Publications

2018-2024 Publications of the OMC in co-authorship with Extramural and Intramural users

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

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

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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. Patange, S., Ball, D. A., Karpova, T. S., Girvan, M., Levens, D., and Larson, D. R. (2022) MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Reports 38, 110292

11. Patange, S., Ball, D. A., Karpova, T. S., Girvan, M., Levens, D., and Larson, D. R. (2022) MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Reports 38, 110292

12. 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

13. 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

14. 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

15. 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

16. 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.

17. Dundr, M., Ball, D. A., Karpova, T. S. Crossing boundaries of light microscopy resolution discerns novel assemblies in the nucleolus (2024) Histochemistry and Cell Biology. Jul;162(1-2):161-183. doi: 10.1007/s00418-024-02297-7

2018-2024 Publications by Extramural and Intramural users using images obtained in OMC

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

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

3. Kim, J., Sturgill, D., Sebastian, R., Khurana, S., Tran, A. D., Edwards, G. B., Kruswick, A., Burkett, S., Hosogane, E. K., Hannon, W. W., Weyemi, U., Bonner, W. M., Luger, K., and Oberdoerffer, P. (2018) Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions. Mol Cell 69, 36-47

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

5. Lee, H-S., Carmena, M., Liskovykh, M., Peat, E., Kim, J-H., Oshimura, M., Masumoto, H., Teulade-Fichou, M-P., Pommier, Y., Earnshaw, W., Larionov, V., and Kouprina, N. (2018) Systematic Analysis of Compounds Specifically Targeting Telomeres and Telomerase for Clinical Implications in Cancer Therapy. Cancer Res 78, 6282-6296.

6. Arango, D., Sturgill, D., Alhusaini, N., Dillman, A. A., Sweet, T. J., Hanson, G., Hosogane, M., Sinclair, W. R., Nanan, K. K., Mandler, M. D., Fox, S. D., Zengeya, T. T., Andresson, T., Meier, J. L., Coller, J., and Oberdoerffer, S. (2018) Acetylation of cytidine in mRNA promotes translation efficiency. Cell 175,1872-1886.

7. 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

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

9. 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.

10. 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.

11. 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.

12. 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

13. 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

14. 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.

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

16. 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

17. 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

18. 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

19. 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.

20. 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.

21. 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.

22. 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.

23. 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.

24. 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