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20072020

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Article
2020

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K. E., Ni, M. & Xu, J., Dec 1 2020, In : Nature communications. 11, 1, 485.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9

Liu, X., Chen, Y., Zhang, Y., Liu, Y., Liu, N., Botten, G. A., Cao, H., Orkin, S. H., Zhang, M. Q. & Xu, J., Mar 5 2020, In : Genome biology. 21, 1, 59.

Research output: Contribution to journalArticle

Open Access

Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies

Li, K., Zhang, Y., Liu, X., Liu, Y., Gu, Z., Cao, H., Dickerson, K. E., Chen, M., Chen, W., Shao, Z., Ni, M. & Xu, J., May 1 2020, In : Cancer discovery. 10, 5, p. 724-745 22 p.

Research output: Contribution to journalArticle

2019

Loss of EZH2 Reprograms BCAA Metabolism to Drive Leukemic Transformation

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. & 1 others, Xu, J., Sep 1 2019, In : Cancer discovery. 9, 9, p. 1228-1247 20 p.

Research output: Contribution to journalArticle

14 Scopus citations

MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes

Li, M., Tu, S., Li, Z., Tan, F., Liu, J., Wang, Q., Zhang, Y., Xu, J., Zhang, Y., Zhou, F. & Shao, Z., Dec 1 2019, In : Cell Discovery. 5, 1, 40.

Research output: Contribution to journalArticle

Open Access
2018

CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9

Liu, X., Zhang, Y., Chen, Y., Li, M., Shao, Z., Zhang, M. Q. & Xu, J., Jul 2018, In : Current Protocols in Molecular Biology. 123, 1, e64.

Research output: Contribution to journalArticle

3 Scopus citations

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

Liu, N., Hargreaves, V. V., Zhu, Q., Kurland, J. V., Hong, J., Kim, W., Sher, F., Macias-Trevino, C., Rogers, J. M., Kurita, R., Nakamura, Y., Yuan, G. C., Bauer, D. E., Xu, J., Bulyk, M. L. & Orkin, S. H., Apr 5 2018, In : Cell. 173, 2, p. 430-442.e17

Research output: Contribution to journalArticle

59 Scopus citations

Dissecting super-enhancer hierarchy based on chromatin interactions

Huang, J., Li, K., Cai, W., Liu, X., Zhang, Y., Orkin, S. H., Xu, J. & Yuan, G. C., Dec 1 2018, In : Nature communications. 9, 1, 943.

Research output: Contribution to journalArticle

40 Scopus citations

GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism

Tanimura, N., Liao, R., Wilson, G. M., Dent, M. R., Cao, M., Burstyn, J. N., Hematti, P., Liu, X., Zhang, Y., Zheng, Y., Keles, S., Xu, J., Coon, J. J. & Bresnick, E. H., Sep 10 2018, In : Developmental cell. 46, 5, p. 581-594.e4

Research output: Contribution to journalArticle

3 Scopus citations

Regulation of embryonic haematopoietic multipotency by EZH1

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., Jan 25 2018, In : Nature. 553, 7689, p. 506-510 5 p.

Research output: Contribution to journalArticle

22 Scopus citations
2017

CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells

Kim, J., Hu, Z., Cai, L., Li, K., Choi, E., Faubert, B., Bezwada, D., Rodriguez-Canales, J., Villalobos, P., Lin, Y. F., Ni, M., Huffman, K. E., Girard, L., Byers, L. A., Unsal-Kacmaz, K., Peña, C. G., Heymach, J. V., Wauters, E., Vansteenkiste, J., Castrillon, D. H. & 6 others, Chen, B. P. C., Wistuba, I., Lambrechts, D., Xu, J., Minna, J. D. & Deberardinis, R. J., Jun 1 2017, In : Nature. 546, 7656, p. 168-172 5 p.

Research output: Contribution to journalArticle

67 Scopus citations

In Situ Capture of Chromatin Interactions by Biotinylated dCas9

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. & Xu, J., Aug 24 2017, In : Cell. 170, 5, p. 1028-1043.e19

Research output: Contribution to journalArticle

78 Scopus citations

Regulation of mitochondrial biogenesis in erythropoiesis by mTORC1-mediated protein translation

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. & Xu, J., May 31 2017, In : Nature cell biology. 19, 6, p. 626-638 13 p.

Research output: Contribution to journalArticle

40 Scopus citations

Temporal dynamics of cardiac hypertrophic growth in response to pressure overload

Wang, Y., Zhang, Y., Ding, G., May, H. I., Xu, J., Gillette, T. G., Wang, H. & Wang, Z. V., Dec 1 2017, In : American Journal of Physiology - Heart and Circulatory Physiology. 313, 6, p. H1119-H1129

Research output: Contribution to journalArticle

8 Scopus citations

The mitochondrial respiratory chain is essential for haematopoietic stem cell function

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. & Chandel, N. S., May 31 2017, In : Nature Cell Biology. 19, 6, p. 614-625 12 p.

Research output: Contribution to journalArticle

75 Scopus citations
2016

Bcl11a Deficiency Leads to Hematopoietic Stem Cell Defects with an Aging-like Phenotype

Luc, S., Huang, J., McEldoon, J. L., Somuncular, E., Li, D., Rhodes, C., Mamoor, S., Hou, S., Xu, J. & Orkin, S. H., Sep 20 2016, In : Cell Reports. 16, 12, p. 3181-3194 14 p.

Research output: Contribution to journalArticle

25 Scopus citations

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis

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. & Xu, J., Jan 11 2016, In : Developmental Cell. 36, 1, p. 9-23 15 p.

Research output: Contribution to journalArticle

85 Scopus citations

Gene regulation: Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin

Masuda, T., Wang, X., Maeda, M., Canver, M. C., Sher, F., Funnell, A. P. W., Fisher, C., Suciu, M., Martyn, G. E., Norton, L. J., Zhu, C., Kurita, R., Nakamura, Y., Xu, J., Higgs, D. R., Crossley, M., Bauer, D. E., Orkin, S. H., Kharchenko, P. V. & Maeda, T., Jan 15 2016, In : Science. 351, 6270, p. 285-289 5 p.

Research output: Contribution to journalArticle

92 Scopus citations

Suppression of the SWI/SNF Component Arid1a Promotes Mammalian Regeneration

Sun, X., Chuang, J. C., Kanchwala, M., Wu, L., Celen, C., Li, L., Liang, H., Zhang, S., Maples, T., Nguyen, L. H., Wang, S. C., Signer, R. A. J., Sorouri, M., Nassour, I., Liu, X., Xu, J., Wu, M., Zhao, Y., Kuo, Y. C., Wang, Z. & 2 others, Xing, C. & Zhu, H., Apr 7 2016, In : Cell Stem Cell. 18, 4, p. 456-466 11 p.

Research output: Contribution to journalArticle

49 Scopus citations
2015

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions

Xu, J., Shao, Z., Li, D., Xie, H., Kim, W., Huang, J., Taylor, J. E., Pinello, L., Glass, K., Jaffe, J. D., Yuan, G. C. & Orkin, S. H., Jan 22 2015, In : Molecular cell. 57, 2, p. 304-316 13 p.

Research output: Contribution to journalArticle

68 Scopus citations

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells

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., De Los Angeles, A., Zhang, Y., Choe, J., Jun, D. L. J., Shen, X., Gregory, R. I., Daley, G. Q. & 5 others, Meissner, A., Kellis, M., Hochedlinger, K., Kim, J. & Orkin, S. H., Sep 1 2015, In : Cell Reports. 12, 9, p. 1456-1470 15 p., 1953.

Research output: Contribution to journalArticle

29 Scopus citations

Role of the clathrin adaptor PICALM in normal hematopoiesis and polycythemia vera pathophysiology

Ishikawa, Y., Maeda, M., Pasham, M., Aguet, F., Tacheva-Grigorova, S. K., Masuda, T., Yi, H., Lee, S. U., Xu, J., Teruya-Feldstein, J., Ericsson, M., Mullally, A., Heuser, J., Kirchhausen, T. & Maeda, T., 2015, In : Haematologica. 100, 4, p. 439-451 13 p.

Research output: Contribution to journalArticle

14 Scopus citations
2014

Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns

Pinello, L., Xu, J., Orkin, S. H. & Yuan, G. C., Jan 21 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 3, p. E344-E353

Research output: Contribution to journalArticle

Open Access
42 Scopus citations

GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient leukemia

Maroz, A., Stachorski, L., Emmrich, S., Reinhardt, K., Xu, J., Shao, Z., Käbler, S., Dertmann, T., Hitzler, J., Roberts, I., Vyas, P., Juban, G., Hennig, C., Hansen, G., Li, Z., Orkin, S., Reinhardt, D. & Klusmann, J. H., Jun 2014, In : Leukemia. 28, 6, p. 1259-1270 12 p.

Research output: Contribution to journalArticle

18 Scopus citations

Inflammatory signaling regulates embryonic hematopoietic stem and progenitor cell production

Li, Y., Esain, V., Teng, L., Xu, J., Kwan, W., Frost, I. M., Yzaguirre, A. D., Cai, X., Cortes, M., Maijenburg, M. W., Tober, J., Dzierzak, E., Orkin, S. H., Tan, K., North, T. E. & Speck, N. A., Dec 1 2014, In : Genes and Development. 28, 23, p. 2597-2612 16 p.

Research output: Contribution to journalArticle

119 Scopus citations

Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner

Xie, H., Xu, J., Hsu, J. H., Nguyen, M., Fujiwara, Y., Peng, C. & Orkin, S. H., Jan 2 2014, In : Cell Stem Cell. 14, 1, p. 68-80 13 p.

Research output: Contribution to journalArticle

165 Scopus citations
2013

An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level

Bauer, D. E., Kamran, S. C., Lessard, S., Xu, J., Fujiwara, Y., Lin, C., Shao, Z., Canver, M. C., Smith, E. C., Pinello, L., Sabo, P. J., Vierstra, J., Voit, R. A., Yuan, G. C., Porteus, M. H., Stamatoyannopoulos, J. A., Lettre, G. & Orkin, S. H., Jan 1 2013, In : Science. 342, 6155, p. 253-257 5 p.

Research output: Contribution to journalArticle

303 Scopus citations

Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A

Xu, J., Bauer, D. E., Kerenyi, M. A., Vo, T. D., Hou, S., Hsu, Y. J., Yao, H., Trowbridge, J. J., Mandel, G. & Orkin, S. H., Apr 16 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 16, p. 6518-6523 6 p.

Research output: Contribution to journalArticle

99 Scopus citations

Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire

Guo, G., Luc, S., Marco, E., Lin, T. W., Peng, C., Kerenyi, M. A., Beyaz, S., Kim, W., Xu, J., Das, P. P., Neff, T., Zou, K., Yuan, G. C. & Orkin, S. H., Oct 3 2013, In : Cell Stem Cell. 13, 4, p. 492-505 14 p.

Research output: Contribution to journalArticle

149 Scopus citations
2012

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

Xu, J., Shao, Z., Glass, K., Bauer, D. E., Pinello, L., Van Handel, B., Hou, S., Stamatoyannopoulos, J. A., Mikkola, H. K. A., Yuan, G. C. & Orkin, S. H., Oct 16 2012, In : Developmental cell. 23, 4, p. 796-811 16 p.

Research output: Contribution to journalArticle

107 Scopus citations

Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number

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., Sicinski, P., Lander, E. S. & Lodish, H. F., Sep 15 2012, In : Genes and Development. 26, 18, p. 2075-2087 13 p.

Research output: Contribution to journalArticle

61 Scopus citations

Generation of a genomic reporter assay system for analysis of γ- and β-globin gene regulation

Chan, K. S. K., Xu, J., Wardan, H., McColl, B., Orkin, S. & Vadolas, J., Apr 1 2012, In : FASEB Journal. 26, 4, p. 1736-1744 9 p.

Research output: Contribution to journalArticle

17 Scopus citations
2011

A functional element necessary for fetal hemoglobin silencing

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. & Bender, M. A., Sep 1 2011, In : New England Journal of Medicine. 365, 9, p. 807-814 8 p.

Research output: Contribution to journalArticle

103 Scopus citations

Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing

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. & Orkin, S. H., Nov 18 2011, In : Science. 334, 6058, p. 993-996 4 p.

Research output: Contribution to journalArticle

186 Scopus citations

Role of ZBP-89 in human globin gene regulation and erythroid differentiation

Woo, A. J., Kim, J., Xu, J., Huang, H. & Cantor, A. B., Sep 29 2011, In : Blood. 118, 13, p. 3684-3693 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

The erythroid/myeloid lineage fate paradigm takes a new player

Xu, J. & Orkin, S. H., Mar 16 2011, In : EMBO Journal. 30, 6, p. 983-985 3 p.

Research output: Contribution to journalArticle

1 Scopus citations
2010

Sumoylation regulates interaction of FOG1 with C-terminal-binding protein (CTBP)

Snow, J. W., Kim, J., Currie, C. R., Xu, J. & Orkin, S. H., Sep 3 2010, In : Journal of Biological Chemistry. 285, 36, p. 28064-28075 12 p.

Research output: Contribution to journalArticle

16 Scopus citations

Transcriptional silencing of γ-globin by BCL11A involves long-range interactions and cooperation with SOX6

Xu, J., Sankaran, V. G., Ni, M., Menne, T. F., Puram, R. V., Kim, W. & Orkin, S. H., Apr 15 2010, In : Genes and Development. 24, 8, p. 783-789 7 p.

Research output: Contribution to journalArticle

216 Scopus citations
2009

Developmental and species-divergent globin switching are driven by BCL11A

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. & Orkin, S. H., Aug 27 2009, In : Nature. 460, 7259, p. 1093-1097 5 p.

Research output: Contribution to journalArticle

252 Scopus citations

Evaluation of the long-term reconstituting subset of hematopoietic stem cells with CD150

Papathanasiou, P., Attema, J. L., Karsunky, H., Jian, X., Smale, S. T. & Weissman, I. L., Oct 1 2009, In : STEM CELLS. 27, 10, p. 2498-2508 11 p.

Research output: Contribution to journalArticle

36 Scopus citations

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

Xu, J., Watts, J. A., Pope, S. D., Gadue, P., Kamps, M., Plath, K., Zaret, K. S. & Smale, S. T., Dec 15 2009, In : Genes and Development. 23, 24, p. 2824-2838 15 p.

Research output: Contribution to journalArticle

123 Scopus citations
2008

Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A

Sankaran, V. G., Menne, T. F., Xu, J., Akie, T. E., Lettre, G., Van Handel, B., Mikkola, H. K. A., Hirschhorn, J. N., Cantor, A. B. & Orkin, S. H., Dec 19 2008, In : Science. 322, 5909, p. 1839-1842 4 p.

Research output: Contribution to journalArticle

487 Scopus citations

Pioneer factors, genetic competence, and inductive signaling: Programming liver and pancreas progenitors from the endoderm

Zaret, K. S., Watts, J., Xu, J., Wandzioch, E., Smale, S. T. & Sekiya, T., Dec 1 2008, In : Cold Spring Harbor symposia on quantitative biology. 73, p. 119-126 8 p.

Research output: Contribution to journalArticle

104 Scopus citations
2007

An inducible enhancer required for Il12b promoter activity in an insulated chromatin environment

Zhou, L., Nazarian, A. A., Xu, J., Tantin, D., Corcoran, L. M. & Smale, S. T., Apr 2007, In : Molecular and cellular biology. 27, 7, p. 2698-2712 15 p.

Research output: Contribution to journalArticle

36 Scopus citations

Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis

Attema, J. L., Papathanasiou, P., Forsberg, E. C., Xu, J., Smale, S. T. & Weissman, I. L., Jul 24 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 30, p. 12371-12376 6 p.

Research output: Contribution to journalArticle

116 Scopus citations

Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells

Xu, J., Pope, S. D., Jazirehi, A. R., Attema, J. L., Papathanasiou, P., Watts, J. A., Zaret, K. S., Weissman, I. L. & Smale, S. T., Jul 24 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 30, p. 12377-12382 6 p.

Research output: Contribution to journalArticle

88 Scopus citations