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Keji Zhao, Ph.D.


Principal Investigator thumbnail image

Keji Zhao
Senior Investigator

P: +1 301 496 2098
F: +1 301 480 0961

Full Publications Listing

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation.
Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K.
Cell Stem Cell. 2013 Feb 7;12(2):180-92.
[Text Abstract on PubMed]

Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.
Leroy G, Chepelev I, Dimaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BA.
Genome Biol. 2012 Aug 16;13(8):R68.
[Text Abstract on PubMed]

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization.
Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K.
Cell Res. 2012 Mar;22(3):490-503.
[Text Abstract on PubMed]

SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome.
Mulholland N, Xu Y, Sugiyama H, Zhao K.
Cell Biosci. 2012;2:3.
[Text Abstract on PubMed]

Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq.
Cui K, Zhao K.
Methods Mol. Biol. 2012;833:413-9.
[Text Abstract on PubMed]

Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis.
Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A.
PLoS Genet. 2012;8(4):e1002649.
[Text Abstract on PubMed]

A novel human polycomb binding site acts as a functional polycomb response element in Drosophila.
Cuddapah S, Roh TY, Cui K, Jose CC, Fuller MT, Zhao K, Chen X.
PLoS ONE. 2012;7(5):e36365.
[Text Abstract on PubMed]

Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.
Wei G, Hu G, Cui K, Zhao K.
Meth. Enzymol. 2012;513:297-313.
[Text Abstract on PubMed]

DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts.
Dmitrieva NI, Cui K, Kitchaev DA, Zhao K, Burg MB.
Proc. Natl. Acad. Sci. U.S.A. 2011 Dec 20;108(51):20796-801.
[Text Abstract on PubMed]

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1.
Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K.
Genome Res. 2011 Oct;21(10):1650-8.
[Text Abstract on PubMed]

ChIP-Seq: technical considerations for obtaining high-quality data.
Kidder BL, Hu G, Zhao K.
Nat. Immunol. 2011 Oct;12(10):918-22.
[Text Abstract on PubMed]

A barrier-only boundary element delimits the formation of facultative heterochromatin in Drosophila melanogaster and vertebrates.
Lin N, Li X, Cui K, Chepelev I, Tie F, Liu B, Li G, Harte P, Zhao K, Huang S, Zhou L.
Mol. Cell. Biol. 2011 Jul;31(13):2729-41.
[Text Abstract on PubMed]

Phosphorylation of H4 Ser 47 promotes HIRA-mediated nucleosome assembly.
Kang B, Pu M, Hu G, Wen W, Dong Z, Zhao K, Stillman B, Zhang Z.
Genes Dev. 2011 Jul 1;25(13):1359-64.
[Text Abstract on PubMed]

Application of ChIP-Seq and related techniques to the study of immune function.
Northrup DL, Zhao K.
Immunity. 2011 Jun 24;34(6):830-42.
[Text Abstract on PubMed]

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells.
Wu H, D'Alessio AC, Ito S, Xia K, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y.
Nature. 2011 May 19;473(7347):389-93.
[Text Abstract on PubMed]

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences.
Tao Y, Xi S, Shan J, Maunakea A, Che A, Briones V, Lee EY, Geiman T, Huang J, Stephens R, Leighty RM, Zhao K, Muegge K.
Proc. Natl. Acad. Sci. U.S.A. 2011 Apr 5;108(14):5626-31.
[Text Abstract on PubMed]

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells.
Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y.
Genes Dev. 2011 Apr 1;25(7):679-84.
[Text Abstract on PubMed]

GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells.
Yu S, Cui K, Jothi R, Zhao DM, Jing X, Zhao K, Xue HH.
Blood. 2011 Feb 17;117(7):2166-78.
[Text Abstract on PubMed]

Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions.
Cuddapah S, Schones DE, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K.
Mol. Cell. Biol. 2011 Feb;31(4):700-9.
[Text Abstract on PubMed]

Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells.
Li L, Jothi R, Cui K, Lee JY, Cohen T, Gorivodsky M, Tzchori I, Zhao Y, Hayes SM, Bresnick EH, Zhao K, Westphal H, Love PE.
Nat. Immunol. 2011 Feb;12(2):129-36.
[Text Abstract on PubMed]

An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data.
Peng W, Zhao K.
Genome Biol. 2011;12(7):120.
[Text Abstract on PubMed]

Genome-wide distribution of macroH2A1 histone variants in mouse liver chromatin.
Changolkar LN, Singh G, Cui K, Berletch JB, Zhao K, Disteche CM, Pehrson JR.
Mol. Cell. Biol. 2010 Dec;30(23):5473-83.
[Text Abstract on PubMed]

PTIP promotes chromatin changes critical for immunoglobulin class switch recombination.
Daniel JA, Santos MA, Wang Z, Zang C, Schwab KR, Jankovic M, Filsuf D, Chen HT, Gazumyan A, Yamane A, Cho YW, Sun HW, Ge K, Peng W, Nussenzweig MC, Casellas R, Dressler GR, Zhao K, Nussenzweig A.
Science. 2010 Aug 20;329(5994):917-23.
[Text Abstract on PubMed]

Epigenome mapping in normal and disease States.
Maunakea AK, Chepelev I, Zhao K.
Circ. Res. 2010 Aug 6;107(3):327-39.
[Text Abstract on PubMed]

Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq.
Gan Q, Chepelev I, Wei G, Tarayrah L, Cui K, Zhao K, Chen X.
Cell Res. 2010 Jul;20(7):763-83.
[Text Abstract on PubMed]

Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes.
Barski A, Chepelev I, Liko D, Cuddapah S, Fleming AB, Birch J, Cui K, White RJ, Zhao K.
Nat. Struct. Mol. Biol. 2010 May;17(5):629-34.
[Text Abstract on PubMed]

Attenuation of Forkhead signaling by the retinal determination factor DACH1.
Zhou J, Wang C, Wang Z, Dampier W, Wu K, Casimiro MC, Chepelev I, Popov VM, Quong A, Tozeren A, Zhao K, Lisanti MP, Pestell RG.
Proc. Natl. Acad. Sci. U.S.A. 2010 Apr 13;107(15):6864-9.
[Text Abstract on PubMed]

Nucleosome dynamics define transcriptional enhancers.
He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS.
Nat. Genet. 2010 Apr;42(4):343-7.
[Text Abstract on PubMed]

Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.
Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X.
Genome Biol. 2010;11(4):R42.
[Text Abstract on PubMed]

Chromatin poises miRNA- and protein-coding genes for expression.
Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K.
Genome Res. 2009 Oct;19(10):1742-51.
[Text Abstract on PubMed]

Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes.
Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K.
Cell. 2009 Sep 4;138(5):1019-31.
[Text Abstract on PubMed]

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W.
Bioinformatics. 2009 Aug 1;25(15):1952-8.
[Text Abstract on PubMed]

H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.
Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G.
Nat. Genet. 2009 Aug;41(8):941-5.
[Text Abstract on PubMed]

Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells.
Araki Y, Wang Z, Zang C, Wood, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP.
Immunity. 2009 Jun 19;30(6):912-25.
[Text Abstract on PubMed]

Genomic location analysis by ChIP-Seq.
Barski A, Zhao K.
J. Cell. Biochem. 2009 May 1;107(1):11-8.
[Text Abstract on PubMed]

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network.
Ho L, Jothi R, Ronan JL, Cui K, Zhao K, Crabtree GR.
Proc. Natl. Acad. Sci. U.S.A. 2009 Mar 31;106(13):5187-91.
[Text Abstract on PubMed]

Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells.
Zhu J, Davidson TS, Wei G, Jankovic D, Cui K, Schones DE, Guo L, Zhao K, Shevach EM, Paul WE.
J. Exp. Med. 2009 Feb 16;206(2):329-41.
[Text Abstract on PubMed]

Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K.
Cell Stem Cell. 2009 Jan 9;4(1):80-93.
[Text Abstract on PubMed]

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.
Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K.
Genome Res. 2009 Jan;19(1):24-32.
[Text Abstract on PubMed]

Chromatin immunoprecipitation (ChIP) for analysis of histone modifications and chromatin-associated proteins.
Milne TA, Zhao K, Hess JL.
Methods Mol. Biol. 2009;538:409-23.
[Text Abstract on PubMed]

Determination of enriched histone modifications in non-genic portions of the human genome.
Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ.
BMC Genomics. 2009;10:143.
[Text Abstract on PubMed]

A novel genetic strategy reveals unexpected roles of the Swi-Snf-like chromatin-remodeling BAF complex in thymocyte development.
Jani A, Wan M, Zhang J, Cui K, Wu J, Preston-Hurlburt P, Khatri R, Zhao K, Chi T.
J. Exp. Med. 2008 Nov 24;205(12):2813-25.
[Text Abstract on PubMed]

Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression.
Liao W, Schones DE, Oh J, Cui Y, Cui K, Roh TY, Zhao K, Leonard WJ.
Nat. Immunol. 2008 Nov;9(11):1288-96.
[Text Abstract on PubMed]

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.
Nucleic Acids Res. 2008 Sep;36(16):5221-31.
[Text Abstract on PubMed]

Combinatorial patterns of histone acetylations and methylations in the human genome.
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K.
Nat. Genet. 2008 Jul;40(7):897-903.
[Text Abstract on PubMed]

Dynamic regulation of nucleosome positioning in the human genome.
Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K.
Cell. 2008 Mar 7;132(5):887-98.
[Text Abstract on PubMed]

Genome-wide approaches to studying chromatin modifications.
Schones DE, Zhao K.
Nat. Rev. Genet. 2008 Mar;9(3):179-91.
[Text Abstract on PubMed]

High-resolution, genome-wide mapping of chromatin modifications by GMAT.
Roh TY, Zhao K.
Methods Mol. Biol. 2008;387:95-108.
[Text Abstract on PubMed]

HMGA1 mediates the activation of the CRYAB promoter by BRG1.
Duncan B, Zhao K.
DNA Cell Biol. 2007 Oct;26(10):745-52.
[Text Abstract on PubMed]

High-resolution profiling of histone methylations in the human genome.
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.
Cell. 2007 May 18;129(4):823-37.
[Text Abstract on PubMed]

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns.
Roh TY, Wei G, Farrell CM, Zhao K.
Genome Res. 2007 Jan;17(1):74-81.
[Text Abstract on PubMed]

The genomic landscape of histone modifications in human T cells.
Roh TY, Cuddapah S, Cui K, Zhao K.
Proc. Natl. Acad. Sci. U.S.A. 2006 Oct 24;103(43):15782-7.
[Text Abstract on PubMed]

The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression.
Liu J, Kouzine F, Nie Z, Chung HJ, Elisha-Feil Z, Weber A, Zhao K, Levens D.
EMBO J. 2006 May 17;25(10):2119-30.
[Text Abstract on PubMed]

Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling.
Liu H, Mulholland N, Fu H, Zhao K.
Mol. Cell. Biol. 2006 Apr;26(7):2550-9.
[Text Abstract on PubMed]

Interleukin-21 receptor gene induction in human T cells is mediated by T-cell receptor-induced Sp1 activity.
Wu Z, Kim HP, Xue HH, Liu H, Zhao K, Leonard WJ.
Mol. Cell. Biol. 2005 Nov;25(22):9741-52.
[Text Abstract on PubMed]

PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes.
Yan Z, Cui K, Murray DM, Ling C, Xue Y, Gerstein A, Parsons R, Zhao K, Wang W.
Genes Dev. 2005 Jul 15;19(14):1662-7.
[Text Abstract on PubMed]

Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.
Roh TY, Cuddapah S, Zhao K.
Genes Dev. 2005 Mar 1;19(5):542-52.
[Text Abstract on PubMed]

High-resolution genome-wide mapping of histone modifications.
Roh TY, Ngau WC, Cui K, Landsman D, Zhao K.
Nat. Biotechnol. 2004 Aug;22(8):1013-6.
[Text Abstract on PubMed]

The chromatin-remodeling BAF complex mediates cellular antiviral activities by promoter priming.
Cui K, Tailor P, Liu H, Chen X, Ozato K, Zhao K.
Mol. Cell. Biol. 2004 May;24(10):4476-86.
[Text Abstract on PubMed]

BRG1 controls the activity of the retinoblastoma protein via regulation of p21CIP1/WAF1/SDI.
Kang H, Cui K, Zhao K.
Mol. Cell. Biol. 2004 Feb;24(3):1188-99.
[Text Abstract on PubMed]

Assay of Z-DNA induction by chromatin remodeling factors.
Liu H, Zhao K.
Meth. Enzymol. 2004;377:412-20.
[Text Abstract on PubMed]

Maximal induction of a subset of interferon target genes requires the chromatin-remodeling activity of the BAF complex.
Liu H, Kang H, Liu R, Chen X, Zhao K.
Mol. Cell. Biol. 2002 Sep;22(18):6471-9.
[Text Abstract on PubMed]

Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes.
Chi TH, Wan M, Zhao K, Taniuchi I, Chen L, Littman DR, Crabtree GR.
Nature. 2002 Jul 11;418(6894):195-9.
[Text Abstract on PubMed]

Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex.
Rando OJ, Zhao K, Janmey P, Crabtree GR.
Proc. Natl. Acad. Sci. U.S.A. 2002 Mar 5;99(5):2824-9.
[Text Abstract on PubMed]

Regulation of CSF1 promoter by the SWI/SNF-like BAF complex.
Liu R, Liu H, Chen X, Kirby M, Brown PO, Zhao K.
Cell. 2001 Aug 10;106(3):309-18.
[Text Abstract on PubMed]

MECP2 truncating mutations cause histone H4 hyperacetylation in Rett syndrome.
Wan M, Zhao K, Lee SS, Francke U.
Hum. Mol. Genet. 2001 May 1;10(10):1085-92.
[Text Abstract on PubMed]

Searching for a function for nuclear actin.
Rando OJ, Zhao K, Crabtree GR.
Trends Cell Biol. 2000 Mar;10(3):92-7.
[Text Abstract on PubMed]

Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling.
Zhao K, Wang W, Rando OJ, Xue Y, Swiderek K, Kuo A, Crabtree GR.
Cell. 1998 Nov 25;95(5):625-36.
[Text Abstract on PubMed]

The scs' boundary element: characterization of boundary element-associated factors.
Hart CM, Zhao K, Laemmli UK.
Mol. Cell. Biol. 1997 Feb;17(2):999-1009.
[Text Abstract on PubMed]

Visualization of chromosomal domains with boundary element-associated factor BEAF-32.
Zhao K, Hart CM, Laemmli UK.
Cell. 1995 Jun 16;81(6):879-89.
[Text Abstract on PubMed]

SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin.
Zhao K, Käs E, Gonzalez E, Laemmli UK.
EMBO J. 1993 Aug;12(8):3237-47.
[Text Abstract on PubMed]