CEMB Faculty Publications
Alisafaei, F., Jokhun, D. S., Shivashankar, G. V., & Shenoy, V. B. (2019). Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors by cell geometric constraints. Proceedings of the National Academy of Sciences of the United States of America, 116(27), 13200–13209. https://doi.org/10.1073/pnas.1902035116
Alisafaei, F., Jokhun, D. S., Shivashankar, G. V., & Shenoy, V. B. (2019). Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors by cell geometric constraints. Proceedings of the National Academy of Sciences of the United States of America, 116(27), 13200–13209. https://doi.org/10.1073/pnas.1902035116
Cho, S., Vashisth, M., Abbas, A., Majkut, S., Vogel, K., Xia, Y., Ivanovska, I. L., Irianto, J., Tewari, M., Zhu, K., Tichy, E. D., Mourkioti, F., Tang, H. Y., Greenberg, R. A., Prosser, B. L., & Discher, D. E. (2019). Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell-cycle arrest. Developmental Cell, 49(6), 920-935.e5. https://doi.org/10.1016/j.devcel.2019.04.020
Cho, S., Vashisth, M., Abbas, A., Majkut, S., Vogel, K., Xia, Y., Ivanovska, I. L., Irianto, J., Tewari, M., Zhu, K., Tichy, E. D., Mourkioti, F., Tang, H. Y., Greenberg, R. A., Prosser, B. L., & Discher, D. E. (2019). Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell-cycle arrest. Developmental Cell, 49(6), 920-935.e5. https://doi.org/10.1016/j.devcel.2019.04.020
Cosgrove, B. D., Loebel, C., Driscoll, T. P., Tsinman, T. K., Dai, E. N., Heo, S.-J., Dyment, N. A., Burdick, J. A., & Mauck, R. L. (2021). Nuclear envelope wrinkling predicts mesenchymal progenitor cell mechano-response in 2D and 3D microenvironments. Biomaterials, 270, 120662. https://doi.org/10.1016/j.biomaterials.2021.120662
Cosgrove, B. D., Loebel, C., Driscoll, T. P., Tsinman, T. K., Dai, E. N., Heo, S.-J., Dyment, N. A., Burdick, J. A., & Mauck, R. L. (2021). Nuclear envelope wrinkling predicts mesenchymal progenitor cell mechano-response in 2D and 3D microenvironments. Biomaterials, 270, 120662. https://doi.org/10.1016/j.biomaterials.2021.120662
Discher, D. E. (2019). From DNA damage to epithelial integrity: New roles for cell forces. Molecular Biology of the Cell, 30 (16), 1879–1881. https://doi.org/10.1091/mbc.E19-06-0338
Discher, D. E. (2019). From DNA damage to epithelial integrity: New roles for cell forces. Molecular Biology of the Cell, 30 (16), 1879–1881. https://doi.org/10.1091/mbc.E19-06-0338
Gardini, L., Woody, M. S., Kashchuk, A. v., Goldman, Y. E., Ostap, E. M., & Capitanio, M. (2022). High-Speed Optical Traps Address Dynamics of Processive and Non-Processive Molecular Motors. Methods in Molecular Biology (Clifton, N.J.), 2478, 513–557. https://doi.org/10.1007/978-1-0716-2229-2_19
Heo, S.-J., Cosgrove, B. D., Dai, E. N., & Mauck, R. L. (2018). Mechano-adaptation of the stem cell nucleus. Nucleus, 9(1), 9–19. https://doi.org/10.1080/19491034.2017.1371398
Heo, S.-J., Cosgrove, B. D., Dai, E. N., & Mauck, R. L. (2018). Mechano-adaptation of the stem cell nucleus. Nucleus, 9(1), 9–19. https://doi.org/10.1080/19491034.2017.1371398
Heo, S.-J., Thakur, S., Chen, X., Loebel, C., Xia, B., McBeath, R., Burdick, J. A., Shenoy, V. B., Mauck, R. L., & Lakadamyali, M. (2022). Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. Nature Biomedical Engineering 2022, 1–15. https://doi.org/10.1038/s41551-022-00910-5
Jing, H., Korasick, D. A., Emenecker, R. J., Morffy, N., Wilkinson, E. G., Powers, S. K., & Strader, L. C. (2022). Regulation of AUXIN RESPONSE FACTOR condensation and nucleo-cytoplasmic partitioning. Nature Communications, 13(4015). https://doi.org/10.1038/s41467-022-31628-2
Kegelman, C. D., Collins, J. M., Nijsure, M. P., Eastburn, E. A., & Boerckel, J. D. (2020). Gone caving: Roles of the transcriptional regulators yap and taz in skeletal development. In Current Osteoporosis Reports (Vol. 18, Issue 5, pp. 526–540). Springer. https://doi.org/10.1007/s11914-020-00605-3
Kegelman, C. D., Collins, J. M., Nijsure, M. P., Eastburn, E. A., & Boerckel, J. D. (2020). Gone caving: Roles of the transcriptional regulators yap and taz in skeletal development. In Current Osteoporosis Reports (Vol. 18, Issue 5, pp. 526–540). Springer. https://doi.org/10.1007/s11914-020-00605-3
Lakadamyali, M. (2022). Single nucleosome tracking to study chromatin plasticity. Current Opinion in Cell Biology, 74, 23–28. https://doi.org/10.1016/J.CEB.2021.12.005
Lakadamyali, M. (2022). Single nucleosome tracking to study chromatin plasticity. Current Opinion in Cell Biology, 74, 23–28. https://doi.org/10.1016/J.CEB.2021.12.005
Linares-Saldana, R., Kim, W., Bolar, N. A., Zhang, H., Koch-Bojalad, B. A., Yoon, S., Shah, P. P., Karnay, A., Park, D. S., Luppino, J. M., Nguyen, S. C., Padmanabhan, A., Smith, C. L., Poleshko, A., Wang, Q., Li, L., Srivastava, D., Vahedi, G., Eom, G. H., Blobel, G. A., Joyce, E. F., and Jain, R. (2021). BRD4 orchestrates genome folding to promote neural crest differentiation. Nature Genetics, 53(10), 1480–1492. https://doi.org/10.1038/s41588-021-00934-8
Linares-Saldana, R., Kim, W., Bolar, N. A., Zhang, H., Koch-Bojalad, B. A., Yoon, S., Shah, P. P., Karnay, A., Park, D. S., Luppino, J. M., Nguyen, S. C., Padmanabhan, A., Smith, C. L., Poleshko, A., Wang, Q., Li, L., Srivastava, D., Vahedi, G., Eom, G. H., Blobel, G. A., Joyce, E. F., and Jain, R. (2021). BRD4 orchestrates genome folding to promote neural crest differentiation. Nature Genetics, 53(10), 1480–1492. https://doi.org/10.1038/s41588-021-00934-8
Liu, S., Yang, H., Lu, T. J., Genin, G. M., & Xu, F. (2019). Electrostatic switching of nuclear basket conformations provides a potential mechanism for nuclear mechanotransduction. Journal of the Mechanics and Physics of Solids, 133, 103705. https://doi.org/10.1016/j.jmps.2019.103705
Liu, S., Yang, H., Lu, T. J., Genin, G. M., & Xu, F. (2019). Electrostatic switching of nuclear basket conformations provides a potential mechanism for nuclear mechanotransduction. Journal of the Mechanics and Physics of Solids, 133, 103705. https://doi.org/10.1016/j.jmps.2019.103705
Mason, D. E., Collins, J. M., Dawahare, J. H., Nguyen, T. D., Lin, Y., Voytik-Harbin, S. L., Zorlutuna, P., Yoder, M. C., & Boerckel, J. D. (2019). YAP and TAZ limit cytoskeletal and focal adhesion maturation to enable persistent cell motility. Journal of Cell Biology, 218(4), 1369–1389. https://doi.org/10.1083/jcb.201806065
Mason, D. E., Collins, J. M., Dawahare, J. H., Nguyen, T. D., Lin, Y., Voytik-Harbin, S. L., Zorlutuna, P., Yoder, M. C., & Boerckel, J. D. (2019). YAP and TAZ limit cytoskeletal and focal adhesion maturation to enable persistent cell motility. Journal of Cell Biology, 218(4), 1369–1389. https://doi.org/10.1083/jcb.201806065
Mathur, J., Shenoy, V., & Pathak, A. (2020). Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity. BioRxiv, 2020.03.20.000802. https://doi.org/10.1101/2020.03.20.000802
Mathur, J., Shenoy, V., & Pathak, A. (2020). Mechanical memory in cells emerges from mechanotransduction with transcriptional feedback and epigenetic plasticity. BioRxiv, 2020.03.20.000802. https://doi.org/10.1101/2020.03.20.000802
Mellis, I. A., Edelstein, H. I., Truitt, R., Goyal, Y., Beck, L. E., Symmons, O., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Pérez-Bermejo, J. A., Padmanabhan, A., Yang, W., Jain, R., & Raj, A. (2021). Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Systems. https://doi.org/10.1016/J.CELS.2021.07.003
Mellis, I. A., Edelstein, H. I., Truitt, R., Goyal, Y., Beck, L. E., Symmons, O., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Pérez-Bermejo, J. A., Padmanabhan, A., Yang, W., Jain, R., & Raj, A. (2021). Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Systems. https://doi.org/10.1016/J.CELS.2021.07.003
Neguembor, M. V., Martin, L., Castells-García, Á., Gómez-García, P. A., Vicario, C., Carnevali, D., AlHaj Abed, J., Granados, A., Sebastian-Perez, R., Sottile, F., Solon, J., Wu, C., Lakadamyali, M., & Cosma, M. P. (2021). Transcription-mediated supercoiling regulates genome folding and loop formation. Molecular Cell, 81(15), 3065-3081.e12. https://doi.org/10.1016/J.MOLCEL.2021.06.009
Neguembor, M. V., Martin, L., Castells-García, Á., Gómez-García, P. A., Vicario, C., Carnevali, D., AlHaj Abed, J., Granados, A., Sebastian-Perez, R., Sottile, F., Solon, J., Wu, C., Lakadamyali, M., & Cosma, M. P. (2021). Transcription-mediated supercoiling regulates genome folding and loop formation. Molecular Cell, 81(15), 3065-3081.e12. https://doi.org/10.1016/J.MOLCEL.2021.06.009
Pfeifer, C. R., Tobin, M. P., Cho, S., Vashisth, M., Dooling, L. J., Vazquez, L. L., Ricci-De Lucca, E. G., Simon, K. T., & Discher, D. E. (2022). Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus, 13(1), 129–143. https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2045726
Pfeifer, C. R., Tobin, M. P., Cho, S., Vashisth, M., Dooling, L. J., Vazquez, L. L., Ricci-De Lucca, E. G., Simon, K. T., & Discher, D. E. (2022). Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus, 13(1), 129–143. https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2045726
Pfeifer, C. R., Tobin, M. P., Cho, S., Vashisth, M., Dooling, L. J., Vazquez, L. L., Ricci-De Lucca, E. G., Simon, K. T., & Discher, D. E. (2022). Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate. Nucleus, 13(1), 129–143. https://doi.org/10.1080/19491034.2022.2045726
Pfeifer, C. R., Vashisth, M., Xia, Y., & Discher, D. E. (2019). Nuclear failure, DNA damage, and cell cycle disruption after migration through small pores: A brief review. Essays in Biochemistry 63(5), 569–577. https://doi.org/10.1042/EBC20190007
Pfeifer, C. R., Vashisth, M., Xia, Y., & Discher, D. E. (2019). Nuclear failure, DNA damage, and cell cycle disruption after migration through small pores: A brief review. Essays in Biochemistry 63(5), 569–577. https://doi.org/10.1042/EBC20190007
Poleshko, A., Shah, P. P., Gupta, M., Babu, A., Morley, M. P., Manderfield, L. J., Ifkovits, J. L., Calderon, D., Aghajanian, H., Sierra-Pagán, J. E., Sun, Z., Wang, Q., Li, L., Dubois, N. C., Morrisey, E. E., Lazar, M. A., Smith, C. L., Epstein, J. A., & Jain, R. (2017). Genome-nuclear lamina interactions regulate cardiac stem cell lineage restriction. Cell, 171(3), 573-587.e14. https://doi.org/10.1016/j.cell.2017.09.018
Poleshko, A., Shah, P. P., Gupta, M., Babu, A., Morley, M. P., Manderfield, L. J., Ifkovits, J. L., Calderon, D., Aghajanian, H., Sierra-Pagán, J. E., Sun, Z., Wang, Q., Li, L., Dubois, N. C., Morrisey, E. E., Lazar, M. A., Smith, C. L., Epstein, J. A., & Jain, R. (2017). Genome-nuclear lamina interactions regulate cardiac stem cell lineage restriction. Cell, 171(3), 573-587.e14. https://doi.org/10.1016/j.cell.2017.09.018
Poleshko, A., Smith, C. L., Nguyen, S. C., Sivaramakrishnan, P., Wong, K. G., Murray, J. I., Lakadamyali, M., Joyce, E. F., Jain, R., & Epstein, J. A. (2019). H3k9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. ELife, 8. https://doi.org/10.7554/eLife.49278
Poleshko, A., Smith, C. L., Nguyen, S. C., Sivaramakrishnan, P., Wong, K. G., Murray, J. I., Lakadamyali, M., Joyce, E. F., Jain, R., & Epstein, J. A. (2019). H3k9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. ELife, 8. https://doi.org/10.7554/eLife.49278
Price, C. C., Mathur, J., Boerckel, J. D., Pathak, A., & Shenoy, V. B. (2021). Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory. Biophysical Journal, 120(22), 5074–5089. https://doi.org/10.1016/J.BPJ.2021.10.006
Price, C. C., Mathur, J., Boerckel, J. D., Pathak, A., & Shenoy, V. B. (2021). Dynamic self-reinforcement of gene expression determines acquisition of cellular mechanical memory. Biophysical Journal, 120(22), 5074–5089. https://doi.org/10.1016/J.BPJ.2021.10.006
Pyrpassopoulos, S., Shuman, H., & Ostap, E. M. (2022). Microtubule Dumbbells to Assess the Effect of Force Geometry on Single Kinesin Motors. Methods in Molecular Biology (Clifton, N.J.), 2478, 559–583. https://doi.org/10.1007/978-1-0716-2229-2_20
See, K., Kiseleva, A. A., Smith, C. L., Liu, F., Li, J., Poleshko, A., & Epstein, J. A. (2020). Histone methyltransferase activity programs nuclear peripheral genome positioning. Developmental Biology, 466(1–2), 90–98. https://doi.org/10.1016/j.ydbio.2020.07.010
See, K., Kiseleva, A. A., Smith, C. L., Liu, F., Li, J., Poleshko, A., & Epstein, J. A. (2020). Histone methyltransferase activity programs nuclear peripheral genome positioning. Developmental Biology, 466(1–2), 90–98. https://doi.org/10.1016/j.ydbio.2020.07.010
See, K., Lan, Y., Rhoades, J., Jain, R., Smith, C. L., & Epstein, J. A. (2019). Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9Me2 domains. Development, 146(3). https://doi.org/10.1242/dev.174078
See, K., Lan, Y., Rhoades, J., Jain, R., Smith, C. L., & Epstein, J. A. (2019). Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9Me2 domains. Development, 146(3). https://doi.org/10.1242/dev.174078
Seo, J., Byun, W. Y., Alisafaei, F., Georgescu, A., Yi, Y. S., Massaro-Giordano, M., Shenoy, V. B., Lee, V., Bunya, V. Y., & Huh, D. (2019). Multiscale reverse engineering of the human ocular surface. Nature Medicine, 25(8), 1310–1318. https://doi.org/10.1038/s41591-019-0531-2
Seo, J., Byun, W. Y., Alisafaei, F., Georgescu, A., Yi, Y. S., Massaro-Giordano, M., Shenoy, V. B., Lee, V., Bunya, V. Y., & Huh, D. (2019). Multiscale reverse engineering of the human ocular surface. Nature Medicine, 25(8), 1310–1318. https://doi.org/10.1038/s41591-019-0531-2
Shah, P. P., Lv, W., Rhoades, J. H., Poleshko, A., Abbey, D., Caporizzo, M. A., Linares-Saldana, R., Heffler, J. G., Sayed, N., Thomas, D., Wang, Q., Stanton, L. J., Bedi, K., Morley, M. P., Cappola, T. P., Owens, A. T., Margulies, K. B., Frank, D. B., Wu, J. C., Rader, D.J., Yang, W., Prosser, B.L., Musunuru, K., Jain, R. (2021). Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell, 28, 1–17. https://doi.org/10.1016/j.stem.2020.12.016
Shah, P. P., Lv, W., Rhoades, J. H., Poleshko, A., Abbey, D., Caporizzo, M. A., Linares-Saldana, R., Heffler, J. G., Sayed, N., Thomas, D., Wang, Q., Stanton, L. J., Bedi, K., Morley, M. P., Cappola, T. P., Owens, A. T., Margulies, K. B., Frank, D. B., Wu, J. C., Rader, D.J., Yang, W., Prosser, B.L., Musunuru, K., Jain, R. (2021). Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell, 28, 1–17. https://doi.org/10.1016/j.stem.2020.12.016
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Smith, C. L., Lan, Y., Jain, R., Epstein, J. A., & Poleshko, A. (2021). Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. Science Advances, 7(39), 3035–3059. https://doi.org/10.1126/SCIADV.ABJ3035
Smith, C. L., Lan, Y., Jain, R., Epstein, J. A., & Poleshko, A. (2021). Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. Science Advances, 7(39), 3035–3059. https://doi.org/10.1126/SCIADV.ABJ3035
Smith, L. R., Irianto, J., Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Constricted migration modulates stem cell differentiation. Molecular Biology of the Cell, 30(16), 1985–1999. https://doi.org/10.1091/mbc.E19-02-0090
Smith, L. R., Irianto, J., Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Constricted migration modulates stem cell differentiation. Molecular Biology of the Cell, 30(16), 1985–1999. https://doi.org/10.1091/mbc.E19-02-0090
Vashisth, M., Cho, S., Irianto, J., Xia, Y., Wang, M., Hayes, B., Wieland, D., Wells, R., Jafarpour, F., Liu, A., & Discher, D. E. (2021). Scaling concepts in ’omics: Nuclear lamin-B scales with tumor growth and often predicts poor prognosis, unlike fibrosis. Proceedings of the National Academy of Sciences of the United States of America, 118(48). https://doi.org/10.1073/PNAS.2112940118/-/DCSUPPLEMENTAL
Vashisth, M., Cho, S., Irianto, J., Xia, Y., Wang, M., Hayes, B., Wieland, D., Wells, R., Jafarpour, F., Liu, A., & Discher, D. E. (2021). Scaling concepts in ’omics: Nuclear lamin-B scales with tumor growth and often predicts poor prognosis, unlike fibrosis. Proceedings of the National Academy of Sciences of the United States of America, 118(48). https://doi.org/10.1073/PNAS.2112940118
Wang, M., Ivanovska, I., Vashisth, M., & Discher, D. E. (2022). Nuclear mechanoprotection: From tissue atlases as blueprints to distinctive regulation of nuclear lamins. APL Bioengineering, 6(2), 021504. https://doi.org/10.1063/5.0080392
Xia, Y., Cho, S., Vashisth, M., Ivanovska, I. L., Dingal, P. C. D. P., & Discher, D. E. (2019). Manipulating the mechanics of extracellular matrix to study effects on the nucleus and its structure. Methods, 157, 3–14. https://doi.org/10.1016/j.ymeth.2018.12.009
Xia, Y., Cho, S., Vashisth, M., Ivanovska, I. L., Dingal, P. C. D. P., & Discher, D. E. (2019). Manipulating the mechanics of extracellular matrix to study effects on the nucleus and its structure. Methods, 157, 3–14. https://doi.org/10.1016/j.ymeth.2018.12.009
Xia, Y., Ivanovska, I. L., Zhu, K., Smith, L., Irianto, J., Pfeifer, C. R., Alvey, C. M., Ji, J., Liu, D., Cho, S., Bennett, R. R., Liu, A. J., Greenberg, R. A., & Discher, D. E. (2018). Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. Journal of Cell Biology, 217(11), 3796–3808. https://doi.org/10.1083/jcb.201711161
Xia, Y., Ivanovska, I. L., Zhu, K., Smith, L., Irianto, J., Pfeifer, C. R., Alvey, C. M., Ji, J., Liu, D., Cho, S., Bennett, R. R., Liu, A. J., Greenberg, R. A., & Discher, D. E. (2018). Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. Journal of Cell Biology, 217(11), 3796–3808. https://doi.org/10.1083/jcb.201711161
Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Nuclear mechanics during and after constricted migration. Acta Mechanica Sinica/Lixue Xuebao, 35(2), 299–308. https://doi.org/10.1007/s10409-018-00836-9
Xia, Y., Pfeifer, C. R., & Discher, D. E. (2019). Nuclear mechanics during and after constricted migration. Acta Mechanica Sinica/Lixue Xuebao, 35(2), 299–308. https://doi.org/10.1007/s10409-018-00836-9
Xia, Y., Pfeifer, C. R., Zhu, K., Irianto, J., Liu, D., Pannell, K., Chen, E. J., Dooling, L. J., Tobin, M. P., Wang, M., Ivanovska, I. L., Smith, L. R., Greenberg, R. A., & Discher, D. E. (2019). Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle. The Journal of Cell Biology, 218(8), 2545–2563. https://doi.org/10.1083/jcb.201811100
Xia, Y., Pfeifer, C. R., Zhu, K., Irianto, J., Liu, D., Pannell, K., Chen, E. J., Dooling, L. J., Tobin, M. P., Wang, M., Ivanovska, I. L., Smith, L. R., Greenberg, R. A., & Discher, D. E. (2019). Rescue of DNA damage after constricted migration reveals a mechano-regulated threshold for cell cycle. The Journal of Cell Biology, 218(8), 2545–2563. https://doi.org/10.1083/jcb.201811100
