Publications

Bhatt, B., Wei, Y., Pradhan, A. K., Dhakshnamoorthy, J., Zofall, M., Xiao, H., Vijayakumari, D., Jain, S., Folco, H. D., Qi, H., Ball, D. A., Karpova, T. S., Wheeler, D., Wong, J., Grewal, S. I. S. (2026) Stress controls heterochromatin inheritance via histone H3 ubiquitylation. Nature. 650:768-778. doi: 10.1038/s41586-025-09899-8

Mazzocca, M., Narducci, D. N., Grosse-Holz, S., Matthias, J., Karpova, T. S., Hansen, A. S. (2026) Integrated MINFLUX tracking reveals two distinct chromatin dynamics classes across cell types. Nat Struct Mol Biol. 33:905-914. doi: 10.1038/s41594-026-01807-6

Balachandra, V., Thomas, M., Shrestha, R. L., Sethi, S. C., Chari, R., Lin, S., Chih-Chien Cheng, K., Karpova, T. S., Caplen, N. J., Basrai, M. A. (2025) Protein Phosphatase 1 Regulatory Subunit PNUTS Prevents CENP-A Mislocalization and Chromosomal Instability. Mol Cell Biol. 45(5):185-197. doi: 10.1080/10985549.2025.2487010

Nehru, V., Ball, D., Mukherjee, A., Kurotaki, D., Karpova, T. S., Ozato, K. (2025) Live cell analysis of mobility and decay kinetics of the histone variant H3.3. J. Biol. Chem. 301:108557. doi: 10.1016/j.jbc.2025.108557

Fettweis, G., Wagh, K., Stavreva, D. A., Jiménez-Panizo, A., Kim, S., Lion, M., Alegre-Martí, A., Rinaldi, L., Johnson, T. A., Krishnamurthy, M., Wang, L., Ball, D. A., Karpova, T. S., Upadhyaya, A., Vertommen, D., Recio, J. F., Estébanez-Perpiñá, E., Dequiedt, F., Hager, G. L. (2025) Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers. Nucleic Acids Research. 53:gkaf415. doi: 10.1093/nar/gkaf415

Sethi, S. C., Shrestha, R. L., Balachandra, V., Hori, T., Corda, L., Ozbun, L., Karpova, T. S., McKinnon, K., Chari, R., Pegoraro, G., Chih-Chien Cheng, K., Giunta, S., Caplen, N. J., Fukagawa, T., Basrai, M. A. (2025) Chromatin remodeling activity of EP400 safeguards chromosomal stability by preventing CENP-A mislocalization. Cell Rep. 44:116423. doi: 10.1016/j.celrep.2025.116423

Balachandra, V., Shrestha, R. L., …, Karpova, T. S., McKinnon, K., Cheng, K., Nielsen, M. L., Groth, A., and Basrai M. A. (2024) DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chain. EMBO J.

Correll, C. C., Rudloff, U., Schmit, J. D., Ball, D. A., Karpova, T. S., Balzer, E., Dundr, M., Crossing boundaries of light microscopy resolution discerns novel assemblies in the nucleolus (2024) Histochemistry and Cell Biology. 162(1-2):161-183.

Sethi, S. C., Shrestha, R. L., Balachandra, V., Durairaj, G., Au, W. C., Nirula, M., Karpova, T. S., Kaiser, P., Basrai, M. A. β-TrCP-Mediated Proteolysis of Mis18β Prevents Mislocalization of CENP-A and Chromosomal Instability (2024) Mol Cell Biol. 13:1-14

Fettweis, G., Johnson TA, Almeida-Prieto B, Weller-Pérez J, Presman DM, Hager GL, Alvarez de la Rosa D.  (2024) The mineralocorticoid receptor forms higher order oligomers upon DNA binding. Protein Sci. 33:e4890. doi: 10.1002/pro.4890.

Zhang, T., Au, W.C., Ohkuni, K., Shrestha, R. L., Kaiser, P., Basrai, M. A. (2024) Mck1-mediated proteolysis of CENP-A prevents mislocalization of CENP-A for chromosomal stability in Saccharomyces cerevisiae. Genetics. 2024 Sep 4;228(1):iyae108. doi: 10.1093/genetics/iyae108

Shrestha, R. L., Balachandra, V., Kim, J. H., Rossi, A., Vadlamani, P., Sethi, S. C., Ozbun, L., Lin, S., Cheng, K. C-C., Chari, R., Karpova, T. S., Pegoraro, G., Foltz, D. R., Caplen, N. J., and Basrai, M. A. (2023) The histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability. J. Cell Sci. 136, jcs260944

Ahn, J., Zhang, L., Ravishankar, H., Fan, L., Zeng, Y., Kirsh, K. P., Park., J-E., Yun, H-Y., Ghirlando, R., Ma, B., Ball, D. A., Ku, B., Nussinov, R., Karpova, T. S., Kim, S. J., Wang, Y-X., and Lee, K. S. (2023) Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in humans . Communications Biology

Wildner, C., Mehta, G. D., Ball, D. A., Karpova, T. S., and Koeppl, H. (2023) Bayesian analysis of non-stationary transcription in CUP1 locus of Saccharomyces cerevisiae. bioRxiv doi: 10.1101/2023.06.20.545522

Ball, D. A., Jalloh, B., and Karpova, T. S. (2022) Impact of Saccharomyces cerevisiae on the field of single molecule biophysics. Int. J. Mol. Sci 23, 10.3390/ijms232415895

Ahn, J., Zhang, L., Ravishankar, H., Fan, L., Zeng, Y., Kirsh, K. P., Park., J-E., Yun, H-Y., Ghirlando, R., Ma, B., Ball, D. A., Ku, B., Nussinov, R., Karpova, T. S., Kim, S. J., Wang, Y-X., and Lee, K. S. (2023) Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in humans . Communications Biology

Shrestha, R., Rossi, A., Wangsa, D., Zaldana, K., Suva, E., Chun, Y., Sanders, C. L., Hogan, A., Difilippantonio, S., Karpova, T. S., Karim, B., Foltz, D. R., Fachinetti, D., Aplan, P., Ried, T., and Basrai, M. (2021) CENP-A overexpression promotes aneuploidy with karyotypic heterogeneity. (2021). J. Cell Biol 220, e202007195

 Patange, S., Ball, D. A., Karpova, T. S., and Larson, D. R.. (2021). Towards a ‘spot on’ understanding of transcription in the nucleus. J Mol Biol 433, 167016

Chen, H., Smith, M., Herz, J., Li, T., Hasley, R., Le Saout, C., Zhu, Z., Cheng, J., Gronda, A., Martina, J. A., Irusta, P. M., Karpova, T.,S., McGavern, D. B., and Catalfamo, M. (2021) The role of protease activated receptor-1 signaling in CD8 T cell effector function. iScience 24, 103387

Chernova, T. A., Yang, Z., Karpova, T. S., Shanks, J. R., Scherbik, N., Wilkinson, K. D., and Chernoff, Y. O. (2020) Aggregation and Prion-Inducing Properties of the G-Protein Gamma Subunit Ste18 are Regulated by Association with the Plasma Membrane. Int J Mol Sci. 21, 5038

Shah, S., Parmiter, D., Constantine, C., Elizalde, P., Naldrett, M., Karpova, T., and Choy, J. (2019) Glucose signaling is connected to chromosome segregation through Protein Kinase A phosphorylation of Dam1 kinetochore subunit in S. cerevisiae. Genetics 211, 531-547

Donovan, B.T., Huyn, A., Ball, D.A., Patel H. P., Poirier, M., Larson, D.R., Ferguson, M.L., Lenstra, TL. (2019) Single-molecule imaging reveals the interplay between transcription factors, nucleosomes, and transcription bursting. EMBO J 38, e100809

Rahman, M.A., McKinnon, K.M., Karpova T.S., Ball D.A., Venzon, D. J. Fan, W., Kang, G, Li, Q., Robert-Guroff, M. Associations of Simian Immunodeficiency Virus (SIV)-Specific follicular CD8 T cells with Other Follicular T cells suggest complex contributions to SIV Viremia control.(2018) J. Immunol. 200: 2714-2726

Serebryannyy, L. A., Ball, D. A., Karpova T. S., Misteli, T. Single molecule analysis of lamin dynamics (2018) Methods, 157:56-65

Mehta G.D., Ball D. A., Eriksson, P. R., Chereji, R. V., Clark D. J., McNally J. G., Karpova, T. S. Single-Molecule analysis reveals linked cycles of RSC chromatin remodeling and Ace1p transcription factor binding in yeast (2018) Molecular Cell 72: 875-887

Shah, S., Parmiter, D., Constantine, C., Elizalde, P., Naldrett, M., Karpova, T., Choy, J. Glucose signaling is connected to chromosome segregation through Protein Kinase A phosphorylation of Dam1 kinetochore subunit in S. cerevisiae. (2018) Genetics, 2011:531-547

Serebryannyy, L. A., Ball, D. A., Karpova T. S., and Misteli, T. (2018) Single molecule analysis of lamin dynamics. Methods 157, 56-65

Fazel, M., Hoseini, R., Saurabh, A., Xu, L. W. Q., Scipioni, L., Tedeschi, G., Gratton, E., Digman, M. A., Pressé, S. (2026) Resolving fluorescently labeled species using highly multiplexed spectral FLIM. Scientific Reports. doi: 10.1038/s41598-026-44023-4

Bryan, J. S. 4th, Tashev, S. A., Fazel, M., Scheckenbach, M., Tinnefeld, P., Herten, D. P., Pressé, S. (2025) Bayesian Inference of Binding Kinetics from Fluorescence Time Series. J Phys Chem B. 129:4670-4681. doi: 10.1021/acs.jpcb.5c01180

Khan, S. A., Pallikkuth, S., Schodt, D. J., Meddens, M. B., Mazloom-Farsibaf, H., Wester, M. J., Liu, S., Taylor, E., Fazel, M., Farzam, F., Lidke, K. A. (2025) A MATLAB-based instrument control (MIC) package for fluorescence imaging. Journal of Open Source Software. 10:7275. doi: 10.21105/joss.07275

Fettweis, G., Johnson TA, Almeida-Prieto B, Weller-Pérez J, Presman DM, Hager GL, Alvarez de la Rosa D.  (2024) The mineralocorticoid receptor forms higher order oligomers upon DNA binding. Protein Sci. 33:e4890. doi: 10.1002/pro.4890.

Zhang, T., Au, W.C., Ohkuni, K., Shrestha, R. L., Kaiser, P., Basrai, M. A. (2024) Mck1-mediated proteolysis of CENP-A prevents mislocalization of CENP-A for chromosomal stability in Saccharomyces cerevisiae. Genetics. 2024 Sep 4;228(1):iyae108. doi: 10.1093/genetics/iyae108

Fettweis, G., Johnson TA, Almeida-Prieto B, Weller-Pérez J, Presman DM, Hager GL, Alvarez de la Rosa D. (2023)The mineralocorticoid receptor forms higher order oligomers upon DNA binding. Protein Sci. Dec 31:e4890. doi: 10.1002/pro.4890.

Wagh K, Stavreva DA, Jensen RAM, Paakinaho V, Fettweis G, Schiltz RL, Wüstner D, Mandrup S, Presman DM, Upadhyaya A, Hager GL. (2023) Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states Sci Adv. Jun 16;9(24):eade1122. doi: 10.1126/sciadv.ade1122. Epub 2023 Jun 14.

Liskovykh, M., Petrov, N. S., Noskov, V. N., Masumoto, H., Earnshaw, W. C., Schlessinger, D., Shabalina, S., Larionov, V., Kouprina, N. (2023) Actively transcribed rRNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci. Apr 12;80(5):121. doi: 10.1007/s00018-023-04770-3

Rinaldi, L., Fettweis, G., Kim, S., Garcia, D. A., Fujiwara, S., Johnson, T. A., Tettey, T. T., Ozbun, L., Pegoraro, G., Puglia, M., Blagoev, B., Upadhyaya, A., Stavreva, D. A., and Hager, G. L. (2022) The glucocorticoid receptor associates with the cohesion loader NIPBL to promote long-range gene regulation. Sci Adv. 2022 Apr;8(13):eabj8360. doi: 10.1126/sciadv.abj8360. Epub 2022 Mar 30.

Zhao, Y., Vartak, S. V., Conte, A., Wang, X., Garcia, D. A., Stevens, E., Kyoung Jung, S., Kieffer-Kwon, K. R., Vian, L., Stodola, T., Moris, F., Chopp, L., Preite, S., Schwartzberg, P. L., Kulinski, J. M., Olivera, A., Harly, C., Bhandoola, A., Heuston, E. F., Bodine, D. M., Urrutia, R., Upadhyaya, A., Weirauch, M. T., Hager, G., Casellas, R. (2022) “Stripe” transcription factors provide accessibility to mammalian genomes.

 Jiménez-Panizo A, Alegre-Martí A, Tettey TT, Fettweis G, Abella M, Antón R, Johnson TA, Kim S, Schiltz RL, Núñez-Barrios I, Font-Díaz J, Caelles C, Valledor AF, Pérez P, Rojas AM, Fernández-Recio J, Presman DM, Hager GL, Fuentes-Prior P, Estébanez-Perpiñá E. (2022) The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Nucleic Acids Res. 2022 Dec 9;50(22):13063-13082. doi: 10.1093/nar/gkac1119.

Garcia, D. A., Fettweis, G., Presman, D. M., Paakinaho, V., Jarzynski, C., Upadhaya, A., and Hager, G.L. (2021) Power-law behavior of transcription factor dynamics at the single molecule level implies a continuum affinity model. Nucleic Acid Res 49, 6605-6620

Garcia, D. A., Johnson, T. A., Presman, D. M., Fettweis, G., Wagh, K., Rinaldi, L., Stavreva, D. A., Paakinaho, V., Jensen, R. A. M., Mandrup, S., Upadhyaya, A., and Hager, G. L. (2021) An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol. Cell 81, 1484-1498

Feric, M., Demarest, T. G., Tian, J., Croteau, D. L., Bohr, V. A., and Misteli, T. (2021) Self-assembly of multi-component mitochondrial nucleoids via phase separation. EMBO J 40, e107165. doi: 10.15252/embj.2020107165.

 Feric, M., and Misteli, T. (2021) Phase separation in genome organization across evolution. Trends Cell Biol 31, 671-685.

Wan, Y., Anastasakis, D. G., Rodriguez, J., Palangat, M., Gudla, P., Zaki, G., Tandon, M., Pegoraro, G., Chow, C. C., Hafner, M., and Larson, D. R. (2021) Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell 184, 2878-2895

Petrov, N., Lee, H-S., Liskovykh, M., Teulade-Fichou, M-P., Masumoto, H., Earnshaw, W. C., Pommier, Y., Larionov, V., and Kouprina, N. (2021) Terpyridine platinum compounds induce telomere dysfunction and chromosome instability in cancer cells. Oncotarget 12, 1444-1456

 Kim, J-H, Noskov, V., Ogurtsov, A. Y., Nagaraja, R., Petrov, N., Liskovykh, M., Walenz, B. P., Lee, H-S., Kouprina, N., Phillippy, A. M., Shabalina, S. A., Schlessinger, D., and Larionov, V. (2021) The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning. Sci Rep 11, 2997

Pooley, J. R., Rivers, C. A., Kilcooley, M.T., Paul, S. N., Cavga, A. D., Kershaw, Y. M., Muratcioglu, S., Gursoy, A., Keskin, O., and Lightman, S. L. (2020) Beyond the Heterodimer Model for Mineralocorticoid and Glucocorticoid Interactions in Nuclei and at DNA. PLoS One 15, e0227520. doi: 10.1371/journal.pone.0227520.

Stavreva, D. A., Garcia, D. A., Fettweis, G., Gudla, P. R., Zaki, G. F., Soni, V., McGowan, A., Williams, G., Huynh, A., Palangat, M., Schiltz, R. L., Johnson, T. A., Presman, D. M., Ferguson, M. L., Pegoraro, G., Upadhyaya, A., and Hager, G. L. (2019) Transcriptional bursting and co-bursting regulation by steroid hormone release pattern and transcription factor mobility. Mol Cell 75, 1161-1177

Meaburn, K. J., and Misteli, T. (2019) Assessment of the Utility of Gene Positioning Biomarkers in the Stratification of Prostate Cancers. Front Genet10, 1029.

Rodrigues, J., Ren, G., Day, C. R., Zhao, K., Choy, C.C., and Larson, D. R. (2019) Intrinsic dynamics of a human gene reveal the basis of expression heterogeneity. Cell 176, 213-226.

Liskovykh, M., Goncharov, N. V., Petrov, N., Aksenova, V., Pegoraro, G., Ozbun, L., Reinhold, W. C., Varma, S., Dasso, M., Kumeiko, V., Matsumoto, H., Earnshaw, W. C., Larionov, V., and Kouprina, N. (2019) A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission. Genome Res 29, 1719–1732.

Lee, N. C. O., Kim, Jung-Hyun, Petrov N. S. , Lee, H-S., Masumoto, H., Earnshaw, W. C., Larionov V., Kouprina, N. Method to assemble Genomic DNA fragments or Genes on human artificial chromosome with regulated kinetochore using a multi-integrase system. ASC Synth. Biol. 2018, 7, 63-74

Pesenti E, Kouprina N, Liskovykh M, Aurich-Costa J, Larionov V, Masumoto H, Earnshaw WC, Molina O. Generation of a Synthetic Human Chromosome with Two Centromeric Domains for Advanced Epigenetic Engineering Studies. ACS Synth Biol. 2018 7:1116-1130

Kim J, Sturgill D, Sebastian R, Khurana S, Tran AD, Edwards GB, Kruswick A, Burkett S, Hosogane EK, Hannon WW, Weyemi U, Bonner WM, Luger K, Oberdoerffer P. Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions. Mol Cell. 2018 69:36-47

Omsland M., Pise-Masison, C, Fujikawa, D., Galli, V., Fenizia, C., Parks, R. W., Gjertsen, B.T., Franchini, G., Andresen, V. Inhibition of Tunneling Nanotube (TNT) Formation and Human T-cell Leucemia virus Type 1 (HTLV-1) Transmission by cytorabine. Sci Rep 2018, 8: 11118