Selected Publications
Botten GA, Zhang Y, Dudnyk K, Liu X, Sanders JT, Imanci A, Droin N, Cao H, Kaphle P, Dickerson KE, Chen M, Chen W, Solary E, Ly P, Zhou J, Xu J. Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription. Blood Mar 22;blood.2022017555, 2023. doi: 10.1182/blood.2022017555. PMID: 36947815
Kim YJ, Jing J, Lee MJ, Lee YT, He L, Botten GA, Lyu J, Zhang Y, Zhou Y, Xu J. Light activated macromolecular phase separation modulates transcription by reconfiguring chromatin interactions. Science Advances Mar 31;9(13):eadg1123, 2023. doi: 10.1126/sciadv.adg1123. PMID: 37000871
Lyu J, Liu Y, Gong L, Chen M, Madanat YF, Zhang Y, Cai F, Gu Z, Cao H, Kaphle P, Kim YJ, Kalkan FN, Stephens H, Dickerson KE, Ni M, Chen W, Patel P, Mims AS, Borate U, Burd A, Cai SF, Yin C, You J, Chung SS, Collins RH, DeBerardinis RJ, Liu X, Xu J. Disabling uncompetitive inhibition of oncogenic IDH mutations drives acquired resistance. Cancer Discov Jan 9;13(1):170-193, 2023. PMID: 36222845
Patrick M, Gu Z, Zhang G, Wynn RM, Kaphle P, Cao H, Vu H, Cai F, Zhang Y, Chen M, Ni M, Chuang DT, DeBerardinis RJ, Xu J. Metabolon formation regulates branched-chain amino acid oxidation and homeostasis. Nature Metabolism 4:1775-1791, 2022. PMID: 36443523
Liu Y, Gu Z, Cao H, Kaphle P, Lyu J, Zhang Y, Hu W, Chung SS, Dickerson KE, Xu J. Convergence of oncogenic cooperation at single-cell and single-gene levels drives leukemic transformation. Nat Commun 12:6323, 2021. PMID: 34732703
Gu Z, Liu Y, Zhang Y, Cao H, Lyu J, Wang X, Wylie A, Newkirk SJ, Jones AE, Lee M, Botten GA, Deng M, Dickerson KE, Zhang CC, An W, Abrams JM, Xu J. Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia. Nat Genet 53:672-682, 2021. PMID: 33833453
Li K, Zhang Y, Liu X, Liu Y, Gu Z, Cao H, Dickerson KE, Chen M, Chen W, Shao Z, Ni M, Xu J. Non-coding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies. Cancer Discov 10:724-745, 2020. PMID: 32188707
Liu X, Chen Y, Zhang Y, Liu Y, Liu N, Botten GA, Cao H, Orkin SH, Zhang MQ, Xu J. Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol 21:59, 2020. PMID: 32138752
Li K, Liu Y, Cao H, Zhang Y, Gu Z, Liu X, Yu A, Kaphle P, Dickerson KE, Ni M, Xu J. Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing. Nat Commun 11:485, 2020. PMID: 31980609
Gu Z, Dickerson KE, Xu J. Therapeutic Response and Outcome Explained by Leukemia Cell of Origin. Cancer Discov 10:1445-1447, 2020. PMID: 33004477
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 KE, Chen W, Ni M, Merritt ME, Morrison SJ, Skoda RC, DeBerardinis RJ, Xu J. Loss of EZH2 reprograms BCAA metabolism to drive leukemic transformation. Cancer Discov 9:1228-1247, 2019. PMID: 31189531
Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trrevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH. Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch. Cell 173:1-13, 2018. PMID: 29606353
Huang J, Li K, Cai W, Liu X, Zhang Y, Orkin SH, Xu J#, Yuan GC#. Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun 9:943, 2018. PMID: 29507293
Vo LT, Kinney MA, Liu X, Zhang Y, Barragan J, Sousa PM, Jha DK, Han A, Cesana M, Shao Z, North TE, Orkin SH, Doulatov S, Xu J, Daley GQ. Regulation of haematopoietic multipotency by EZH1. Nature 553:506-510, 2018. PMID: 29342143
Liu X, Zhang Y, Chen Y, Li M, Zhou F#, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, Shao Z, Xu J#. In situ capture of chromatin interactions by biotinylated dCas9. Cell 170:1028-1043, 2017. PMID: 28841410
Liu X, Zhang Y, Ni M, Cao H, Signer RAJ, Li D, Li M, Gu Z, Hu Z, Dickerson KE, Weinberg SE, Chandel NS, DeBerardinis RJ, Zhou F#, Shao Z#, Xu J#. Regulation of mitochondrial biogenesis in erythropoiesis by mTORC1-mediated protein translation. Nat Cell Biol 19:626-638, 2017. PMID: 28504707
Ansó E, Weinberg SE, Diebold LP, Thompson BJ, Malinge S, Schumacker PT, Liu X, Zhang Y, Shao Z, Steadman M, Marsh KM, Xu J, Crispino JD, Chandel NS. The mitochondrial respiratory chain is essential for hematopoietic stem cell function. Nat Cell Biol 19:614-625, 2017. PMID: 28504706
Kim J, Hu Z, Cai L, Li K, Choi E, Faubert B, Bezwada D, Rodriguez-Canales J, Villalobos P, Lin YF, Ni M, Huffman KE, Girard L, Byers LA, Unsal-Kacmaz K, Peña CG, Heymach JV, Wauters E, Vansteenkiste J, Castrillon DH, Chen B, Wistuba I, Lambrechts D, Xu J, Minna JD, DeBerardinis RJ. CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells. Nature 546:168-172, 2017. PMID: 28538732
Luc S, Huang J, McEldoon JL, Somuncular E, Li D, Rhodes C, Mamoor S, Hou S, Xu J#, Orkin SH#. Bcl11a deficiency leads to hematopoietic stem cell defects with an aging-like phenotype. Cell Rep 16(12):3181-94, 2016. PMID: 27653684
Huang J, Liu X, Li D, Shao Z, Zhang Y, Trompouki E, Bowman TV, Zon LI, Yuan GC, Orkin SH#, and Xu J#. Dynamic control of enhancer repertoires drives lineage and stage-specific transcription during hematopoiesis. Dev Cell 36(1):9-23, 2016. PMID: 26766440
Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell AP, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T. Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science 351(6270):285-289, 2016. PMID: 26816381
Xu J*, Shao Z*, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, and Orkin SH. Developmental control of Polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell 57(2):304-316, 2015. PMID: 25578878
Pinello L*, Xu J*, Orkin SH, and Yuan GC. Analysis of chromatin state plasticity identifies cell-type specific regulators of H3K27me3 patterns. PNAS 111(3):E344-53, 2014. PMID: 2439579
Xie H, Xu J, Hsu JH, Nguyen M, Fujiwara Y, Peng C, and Orkin SH. Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner. Cell Stem Cell 14:68-80, 2014. PMID: 24239285
Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, and Orkin SH. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 342:253-257, 2013. PMID: 24115442
Xu J, Bauer DE, Kerenyi MA, Vo TD, Hou S, Hsu YJ, Yao H, Trowbridge JJ, Mandel G, and Orkin SH. Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A. PNAS 110:6518-23, 2013. PMID: 23576758
Xu J*, Shao Z*, Glass K, Bauer DE, Pinello L, Handel BV, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Developmental Cell 23(4):796-811, 2012. PMID: 23041383
Xu J, Smale ST. Designing an enhancer landscape. Cell 151(5):929-931, 2012.
Xu J, Peng C, Sankaran VG, Shao Z, Esrick EB, Chong BG, Ippolito GC, Fujiwara Y, Ebert BL, Tucker PW, Orkin SH. Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science 334(6058):993-996, 2011. PMID: 21998251
Sankaran VG, Xu J, Byron R, Greisman HA, Fisher C, Weatherall DJ, Sabath DE, Groudine M, Orkin SH, Premawardhena A, Bender MA. A functional element necessary for fetal hemoglobin silencing. New England Journal of Medicine 365:807-814, 2011. PMID: 21879898
Xu J, Sankaran VG, Ni M, Menne TF, Puram RV, Kim W, Orkin SH. Transcriptional silencing of g-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes & Development 24(8):783-798, 2010. PMID: 20395365
Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, and Smale ST. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes & Development 23(24):2824-2838, 2009. PMID: 20008934
Sankaran VG, Menne TF, Xu J, Akie TE, Lettre G, Handel BV, Mikkola HKA, Hirschhorn JN, Cantor AB, Orkin SH. Human fetal hemoglobin expression is regulated by the development stage-specific repressor BCL11A. Science 322: 1839-1842, 2008. PMID: 19056937
Sankaran VG*, Xu J*, Ragoczy T, Ippolito GC, Walkley CR, Maika SD, Fujiwara Y, Ito M, Groudine M, Bender MA, Tucker PW, Orkin SH. Developmental and species-divergent globin switching are driven by BCL11A. Nature 460: 1093-1097, 2009. PMID: 19657335
Xu J, Pope SD, Jazirehi AR, Attema JL, Papathanasiou P, Watts JA, Zaret KS, Weissman IL, and Smale ST. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. PNAS 104:12377-12382, 2007. PMID: 17640912
Last update: May 2023