Publications

  1. Cheng L, Zhang X, Wang Y, Gan H, Xu X, Lv X, Hua X, Que J, Ordog T, Zhang Z. Chromatin Assembly Factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit. Nucleic Acids Res. 2019 Dec 2; 47 (21):11114-11131
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  2. Lee JS, Mo Y, Gan H, Burgess RJ, Baker DJ, van Deursen JM, Zhang Z. Pak2 kinase promotes cellular senescence and organismal aging. Proc Natl Acad Sci U S A. 2019 Jul 2; 116 (27):13311-13319 Epub 2019 June 17
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  3. Zhong J, Ye Z, Clark CR, Lenz SW, Nguyen JH, Yan H, Robertson KD, Farrugia G, Zhang Z, Ordog T, Lee JH. Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq. BMC Genomics. 2019 Mar 29; 20 (1):249
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  4. Gan H, Serra-Cardona A, Hua X, Zhou H, Labib K, Yu C, Zhang Z. The Mcm2-Ctf4-Polalpha Axis Facilitates Parental Histone H3-H4 Transfer to Lagging Strands. Mol Cell. 2018 Oct 4; 72 (1):140-151.e3 Epub 2018 Sept 20
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  5. Yu C, Gan H, Serra-Cardona A, Zhang L, Gan S, Sharma S, Johansson E, Chabes A, Xu RM, Zhang Z. A mechanism for preventing asymmetric histone segregation onto replicating DNA strands. Science. 2018 Sep 28; 361 (6409):1386-1389 Epub 2018 Aug 16
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  6. Chen X, Zhang M, Gan H, Wang H, Lee JH, Fang D, Kitange GJ, He L, Hu Z, Parney IF, Meyer FB, Giannini C, Sarkaria JN, Zhang Z. A novel enhancer regulates MGMT expression and promotes temozolomide resistance in glioblastoma. Nat Commun. 2018 Jul 27; 9 (1):2949 Epub 2018 July 27
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  7. Gao Y, Gan H, Lou Z, Zhang Z. Asf1a resolves bivalent chromatin domains for the induction of lineage-specific genes during mouse embryonic stem cell differentiation. Proc Natl Acad Sci U S A. 2018 Jul 3; 115 (27):E6162-E6171 Epub 2018 June 18
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  8. Fang D, Gan H, Cheng L, Lee JH, Zhou H, Sarkaria JN, Daniels DJ, Zhang Z. H3.3K27M mutant proteins reprogram epigenome by sequestering the PRC2 complex to poised enhancers. Elife. 2018 Jun 22; 7 Epub 2018 June 22
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  9. Yu C, Gan H, Zhang Z. Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast. Methods Mol Biol. 2018; 1672:227-238
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  10. Zhong J, Ye Z, Lenz SW, Clark CR, Bharucha A, Farrugia G, Robertson KD, Zhang Z, Ordog T, Lee JH. Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application. BMC Genomics. 2017 Dec 21; 18 (1):985
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  11. Yu C, Gan H, Zhang Z. Both DNA Polymerases delta and epsilon Contact Active and Stalled Replication Forks Differently. Mol Cell Biol. 2017 Nov 1; 37 (21) Epub 2017 Oct 13
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  12. Gan H, Yu C, Devbhandari S, Sharma S, Han J, Chabes A, Remus D, Zhang Z. Checkpoint Kinase Rad53 Couples Leading- and Lagging-Strand DNA Synthesis under Replication Stress. Mol Cell. 2017 Oct 19; 68 (2):446-455.e3 Epub 2017 Oct 12
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  13. Winkler DD, Zhou H, Dar MA, Zhang Z, Luger K. Yeast CAF-1 assembles histone (H3-H4) 2 tetramers prior to DNA deposition. Nucleic Acids Res. 2017 Sep 19; 45 (16):9811-9812
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  14. Zhang H, Gan H, Wang Z, Lee JH, Zhou H, Ordog T, Wold MS, Ljungman M, Zhang Z. RPA Interacts with HIRA and Regulates H3.3 Deposition at Gene Regulatory Elements in Mammalian Cells. Mol Cell. 2017 Jan 19; 65 (2):272-284
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  15. Wu R, Wang Z, Zhang H, Gan H, Zhang Z. H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication. Nucleic Acids Res. 2017 Jan 9; 45 (1):169-180 Epub 2016 Sept 26
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  16. Yokoyama Y, Zhu H, Lee JH, Kossenkov AV, Wu SY, Wickramasinghe JM, Yin X, Palozola KC, Gardini A, Showe LC, Zaret KS, Liu Q, Speicher D, Conejo-Garcia JR, Bradner JE, Zhang Z, Sood AK, Ordog T, Bitler BG, Zhang R. BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer. Cancer Res. 2016 Nov 1; 76 (21):6320-6330
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  17. Li W, Chen P, Yu J, Dong L, Liang D, Feng J, Yan J, Wang PY, Li Q, Zhang Z, Li M, Li G. FACT Remodels the Tetranucleosomal Unit of Chromatin Fibers for Gene Transcription. Mol Cell. 2016 Oct 6; 64 (1):120-133 Epub 2016 Sept 22
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  18. Choi CI, Yoo KH, Hussaini SM, Jeon BT, Welby J, Gan H, Scarisbrick IA, Zhang Z, Baker DJ, van Deursen JM, Rodriguez M, Jang MH. The progeroid gene BubR1 regulates axon myelination and motor function. Aging (Albany NY). 2016 Sep 12; 8 (11):2667-2688
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  19. Feng J, Gan H, Eaton ML, Zhou H, Li S, Belsky JA, MacAlpine DM, Zhang Z, Li Q. Noncoding Transcription Is a Driving Force for Nucleosome Instability in spt16 Mutant Cells. Mol Cell Biol. 2016 Jul 1; 36 (13):1856-67 Epub 2016 June 15
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  20. Zhang K, Gao Y, Li J, Burgess R, Han J, Liang H, Zhang Z, Liu Y. A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks. Nucleic Acids Res. 2016 Jun 20; 44 (11):5083-94 Epub 2016 Feb 22
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  21. Fang D, Gan H, Lee JH, Han J, Wang Z, Riester SM, Jin L, Chen J, Zhou H, Wang J, Zhang H, Yang N, Bradley EW, Ho TH, Rubin BP, Bridge JA, Thibodeau SN, Ordog T, Chen Y, van Wijnen AJ, Oliveira AM, Xu RM, Westendorf JJ, Zhang Z. The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas. Science. 2016 Jun 10; 352 (6291):1344-8 Epub 2016 May 26
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  22. Lee JS, Zhang Z. O-linked N-acetylglucosamine transferase (OGT) interacts with the histone chaperone HIRA complex and regulates nucleosome assembly and cellular senescence. Proc Natl Acad Sci U S A. 2016 Jun 7; 113 (23):E3213-20 Epub 2016 May 23
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  23. Wang Z, Zhang H, Liu J, Cheruiyot A, Lee JH, Ordog T, Lou Z, You Z, Zhang Z. USP51 deubiquitylates H2AK13,15ub and regulates DNA damage response. Genes Dev. 2016 Apr 15; 30 (8):946-59
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  24. Kitange GJ, Mladek AC, Schroeder MA, Pokorny JC, Carlson BL, Zhang Y, Nair AA, Lee JH, Yan H, Decker PA, Zhang Z, Sarkaria JN. Retinoblastoma Binding Protein 4 Modulates Temozolomide Sensitivity in Glioblastoma by Regulating DNA Repair Proteins. Cell Rep. 2016 Mar 22; 14 (11):2587-98 Epub 2016 Mar 10
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  25. Zhang R, Han J, Daniels D, Huang H, Zhang Z. Detecting the H3F3A mutant allele found in high-grade pediatric glioma by real-time PCR. J Neurooncol. 2016 Jan; 126 (1):27-36 Epub 2015 Sept 16
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  26. Dahlin JL, Nissink JWM, Francis S, Strasser JM, John K, Zhang Z, Walters MA. Post-HTS case report and structural alert: Promiscuous 4-aroyl-1,5-disubstituted-3-hydroxy-2H-pyrrol-2-one actives verified by ALARM NMR. Bioorg Med Chem Lett. 2015 Nov 1; 25 (21):4740-4752 Epub 2015 Aug 10
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  27. Dahlin JL, Nissink JW, Strasser JM, Francis S, Higgins L, Zhou H, Zhang Z, Walters MA. PAINS in the assay: chemical mechanisms of assay interference and promiscuous enzymatic inhibition observed during a sulfhydryl-scavenging HTS. J Med Chem. 2015 Mar 12; 58 (5):2091-113 Epub 2015 Feb 21
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  28. Dahlin JL, Chen X, Walters MA, Zhang Z. Histone-modifying enzymes, histone modifications and histone chaperones in nucleosome assembly: Lessons learned from Rtt109 histone acetyltransferases. Crit Rev Biochem Mol Biol. 2015 Jan-Feb; 50 (1):31-53 Epub 2014 Nov 03
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  29. Hashizume R, Andor N, Ihara Y, Lerner R, Gan H, Chen X, Fang D, Huang X, Tom MW, Ngo V, Solomon D, Mueller S, Paris PL, Zhang Z, Petritsch C, Gupta N, Waldman TA, James CD. Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat Med. 2014 Dec; 20 (12):1394-6 Epub 2014 Nov 17
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  30. Yu C, Gan H, Han J, Zhou ZX, Jia S, Chabes A, Farrugia G, Ordog T, Zhang Z. Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall. Mol Cell. 2014 Nov 20; 56 (4):551-63 Epub 2014 Oct 23
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  31. Tiedemann RL, Putiri EL, Lee JH, Hlady RA, Kashiwagi K, Ordog T, Zhang Z, Liu C, Choi JH, Robertson KD. Acute depletion redefines the division of labor among DNA methyltransferases in methylating the human genome. Cell Rep. 2014 Nov 20; 9 (4):1554-66 Epub 2014 Nov 06
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  32. Dahlin JL, Kottom T, Han J, Zhou H, Walters MA, Zhang Z, Limper AH. Pneumocystis jirovecii Rtt109, a novel drug target for Pneumocystis pneumonia in immunosuppressed humans. Antimicrob Agents Chemother. 2014 Jul; 58 (7):3650-9 Epub 2014 Apr 14
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  33. Burgess RJ, Han J, Zhang Z. The Ddc1-Mec3-Rad17 sliding clamp regulates histone-histone chaperone interactions and DNA replication-coupled nucleosome assembly in budding yeast. J Biol Chem. 2014 Apr 11; 289 (15):10518-10529 Epub 2014 Feb 25
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  34. Han J, Zhang H, Zhang H, Wang Z, Zhou H, Zhang Z. A Cul4 E3 ubiquitin ligase regulates histone hand-off during nucleosome assembly. Cell. 2013 Nov 7; 155 (4):817-29
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  35. Zhang H, Wang Z, Zhang Z. PP1alpha, PP1beta and Wip-1 regulate H4S47 phosphorylation and deposition of histone H3 variant H3.3. Nucleic Acids Res. 2013 Sep; 41 (17):8085-93 Epub 2013 July 04
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  36. Chan KM, Han J, Fang D, Gan H, Zhang Z. A lesson learned from the H3.3K27M mutation found in pediatric glioma: a new approach to the study of the function of histone modifications in vivo? Cell Cycle. 2013 Aug 15; 12 (16):2546-52 Epub 2013 July 10
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  37. Chan KM, Fang D, Gan H, Hashizume R, Yu C, Schroeder M, Gupta N, Mueller S, James CD, Jenkins R, Sarkaria J, Zhang Z. The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. Genes Dev. 2013 May 1; 27(9):985-90. Epub 2013 Apr 19.
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  38. Li Q, Burgess R, Zhang Z. All roads lead to chromatin: multiple pathways for histone deposition. Biochim Biophys Acta. 2013 Mar-Apr; 1819 (3-4):238-46
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  39. Dahlin JL, Sinville R, Solberg J, Zhou H, Han J, Francis S, Strasser JM, John K, Hook DJ, Walters MA, Zhang Z. A cell-free fluorometric high-throughput screen for inhibitors of Rtt109-catalyzed histone acetylation. PLoS One. 2013; 8 (11):e78877 Epub 2013 Nov 18
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  40. Burgess RJ, Zhang Z. Histone chaperones in nucleosome assembly and human disease. Nat Struct Mol Biol. 2013 Jan; 20 (1):14-22
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  41. Liu CP, Xiong C, Wang M, Yu Z, Yang N, Chen P, Zhang Z, Li G, Xu RM. Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX. Nat Struct Mol Biol. 2012 Dec; 19(12):1287-92. Epub 2012 Nov 11.
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  42. Winkler DD, Zhou H, Dar MA, Zhang Z, Luger K. Yeast CAF-1 assembles histone (H3-H4)2 tetramers prior to DNA deposition. Nucleic Acids Res. 2012 Nov 1; 40 (20):10139-49 Epub 2012 Aug 31
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  43. Chan KM, Zhang Z. Leucine-rich repeat and WD repeat-containing protein 1 is recruited to pericentric heterochromatin by trimethylated lysine 9 of histone H3 and maintains heterochromatin silencing. J Biol Chem. 2012 Apr 27; 287 (18):15024-33 Epub 2012 Mar 15
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  44. Weintraub WS, Grau-Sepulveda MV, Weiss JM, O'Brien SM, Peterson ED, Kolm P, Zhang Z, Klein LW, Shaw RE, McKay C, Ritzenthaler LL, Popma JJ, Messenger JC, Shahian DM, Grover FL, Mayer JE, Shewan CM, Garratt KN, Moussa ID, Dangas GD, Edwards FH. Comparative effectiveness of revascularization strategies. N Engl J Med. 2012 Apr 19; 366(16):1467-76. Epub 2012 Mar 27.
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  45. Fazly A, Li Q, Hu Q, Mer G, Horazdovsky B, Zhang Z. Histone chaperone Rtt106 promotes nucleosome formation using (H3-H4)2 tetramers. J Biol Chem. 2012 Mar 30; 287 (14):10753-60 Epub 2012 Feb 15
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  46. Li Q, Burgess R, Zhang Z. All roads lead to chromatin: Multiple pathways for histone deposition. Biochim Biophys Acta. 2012 Mar; 1819(3-4):238-46. Epub 2011 Jul 07.
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  47. Zhang H, Han J, Kang B, Burgess R, Zhang Z. Human histone acetyltransferase 1 protein preferentially acetylates H4 histone molecules in H3.1-H4 over H3.3-H4. J Biol Chem. 2012 Feb 24; 287 (9):6573-81 Epub 2012 Jan 07
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  48. Su D, Hu Q, Li Q, Thompson JR, Cui G, Fazly A, Davies BA, Botuyan MV, Zhang Z, Mer G. Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106. Nature. 2012 Feb 5; 483 (7387):104-7 Epub 2012 Feb 05
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  49. Li Q, Zhang Z. Linking DNA replication to heterochromatin silencing and epigenetic inheritance. Acta Biochim Biophys Sin (Shanghai). 2012 Jan; 44 (1):3-13
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  50. Burgess RJ, Zhou H, Han J, Li Q, Zhang Z. The SCFDia2 ubiquitin E3 ligase ubiquitylates Sir4 and functions in transcriptional silencing. PLoS Genet. 2012; 8 (7):e1002846 Epub 2012 July 26
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  51. Chan KM, Zhang H, Malureanu L, van Deursen J, Zhang Z. Diverse factors are involved in maintaining X chromosome inactivation. Proc Natl Acad Sci U S A. 2011 Oct 4; 108 (40):16699-704 Epub 2011 Sept 21
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  52. Lau AT, Lee SY, Xu YM, Zheng D, Cho YY, Zhu F, Kim HG, Li SQ, Zhang Z, Bode AM, Dong Z. Phosphorylation of histone H2B serine 32 is linked to cell transformation. J Biol Chem. 2011 Jul 29; 286(30):26628-37. Epub 2011 Jun 06.
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  53. Kang B, Pu M, Hu G, Wen W, Dong Z, Zhao K, Stillman B, Zhang Z. Phosphorylation of H4 Ser 47 promotes HIRA-mediated nucleosome assembly. Genes Dev. 2011 Jul 1; 25 (13):1359-64
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  54. Kottom TJ, Han J, Zhang Z, Limper AH. Pneumocystis carinii expresses an active Rtt109 histone acetyltransferase. Am J Respir Cell Mol Biol. 2011 Jun; 44 (6):768-76 Epub 2010 July 23
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  55. Su D, Hu Q, Zhou H, Thompson JR, Xu RM, Zhang Z, Mer G. Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex. J Biol Chem. 2011 May 6; 286 (18):15625-9 Epub 2011 Mar 22
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  56. Li Q, Zhang Z. Linking DNA replication to heterochromatin silencing and inheritance. ABBS. 2011.
  57. Burgess RJ, Zhang Z. Roles for Gcn5 in promoting nucleosome assembly and maintaining genome integrity. Cell Cycle. 2010 Aug 1; 9 (15):2979-85 Epub 2010 Aug 23
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  58. Han J, Li Q, McCullough L, Kettelkamp C, Formosa T, Zhang Z. Ubiquitylation of FACT by the cullin-E3 ligase Rtt101 connects FACT to DNA replication. Genes Dev. 2010 Jul 15; 24 (14):1485-90
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  59. Burgess RJ, Zhang Z. Histones, histone chaperones and nucleosome assembly. Protein Cell. 2010 Jul; 1 (7):607-12
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  60. Burgess RJ, Zhou H, Han J, Zhang Z. A role for Gcn5 in replication-coupled nucleosome assembly. Mol Cell. 2010 Feb 26; 37 (4):469-80
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  61. Falbo KB, Alabert C, Katou Y, Wu S, Han J, Wehr T, Xiao J, He X, Zhang Z, Shi Y, Shirahige K, Pasero P, Shen X. Involvement of a chromatin remodeling complex in damage tolerance during DNA replication. Nat Struct Mol Biol. 2009 Nov; 16(11):1167-72. Epub 2009 Oct 25.
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  62. Li Q, Fazly AM, Zhou H, Huang S, Zhang Z, Stillman B. The elongator complex interacts with PCNA and modulates transcriptional silencing and sensitivity to DNA damage agents. PLoS Genet. 2009 Oct; 5 (10):e1000684 Epub 2009 Oct 16
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  63. Yuan J, Pu M, Zhang Z, Lou Z. Histone H3-K56 acetylation is important for genomic stability in mammals. Cell Cycle. 2009 Jun 1; 8 (11):1747-53 Epub 2009 June 03
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  64. Burgess R, Jenkins R, Zhang Z. Epigenetic changes in gliomas. Cancer Biol Ther. 2008 Sep; 7 (9):1326-34 Epub 2008 Sept 18
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  65. Li Q, Zhou H, Wurtele H, Davies B, Horazdovsky B, Verreault A, Zhang Z. Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly. Cell. 2008 Jul 25; 134 (2):244-55
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  66. Han J, Zhou H, Li Z, Xu RM, Zhang Z. Acetylation of lysine 56 of histone H3 catalyzed by RTT109 and regulated by ASF1 is required for replisome integrity. J Biol Chem. 2007 Sep 28; 282 (39):28587-28596 Epub 2007 Aug 09
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  67. Han J, Zhou H, Li Z, Xu RM, Zhang Z. The Rtt109-Vps75 histone acetyltransferase complex acetylates non-nucleosomal histone H3. J Biol Chem. 2007 May 11; 282 (19):14158-64 Epub 2007 Mar 16
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  68. Huang S, Zhou H, Tarara J, Zhang Z. A novel role for histone chaperones CAF-1 and Rtt106p in heterochromatin silencing. EMBO J. 2007 May 2; 26 (9):2274-83 Epub 2007 Apr 05
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  69. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007 Apr 12; 446(7137):806-10. Epub 2007 Feb 21.
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  70. Han J, Zhou H, Horazdovsky B, Zhang K, Xu RM, Zhang Z. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science. 2007 Feb 2; 315(5812):653-5.
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  71. Zhou H, Madden BJ, Muddiman DC, Zhang Z. Chromatin assembly factor 1 interacts with histone H3 methylated at lysine 79 in the processes of epigenetic silencing and DNA repair. Biochemistry. 2006 Mar 7; 45 (9):2852-61
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  72. Huang S, Zhou H, Katzmann D, Hochstrasser M, Atanasova E, Zhang Z. Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing. Proc Natl Acad Sci U S A. 2005 Sep 20; 102 (38):13410-5 Epub 2005 Sept 12
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  73. Zhang Z, Hayashi MK, Merkel O, Stillman B, Xu RM. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J. 2002 Sep 2; 21(17):4600-11.
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  74. Zhang Z, Shibahara K, Stillman B. PCNA connects DNA replication to epigenetic inheritance in yeast. Nature. 2000 Nov 9; 408(6809):221-5.
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  75. Zhang Z, Krutchinsky A, Endicott S, Realini C, Rechsteiner M, Standing KG. Proteasome activator 11S REG or PA28: recombinant REG alpha/REG beta hetero-oligomers are heptamers. Biochemistry. 1999 Apr 27; 38(17):5651-8.
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  76. Zhang Z, Clawson A, Rechsteiner M. The proteasome activator 11 S regulator or PA28. Contribution By both alpha and beta subunits to proteasome activation. J Biol Chem. 1998 Nov 13; 273(46):30660-8.
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  77. Zhang Z, Realini C, Clawson A, Endicott S, Rechsteiner M. Proteasome activation by REG molecules lacking homolog-specific inserts. J Biol Chem. 1998 Apr 17; 273(16):9501-9.
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  78. Zhang Z, Clawson A, Realini C, Jensen CC, Knowlton JR, Hill CP, Rechsteiner M. Identification of an activation region in the proteasome activator REGalpha. Proc Natl Acad Sci U S A. 1998 Mar 17; 95(6):2807-11.
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  79. Knowlton JR, Johnston SC, Whitby FG, Realini C, Zhang Z, Rechsteiner M, Hill CP. Structure of the proteasome activator REGalpha (PA28alpha). Nature. 1997 Dec 11; 390(6660):639-43.
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  80. Realini C, Jensen CC, Zhang Z, Johnston SC, Knowlton JR, Hill CP, Rechsteiner M. Characterization of recombinant REGalpha, REGbeta, and REGgamma proteasome activators. J Biol Chem. 1997 Oct 10; 272(41):25483-92.
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