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NCI Optical Microscopy Laboratory

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Publications (2016 – present)

2016-2020 Publications of the OMC in co-aurthorship with Extramural and Intramural users

1. 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 )

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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.

12. 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

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

14. 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

15. 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

2012-2020 Publications with imaging supported by OMC
(By Extramural and Intramural users using images obtained in the Core)

1. 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

2. 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.

3. 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

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

5. 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.

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

7. 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

8. 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

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

10. 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

11. 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.

12. 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.

13. 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

14. 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

15. 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

16. 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