Perelman School of Medicine at the University of Pennsylvania

Jain Lab

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Selected Publications

A complete list of publications can be found here.

Jiang, C.L., Goyal, Y., Jain, N., Wang, Q., Truitt, R.E., Coté, A.J., Emert, B., Mellis, I.A., Kiani, K., Yang, W., Jain, R.*, Raj, A.* Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. Genome Biology 2022. *Co-corresponding author

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.,  Padamanabhan, A.,  Smith, C.L.,  Polseshko, A.,  Wang, Q.,  Li, L.,  Srivastava, D., Vahedi, G.,  Eom, G.H.,  Blobel, G.A.,  Joyce, E.F.,  Jain, R.  BRD4 orchestrates genome folding to promote neural crest progenitor differentiation. Nature Genetics 2021. (Feature in Perspective in Nature Genetics) 

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.**  Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell 2021.

Mellis, I.A., Edelstein, H.I., Truitt, R., Beck, L.E., Symmons, O., Goyal, Y., Dunagin, M.C., Linares-Saldana, R.A., Shah, P.P., Yang, W., Jain, R.*, Raj, A.* Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity. Cell Systems 2021. *Co-corresponding author

Jain R.*, Epstein J.A.* Not all stress is bad for your heart. Science 2021. *Co-corresponding author

Keough, K.C.*, Shah, P.P.*,  Gjoni, K., Santini, G.T., Wickramasinghe, N.M., Dundes, C.E., Karnay, A., Chen, A., Salomon, R.E.A., Walsh, P.J., Nguyen, S.C., Whalen, S.,  Joyce, E.F., Loh, K.M., Dubois, N.C.,  Pollard, K.S.**,  Jain, R.** An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. bioRxiv (In Revision).

Smith, C.L., Lan, Y., Jain, R., Epstein, J.A., Poleshko, A.. Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. Science Advances 2021.

Alexanian, M., Prztycki, P., Micheletti, R., Padmanabhan, A., Ye, L., Travers, J.G., Teran, B.G., Duan, Q.,  Ranade, S.S., Felix, F.,  Linares-Saldana, R., Huang, Y., Andreoletti, G., Yang, J., Ivey, K.,  Jain, R., McKinsey, T.A., Gifford, C., Pollard, K.S., Haldar, S.M.,  Srivastava, D., A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease. Nature. 2021. 

Bose, S.K., White, B.M., Kashyap, M.V., Dave, A., De Bie, F.R., Li, H., Singh, K., Menon, P., Wang, T., Teerdhala, S., Swaminathan, V., Hartman, H.A., Jayachandran, S., Chandrasekaran, P., Musunuru, K., Jain, R., Frank, D.B., Zoltick, P., Peranteau, W.H. In utero adenine base editing corrects multi-organ pathology in a lethal lysosomal storage disease. Nature Communications 2021.

Yoon, S., Kim, M., Lee, H., Kang, G., Bedi, K., Margulies, K.B., Jain, R., Nam, K.I., Kook, H., Eom, G.H. S-Nitrosylation of Histone Deacetylase 2 by Neuronal Nitric Oxide Synthase as a Mechanism of Diastolic Dysfunction. Circulation 2021.

Padmanabhan, A.*, Alexanian, M.*, Linares-Saldana, R.A.*, Gonzalez-Teran, B., Andreoletti, G., Huang, Y., Connolly, A.J., Kim, W.K., Hsu, A., Duan, Q, Winchester, S., Haldar, S.M., Jain, R.**, Srivastava, D.** BRD4 Interacts with GATA4 to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes. Circulation 2020. **Co-corresponding author

Kim, W. and Jain, R., Picking Winners and Losers: The Role of Cell Competition in Tissue Development and Homeostasis. Trends in Genetics 2020. 

Chakravarti Dilley, L.,  Szuperak, M.,  Gong., N.N.,  Williams, C.E.,  Saldana, R.L.,  Garbe, D.S.,  Syed, M.H.,  Jain, R.,  Kayser, M.S. Identification of a molecular basis for the juvenile sleep state. Elife 2020.

Heffler, J., Shah, P.P., Robison, P., Phyo, S., Veliz, K., Uchida, K., Bogush, A., Rhoades, J., Jain, R., Prosser, B.L. A Balance Between Intermediate Filaments and Microtubules Maintains Nuclear Architecture in the Cardiomyocyte. Circulation Research 2020.

Gozalo, A., Duke A., Lan, Y., Pascual-Garcia, P., Talamas, J.A., Nguyen, S.C., Shah, P.P., Jain, R., Joyce, E.F., Capelson, M.. Core Components of the Nuclear Pore Bind Distinct States of Chromatin and Contribute to Polycomb Repression. Molecular Cell 2020.

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.*H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. Elife 2019. *Co-corresponding author

Aghajanian, H., Kimura, T., Rurik, J.G., Hancock, A.S., Leibowitz, M.S., Li, L., Scholler, J., Monslow, J., Lo, A., Han, W., Wang, T., Bedi, K., Morley, M.P., Linares Saldana, R.A., Bolar, N.A., McDaid, K., Assenmacher, C.A., Smith, C.L., Wirth, D., June, C.H., Margulies, K.B., Jain, R., Puré, E., Albelda, S.M., Epstein, J.A. Targeting cardiac fibrosis with engineered T cells. Nature 2019. 

Berg DA, Su Y, Jimenez-Cyrus D, Patel A, Huang N, Morizet D, Lee S, Shah R, Ringeling FR, Jain R, Epstein JA, Wu QF, Canzar S, Ming GL, Song H, Bond AM. A Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis. Cell 2019.

Frank, D.B.*, Penkala, I.J., Zepp, J.A., Sivakumar, A., Linares-Saldana, R., Zacharias, W.J., Stolz, K.G., Pankin, J., Lu, M., Wang, Q., Babu, A., Li, L., Zhou, S., Morley, M.P., Jain, R.*, Morrisey, E.E.* Early lineage specification defines alveolar epithelial ontogeny in the murine lung. PNAS 2019. *Co-corresponding author

Rossidis, A.C., Stratigis, J.D., Chadwick, A.C., Hartman, H.A., Ahn, N.J., Li, H., Singh, K., Coons, B.E., Li, L., Lv, W., Zoltick, P.W., Alapati, D., Zacharias, W., Jain, R., Morrisey, E.E., Musunuru, K., Peranteau, W.H. In utero CRISPR-mediated therapeutic editing of metabolic genes. Nature Medicine 2018.

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.**. Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction. Cell 2017.

Aghajanian, H., Cho, Y.K., Rizer, N.W., Wang, Q., Li, L., Degenhardt, K., Jain, R.  Pdgfrα functions in endothelial-derived cells to regulate neural crest cells and the development of the great arteries. Disease Models & Mechanisms 2017. Featured on cover

Kook, H., Seo, S.B., Jain, R.  EZ Switch From EZH2 to EZH1: Histone Methylation Opens a Window of Cardiac Regeneration. Circulation research 2017.

Ramjee, V.*, Li, D.*, Manderfield, L.J., Liu, F., Engleka, K.A., Aghajanian, H., Rodell, C.B., Lu, W., Ho, V., Wang, T., Li, L., Singh, A., Cibi, D.M., Burdick, J.A., Singh, M.K.**, Jain, R.**, Epstein, J.A.** Epicardial YAP/TAZ orchestrate an immunosuppressive response following myocardial infarction. JCI 2017.  **Co-corresponding author.

Bardot, E., Calderon, D., Santoriello, F., Han, S., Cheung, K., Jadhav, B., Burtscher, I., Artap, S., Jain, R., Epstein, J.A., Lickert, H., Gouon-Evans, V., Sharp, A.J., Dubois, N.C. Foxa2 identifies a cardiac progenitor population with ventricular differentiation potential. Nature Communications 2017.

Loh, K.M., Chen, A., Koh, P.W., Deng, T.Z., Sinha, R., Tsai, J.M., Barkal, A.A., Shen, K.Y., Jain, R., Morganti, R.M., Shyh-Chang, N., Fernhoff, N.B., George, B.M., Wernig, G., Salomon, R.E., Chen, Z., Vogel, H., Epstein, J.A., Kundaje, A., Talbot, W.S., Beachy, P.A., Ang, L.T., Weissman, I.L. Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types. Cell 2016.  *Commentary in Cell Stem Cell

Jain, R.*, Li, D.*, Gupta, M., Manderfield, L.J., Ifkovits, J.L., Wang, Q., Liu, F., Liu, Y., Poleshko, A., Padmanabhan, A., Raum, J.C., Li, L., Lu, M.M., Won, K., Epstein, J.A. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts. Science 2015. *Featured on cover; Commentary in Molecular Therapy; Faculty of 1000 selection. 

Jain, R.*, Barkauskas, C.E.*, Takeda, N., Wang, Q., Aghajanian, H., Manderfield, L.M., Gupta, M., Padmanabhan, A., Li, D.Q., Li, L., Trivedi, C.M., Hogan, B.L., Epstein, J.A. Plasticity of Hopx+ Type I alveolar cells to regenerate Type II cells in the lung. Nature Communications 2015.

Hogan, B.L., Barkauskas, C.E., Chapman, H.A., Epstein, J.A., Jain, R., Hsia, C.C., Niklason, L., Calle, E., Le, A., Randell, S.H., Rock, J., Snitow, M., Krummel, M., Stripp, B.R., Vu, T., White, E.S., Whitsett, J.A., Morrisey, E.E. Repair and regeneration of the respiratory system: complexity, plasticity, and mechanisms of lung stem cell function. Cell Stem Cell 2014.

Takeda, N.*, Jain, R.*, LeBoeuf, M.R., Padmanabhan, A, Wang, Q., Li, L., Lu, M.M., Millar S., Epstein, J.A. Hopx expression defines a subset of multipotent hair follicle stem and progenitor cells primed to give rise to the niche. Development 2013. *Co-first author.

Takeda, N.*, Jain, R.*, LeBoeuf, M.R., Wang, Q., Lu, M.M., Epstein, J.A. Inter-conversion between intestinal stem cell populations in distinct niches. Science 2011. *Co-first author; Faculty of 1000 selection; Commentary in Cell Stem Cell

Jain, R., Engleka, K.A., Rentschler, S.L., Manderfield, L.J., Li, L., Yuan, L., Epstein, J.A. Cardiac neural crest orchestrates remodeling and functional maturation of mouse semilunar valves. JCI 2011.

Jain, R.*, Rentschler, S.*, Epstein, J.A. Notch and Outflow Tract Development. Annals of the New York Academy of Sciences 2010.

High, F.A.*, Jain, R.*, Stoller, J.Z., Antonucci, N.A., Lu, M.M., Epstein, J.A. Murine Jagged1/Notch signaling in the second heart field directs Fgf8 expression and tissue-tissue interactions during outflow tract development. JCI 2009. *Co-first author; Faculty of 1000 selection

Ladurner, A.G., Inouye, C., Jain, R., Tjian, R. Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol Cell. 2003.