Selected Xu Lab Publications


Liu, Y., Gu, Z., Cao, H., Kaphle, P., Lyu, J., Zhang, Y., Hu, W., Chung, S.S., Dickerson, K.E., and Xu, J. (2021). Convergence of oncogenic cooperation at single-cell and single-gene levels drives leukemic transformation. Nat. Comm., 12, 6323. (PubMed)

Gu, Z., Liu, Y., Zhang, Y., Cao, H., Lyu, J., Wang, X., Wylie, A., Newkirk, S.J., Jones, A.E., Lee, M., Botten, G.A., Deng, M., Dickerson, K.E., Zhang, C.C., An, W., Abrams, J.M., and Xu J. (2021). Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia. Nat Genet. 53, 672-682. (PubMed)


Gu, Z., Dickerson, K.E., NS Xu, J. (2020). Therapeutic response and outcome explained by leukemia cell of origin.  Cancer Discov. 10, 445-1447. (PubMed)

Li, K., Zhang, Y., Liu, X., Liu, Y., Gu, Z., Cao, H., Dickerson, K.E., Chen, M., Chen, W., Shao, Z., Ni, M., and Xu, J. (2020). Non-coding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies. Cancer Discov. 10, 724-745. (PubMed

Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K.E., Ni, M., and Xu, J. (2020) Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing. Nat Commun. 11, 485. (PubMed)

Liu, X., Chen, Y., Zhang, Y., Liu, Y., Liu, N., Botten, G.A., Cao, H., Orkin, S.H., Zhang, M.Q., and Xu, J. (2020). Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol. 21, 59 (PubMed)


Gu, Z., Liu, Y., Cai, F., Patrick, M., Zmajkovic, J., Cao, H., Zhang, Y., Tasdogan, A., Chen, M., Qi, L., Liu, X., Li, K., Lyu, J., Dickerson, K.E., Chen, W., Ni, M., Merritt, M.E., Morrison. S.J., Skoda, R.C., DeBerardinis, R.J., and Xu, J. (2019) Loss of EZH2 reprograms BCAA metabolism to drive leukemic transformation. Cancer Discovery 9, 1228-1247.  (PubMed)


Vo, L.T., Kinney, M.A., Liu, X., Zhang, Y., Barragan, J., Sousa, P.M., Jha, D.K., Han, A., Cesana, M., Shao, Z., North, T.E., Orkin, S.H., Doulatov, S., Xu, J., Daley, G.Q. (2018). Regulation of haematopoietic multipotency by EZH1. Nature 553, 506-510. (PubMed)

Huang, J., Li, K., Cai, W., Liu, X., Zhang, Y., Orkin, S.H., Xu, J.#, Yuan, G.C.#. (2018). Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun. 9, 943. (PubMed) #corresponding author

Liu, X., Zhang, Y., Chen, Y., Li, M., Shao, Z., Zhang, M.Q., Xu, J. (2018). CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9. Curr Protoc Mol Biol.  123, e64. (PubMed)

Liu, N., Hargreaves, V.V., Zhu, Q., Kurland, J.V., Hong, J., Kim, W., Sher, F., Macias-Trrevino, C., Rogers, J.M., Kurita, R., Nakamura, Y., Yuan, G.C., Bauer, D.E., Xu, J., Bulyk, M.L., Orkin, S.H. (2018). Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch. Cell 173, 1-13. (PubMed)


Liu, X., Zhang, Y., Chen, Y., Li, M., Zhou, F.#, Li ,K., Cao, H., Ni, M., Liu, Y., Gu, Z., Dickerson, K.E., Xie, S., Hon, G.C., Xuan, Z., Zhang, M.Q., Shao, Z., and Xu, J#. (2017) In situ capture of chromatin interactions by biotinylated dCas9. Cell  170, 1028–1043.  (PudMed)  #corresponding author

Liu, X., Zhang, Y., Ni, M., Cao, H., Signer, R.A.J., Li, D., Li, M., Gu, Z., Hu, Z., Dickerson, K.E., Weinberg, S.E., Chandel, N.S., DeBerardinis, R.J., Zhou, F.#, Shao, Z.#., and Xu, J.#. (2017). Mitochondrial biogenesis in erythropoiesis is regulated by mTORC1-mediated protein translation. Nat. Cell Biol. 19, 626-638. (PubMed) #corresponding author

Ansó, E., Weinberg, S.E., Diebold, L.P., Thompson, B.J., Malinge, S., Schumacker, P.T., Liu, X., Zhang, Y., Shao, Z., Steadman, M., Marsh, K.M., Xu J, Crispino, J.D., and Chandel, N.S. (2017). Mitochondrial respiratory chain is essential for hematopoietic stem cell function. Nat. Cell Biol19, 614- 625. (PubMed)

Kim, J., Hu, Z., Cai, L., Li, K., Choi, E., Faubert, B., Bezwada, D., Rodriguez-Canales, J., Villalobos, P., Lin, Y.F., et al. (2017). CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells. Nature 546, 168-172. (PubMed)


Sun, X., Chuang, J.C., Kanchuala, M., Wu, L., Celen, C., Li, L., Liang, H., Zhang, S., Maples, T., Nguyen, L.H., Wang, S.C., Sanger, R.A., Sorouri, M., Nassour, I., Liu, X., Xu, J., et al. (2016). Suppression of the SWI/SNF component Arid1a promotes mammalian regeneration. Cell Stem Cell 18, 456-466. (PubMed)

Huang, J., Liu, X., Li, D., Shao, Z., Cao, H., Zhang, Y., Trompouki, E., Bowman, T.V., Zon, L.I., Yuan, G.C., Orkin, S.H.#., and Xu, J.#. (2016). Dynamic control of enhancer repertoires drives lineage and stage-specific transcription during hematopoiesis. Dev. Cell 36, 9—23. (PubMed) #corresponding author

Masuda, T., Wang, X., Maeda, M., Canver, M.C., Sher, F., Funnell, A.P., Fisher, C., Suciu, M., Martyn, G.E., Norton, L.J., Zhu, C., Kurita, R., Nakamura, Y., Xu, J., et al. (2016). Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science 351, 285-289. (PubMed)


Das, P.P., Hendrix, D.A., Apostolou, E., Buchner, A.H., Canver, M.C., Beyaz, S., Ljuboja, D., Kuintzle, R., Kim, W., Karnik, R., Shao, Z., Xie, H., Xu, J., et al. (2015). PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 12, 1456-1470. (PubMed)

Xu, J.*, Shao, Z.*, Li, D., Xie, H., Kim, W., Huang, J., Taylor, J.E., Pinello, L., Glass, K., Jaffe, J.D., et al. (2015). Developmental control of Polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol. Cell 57, 304—316. (PubMed) *co-first author

Ishikawa, Y., Maeda, M., Pasham, M., Aguet, F., Tacheva-Grigorova, S.K., Masuda, T., Yi, H., Lee, S.U., Xu, J., Teruya-Feldstein, J., et al. (2015). Role of the clathrin adaptor PICALM in normal hematopoiesis and polycythemia vera pathophysiology. Haematologica 100, 439-451. (PubMed)


Li, Y., Esain, V., Teng, L., Xu, J., Kwan, W., Frost, I.M., Yzaguirre, A.D., Cai, X., Cortes, M., Maijenberg, M.W., et al. (2014). Inflammatory signaling regulates embryonic hematopoiesis. Genes Dev. 28, 2597-2612. (PubMed)

Pinello, L.*, Xu, J.*, Orkin, S.H., and Yuan, G.C. (2014). Analysis of chromatin state plasticity identifies cell-type specific regulators of H3K27me3 patterns. Proc. Natl. Acad. Sci. U. S. A. 111, E344-E353. *co-first author (PubMed)

Maroz, A., Stachorski, L., Emmrich, S., Reinhardt, K., Xu, J., Shao, Z., Käbler, S., Dertmann, T., Hitzler, J., Roberts, I., et al. (2014). GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient leukemia. Leukemia 28, 1259-1270. (PubMed)

Xie, H., Xu, J.Hsu, J.H., Nguyen, M., Fujiwara, Y., Peng, C., and Orkin, S.H. (2014). Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner. Cell Stem Cell 14, 68—80. (PubMed)


Bauer, D.E., Kamran, S.C., Lessard, S., Xu, J., Fujiwara, Y., Lin, C., Shao, Z., Canver, M.C., Smith, E.C., Pinello, L., et al. (2013). An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 342, 253—257. (PubMed)

Xu, J., Bauer, D.E., Kerenyi, M.A., Vo, T.D., Hou, S., Hsu, Y.J., Yao, H., Trowbridge, J.J., Mandel, G., and Orkin, S.H. (2013). Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A Proc. Natl. Acad. Sci. U. S. A. 110, 6518—6523. (PubMed)

Guo, G., Luc, S., Marco, E., Lin, T.W., Peng, C., Kerenyi, M.A., Beyaz, S., Kim, W., Xu, J., Das, P.P., et al. (2013). Mapping cellular hierarchy by single cell analysis of the cell surface repertoire. Cell Stem Cell 12, 492—505. (PubMed)


Xu, J.and Smale S.T. (2012). Designing an enhancer landscape. Cell 151, 929—931. (PubMed)

Xu. J.*., Shao, Z.*., Glass, K., Bauer, D.E., Pinello, L., Handel, B.V., Hou, S., Stamatoyannopoulos, J.A., Mikkola, H.K.A., Yuan, G.C., and Orkin, S.H. (2012). Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev. Cell 23, 796-811. (PubMed) *co-first author

Sankaran, V.G., Ludwig, L.S., Sicinska, E., Xu, J., Bauer, D.E., Eng, J.C., Patterson, H.C., Metcalf, R.A., Natkunam, Y., Orkin, S.H., et al. (2012). Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number. Gen. Dev. 26, 2075-2087. (PubMed)

Chan, K.S., Xu, J., Wardan, H., McColl, B., Orkin, S., and Vadolas, J. (2012). Generation of a genomic reporter assay system for analysis of g- and b-globin gene regulation. FASEB J. 26, 1736-1744. (PubMed)


Xu, J., and Orkin, S.H. (2011). The erythroid/myeloid lineage fate paradigm takes a new player. EMBO J. 30, 983-985. (PubMed)

Xu, J., Peng, C., Sankaran, V.G., Shao, Z., Esrick, E.B., Chong, B.G., Ippolito, G.C., Fujiwara, Y., Ebert, B.L., Tucker, P.W., et al. (2011). Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science 334, 993—996. (PubMed)

Sankaran, V.G, Xu, J., Byron, R., Greisman, H.A., Fisher, C., Weatherall, D.J., Sabath, D.E., Groudine, M., Orkin, S.H., Premawardhena, A., et al. (2011). A functional element necessary for fetal hemoglobin silencing. N. Engl. J. Med. 365, 807-814. (PubMed)

Woo, A.J., Kim, J., Xu, J., Huang, H., and Cantor, A.B. (2011). Role of ZBP-89 in human globin gene regulation and erythroid differentiation. Blood 118, 3684-3693. (PubMed)


Sankaran, V.G., Xu, J., and Orkin, S.H. (2010). Transcriptional silencing of fetal hemoglobin by BCL11A. Ann. N. Y. Acad. Sci. 1202, 64-68. (PubMed)

Sankaran, V.G.*, Xu, J.*, and Orkin, S.H. (2010). Advances in the understanding of haemoglobin switching. Br J Haematol 149, 181—194. Review. (PubMed) *co-first author

Snow, J.W., Kim, J., Currie, C.R., Xu, J., and Orkin, S.H. (2010). Sumoylation regulates interaction of FOG1 with CTBP. J. Biol. Chem. 285, 28064-28075. (PubMed)

Xu, J., Sankaran, V.G., Ni, M., Menne, T.F., Puram, R.V., Kim, W., and Orkin, S.H. (2010). Transcriptional silencing of g-globin by BCL11A involves long-range interactions and cooperation with SOX6. Gen. Dev. 24, 783—798. (PubMed)


Xu, J., Watts, J.A., Pope, S.D., Gadue, P., Kamps, M., Plath, K., Zaret, K.S., and Smale, S.T. (2009). Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Gen. Dev. 23, 2824—2838. (PubMed)

Sankaran, V.G.*., Xu, J.*., Ragoczy, T., Ippolito, G.C., Walkley, C.R., Maika, S.D., Fujiwara, Y., Ito, M., Groudine, M., Bender, M.A., Tucker, P.W., and Orkin, S.H. (2009). Developmental and species-divergent globin switching are driven by BCL11A. Nature 460, 1093-1097. (PubMed) *co-first author

Papathanasiou, P., Attema, J.L., Karsunky, H., Xu, J., Smale, S.T., and Weissman, I.L. (2009). Evaluation of the long-term reconstituting subset of hematopoietic stem cells with CD150. Stem Cells 27, 2498-2508. (PubMed)


Zaret, K.S., Watts, J., Xu, J., Wandzioch, E., Smale, S.T., and Sekiya, T. (2008). Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. Cold Spr. Harbor Symp. Quant. Biol. 73, 119-126. (PubMed)

Sankaran, V.G., Menne, T.F., Xu, J., Akie, T.E., Lettre, G., Handel, B.V., Mikkola, H.K.A., Hirschhorn, J.N., Cantor, A.B., and Orkin, S.H. (2008). Human fetal hemoglobin expression is regulated by the development stage-specific repressor BCL11A. Science 322, 1839—1842. (PubMed)


 Xu, J., Pope, S.D., Jazirehi, A.R., Attema, J.L., Papathanasiou, P., Watts, J.A., Zaret, K.S., Weissman, I.L., and Smale, S.T. (2007). Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc. Natl. Acad. Sci. U. S. A. 104, 12377—12382. (PubMed)

Attema, J.L., Papathanasiou, P., Forsberg, E.C., Xu, J., Smale, S.T., and Weissman, I.L. (2007). Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl. Acad. Sci. U. S. A. 104, 12371-12376. (PubMed)

Zhou, L., Nazarian, A.A., Xu, J., Tantin, D., Corcoran, L.M., and Smale, S.T. (2007). An inducible enhancer required for Il12b promoter activity in an insulated chromatin environment. Mol. Cell. Biol. 27, 2698-2712. (PubMed)