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CEMB Faculty Publications

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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

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

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

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., 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

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

**  NOTE:  new video for this publication HERE.

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

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

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