Publications

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

Presman, D., Ball, D., Paakinaho, V., Grimm, J., Lavis, L., Karpova, T., Hager, G.: Quantifying transcription factor dynamics at the single-molecule level in live cells. (2017) Methods 123: 76-88

Kannan R., Song JK, Karpova T, Clarke A, Shivalkar M, Wang B, Kotlyanskaya L, Kuzina I, Gu Q, Giniger E. The Abl pathway bifurcates to balance Enabled and Rac signaling in axon patterning in Drosophila. The Abl pathway bifurcates to balance Enabled and Rac signaling in axon patterning in Drosophila.(2017) Development 144: 487-498

Keyvan Torabi, Darawalee Wangsa, Immaculada Ponsa, Markus Brown, Anna Bosch, Maria Vila-Casadesús, Tatiana S. Karpova, Maria Calvo, Antoni Castells, Rosa Miró, , Thomas Ried, and Jordi Camps. Transcription-dependent radial distribution of TCF7L2 regulated genes in chromosome territories.2017. Chromosoma. 126: 655-667

Paakinaho, V., Presman DM, Ball D, Schiltz, RL, Levitt, P, Johnson, T, Mazza D., Morisaki T, Karpova TS, Hager GL. Single-Molecule analysis of Glucocorticoid Receptor and cofactor actin in living cells. 2017 Nat Commun 8:15896

Morales-Kastresana, A, Telford, B., Musich, TA, McKinnon K, Clayborne, K, Braig, Z, Rosner, A, Demberg, T, Watson DC, Karpova TS, Freeman GJ, DeKruyff RH, Pavlakis GN, Terabe M, Robert-Guroff M, Berzofsky JA, Jones JA. Labeling extracellular vesicles for nanoscale flow cytometry (2017) Sci Rep 7:1878

Shrestha RL, Ahn GS, Staples MI, Sathyan KM, Karpova TS, Foltz DR, Basrai MA. Mislocalization of centromeric Histone H3 variant, CENP-A contributes to chromosomal instability (CIN) in human cells (2017) Oncotarget 8: 46781-46800.

Vargas-Inchaustegui Diego A., Demers Andrew, Shaw Julia M., Kang Guobin, Ball David, Tuero Iskra, Musich Thomas, Mohanram Venkatramanan, Demberg Thorsten, Karpova Tatiana S., Li Qingsheng, Robert-Guroff Marjorie. Vaccine-induction of Lymph Node-resident SIV Env-specific T-follicular helper cells in rhesus macaques . J Immunol, 196: 1700-1710 (2016 )

Swinstead EE, Miranda TB, Paakinaho V, Baek S, Goldstein I, Hawkins M, Karpova TS, Ball D, Mazza D, Grimm JB, Lavis LD, Morisaki T, Grøntved L, Presman DM, Hager GL. (2016) Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions. Cell 165: 593-605

Presman, D. M., Ganguly S., Schiltz, L., Karpova T. S., Hager, Gordon. (2016).DNA binding triggers the teramerization of the glucocorticoid receptor in new cells. PNAS 113:8236-8241

Ball, D.A., Mehta, G. D., Salomon-Kent, R., Mazza, D., Morisaki, T., Mueller, F., McNally, J.G., Karpova, T. S. Single Molecule Tracking Of Ace1p In Saccharomyces cerevisiae Defines A Characteristic Residence Time For Non-specific Interactions Of Transcription Factors With Chromatin  2016 Nucleic Acids Res doi:10.1093/nar/gkw744

Barik, D., Ball, D., Peccoud, J., Tyson, J.: A stochastic model of the yeast cell cycle reveals roles for feedback regulation in limiting cellular variability, PLoS Comput. Biol. 12: e1005230, 2016

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

Goldstein I, Baek S, Presman DM, Paakinaho V, Swinstead EE, Hager GL. Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response. Genome Res. 2017 27(3):427-439.

DeBoy E, Puttaraju M, Jailwala P, Kasoji M, Cam M, Misteli T. Identification of novel RNA isoforms of LMNA. Nucleus. 2017 Sep 3;8(5):573-582.

Wang, Q., Sawyer, I.A., Sung, M-H., Sturgill, D., Shevtsov, S.P., Pegoraro, G., Hakim, O., Baek, S., Hager, G.L., and Dundr, M. (2016) Cajal bodies influence genome conformation. Nature Commun. 7:10966

Ji X, Dadon DB, Powell BE, Fan ZP, Borges-Rivera D, Shachar S, Weintraub AS, Hnisz D, Pegoraro G, Lee TI, Misteli T, Jaenisch R, Young RA. (2016) 3D Chromosome Regulatory Landscape of Human Pluripotent Cells. Cell Stem Cell. 18:262-75.

Leshner M, Devine M, Roloff GW, True LD, Misteli T, Meaburn KJ. (2016) Locus-specific gene repositioning in prostate cancer. Mol Biol Cell. 27:236-46

Stavreva, D.A., and Hager, G.L. (2016)  Chromatin structure and gene regulation: A dynamic view of enhancer function. Nucleus. 6:442-448

Meaburn KJ, Agunloye O, Devine M, Leshner M, Roloff GW, True LD, Misteli T. (2016) Tissue-of-origin-specific gene repositioning in breast and prostate cancer. Histochem Cell Biol. 145:433-46.

Quenet D, Sturgill D, Dalal Y. (2016) Identifying centromeric RNAs involved in histone dynamics in vivo. Methods Enzymol. 573:445-466

Liskovykh, M., Lee N.C., Larionov V., Kouprina N. (2016) Moving toward a higher efficiency of microcell-mediated chromosome transfer. Mol Ther Methods Clin Dev, 3: 16043

Martins NM, Bergmann JH, Shono N, Kimura H, Larionov V, Masumoto H, Earnshaw WC. (2016) Epigenetic engineering shows that a human centromere resists silencing mediated by H3K27me3/K9me3. Mol Biol Cell 27: 177-196

Sawyer, Iain A. , Shevtsov, Sergei P., Dundr, Miroslav. (2016) Spectral imaging to visualize higher-order genomic organization. Nucleus. 2016 7:325-338

Sawyer I.A., Sturgill D., Sung MH, Hager GL, Dundr M. Cajal body function in genome organization and transcriptome diversity. Bioessays 2016 38:1197-1208