E., Benner, C., Dubois, W., Nelson, S., Vian, L., Oliveira, TY., Jankovic, M., Hakim, O., Gazumyan, A., Pavri, R., Awasthi, P., Song, B., Liu, G., Chen, L., Zhu, S., Feigenbaum, L., Staudt, L., Murre, C., Ruan, Y., Robbiani, DF., Pan-Hammarström, Q., Nussenzweig, MC., Casellas, R. (2014)

B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity.

 Cell. 159(7):1524-37
Wang, Q., Oliveira, T., Jankovic, M., Silva, IT., Hakim, O., Yao, K., Gazumyan, A., Mayer, CT., Pavri, R., Casellas, R., Nussenzweig, MC., Robbiani, DF. (2014)

Epigenetic targeting of activation-induced cytidine deaminase.

 Proc Natl Acad Sci U S A. 111(52):18667-72

2011

Pavri, R., Nussenzweig, MC. (2011)

AID targeting in antibody diversity.

 Adv Immunol. 110:1-26

2010

Pavri, R., Gazumyan, A., Jankovic, M., Di Virgilio, M., Klein, I., Ansarah-Sobrinho, C., Resch, W., Yamane, A., Reina San-Martin, B., Barreto, V., Nieland, TJ., Root, DE., Casellas, R., Nussenzweig, MC. (2010)

Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5.

 Cell. 143(1):122-33

2006

Pavri, R., Zhu, B., Li, G., Trojer, P., Mandal, S., Shilatifard, A., Reinberg, D. (2006)

Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II.

 Cell. 125(4):703-17

2005

Pavri, R., Lewis, B., Kim, TK., Dilworth, FJ., Erdjument-Bromage, H., Tempst, P., de Murcia, G., Evans, R., Chambon, P., Reinberg, D. (2005)

PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of mediator.

 Mol Cell. 18(1):83-96