Keji Zhao

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Raja Jothi
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:5221-31. 2008
  2. pmc Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
    Alika K Maunakea
    1 Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA 2 Current address Department of Native Hawaiian Health, John A Burns School of Medicine, University of Hawai i at Manoa, Honolulu, HI 96813, USA
    Cell Res 23:1256-69. 2013
  3. pmc An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data
    Weiqun Peng
    Department of Physics, The George Washington University, 725 21st Street NW, Washington, DC 20052, USA
    Genome Biol 12:120. 2011
  4. pmc An anti-cancer Smurf
    Keji Zhao
    Systems Biology Center, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    Cell Biosci 2:10. 2012
  5. pmc SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome
    Niveen Mulholland
    Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Maryland, USA
    Cell Biosci 2:3. 2012
  6. pmc Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
    Qiang Gan
    Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    Genome Biol 11:R42. 2010
  7. pmc Profiling RE1/REST-mediated histone modifications in the human genome
    Deyou Zheng
    Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Rose F Kennedy Center for the Study of Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Biol 10:R9. 2009
  8. pmc Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
    Gangqing Hu
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 21:1650-8. 2011
  9. pmc Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 31:700-9. 2011
  10. pmc Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types
    Gang Wei
    Laboratory of Molecular Immunology, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Immunity 35:299-311. 2011

Detail Information

Publications68

  1. pmc Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    Raja Jothi
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:5221-31. 2008
    ..Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding...
  2. pmc Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
    Alika K Maunakea
    1 Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA 2 Current address Department of Native Hawaiian Health, John A Burns School of Medicine, University of Hawai i at Manoa, Honolulu, HI 96813, USA
    Cell Res 23:1256-69. 2013
    ....
  3. pmc An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data
    Weiqun Peng
    Department of Physics, The George Washington University, 725 21st Street NW, Washington, DC 20052, USA
    Genome Biol 12:120. 2011
    ..A novel integrative approach has been developed by Lieb and colleagues for analyzing genome-wide datasets of different chromatin-binding factors and epigenetic states that exhibit both sharp and diffuse signals on the genome...
  4. pmc An anti-cancer Smurf
    Keji Zhao
    Systems Biology Center, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    Cell Biosci 2:10. 2012
    ..ABSTRACT: A novel, cancer-fighting function was recently discovered for Smad ubiquitination regulatory factor 2 (Smurf2)...
  5. pmc SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome
    Niveen Mulholland
    Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Maryland, USA
    Cell Biosci 2:3. 2012
    ..abstract:..
  6. pmc Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
    Qiang Gan
    Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    Genome Biol 11:R42. 2010
    ..Previous studies have been performed using cultured mammalian embryonic stem cells. To a lesser extent, chromatin structure has been delineated in other model organisms, such as Drosophila, to open new avenues for genetic analyses...
  7. pmc Profiling RE1/REST-mediated histone modifications in the human genome
    Deyou Zheng
    Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Rose F Kennedy Center for the Study of Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Biol 10:R9. 2009
    ....
  8. pmc Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
    Gangqing Hu
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 21:1650-8. 2011
    ..Intriguingly, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1 and is linked to subsequent transcriptional regulation of target genes...
  9. pmc Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 31:700-9. 2011
    ..Our results suggest that HMGN1 is part of the cellular machinery that modulates transcriptional fidelity by generating, maintaining, or preferentially interacting with specific sites in chromatin...
  10. pmc Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types
    Gang Wei
    Laboratory of Molecular Immunology, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Immunity 35:299-311. 2011
    ....
  11. pmc Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
    Kairong Cui
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Cell Stem Cell 4:80-93. 2009
    ..Thus, our data suggest that gene expression changes during differentiation are programmed by chromatin modifications present at the HSC/HPC stage and provide a resource for enhancer and promoter identification...
  12. pmc Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells
    Jinfang Zhu
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    J Exp Med 206:329-41. 2009
    ..Thus, Gfi-1 plays a critical role both in enhancing Th2 cell expansion and in repressing induction of Th17 and CD103(+) iTreg cells...
  13. pmc Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 19:24-32. 2009
    ..Our data indicate that CTCF may play important roles in the barrier activity of insulators, and this study provides a resource for further investigation of the CTCF function in organizing chromatin in the human genome...
  14. pmc Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
    Zhibin Wang
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 138:1019-31. 2009
    ..Silent genes without any H3K4 methylation signal show no evidence of being bound by HDACs...
  15. pmc Combinatorial patterns of histone acetylations and methylations in the human genome
    Zhibin Wang
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Genet 40:897-903. 2008
    ..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
  16. ncbi request reprint High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
    ..Our data provide new insights into the function of histone methylation and chromatin organization in genome function...
  17. pmc The transcription factor GATA3 actively represses RUNX3 protein-regulated production of interferon-gamma
    Ryoji Yagi
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Immunity 32:507-17. 2010
    ..Thus, the Runx3-mediated pathway, actively suppressed by GATA3, induces IFN-gamma production in a STAT4- and T-bet-independent manner...
  18. doi request reprint Dynamic regulation of nucleosome positioning in the human genome
    Dustin E Schones
    Laboratory of Molecular Immunology, The National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 132:887-98. 2008
    ..Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome...
  19. ncbi request reprint High-resolution, genome-wide mapping of chromatin modifications by GMAT
    Tae Young Roh
    National Institute of Health, Bethesda, MD, USA
    Methods Mol Biol 387:95-108. 2008
    ....
  20. ncbi request reprint Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology
    Gang Wei
    Systems Biology Center, NHLBI, NIH, Bethesda, Maryland, USA
    Methods Enzymol 513:297-313. 2012
    ..We also describe RNA-Seq protocols used to map global gene expression profiles...
  21. pmc Dynamic regulation of epigenomic landscapes during hematopoiesis
    Brian J Abraham
    Systems Biology Center, NHLBI, NIH, Rockville Pike, Bethesda, MD, USA
    BMC Genomics 14:193. 2013
    ..Transcriptional regulation has been mostly studied using in vitro systems while epigenetic changes occurring during in vivo development remain poorly understood...
  22. pmc Chromatin poises miRNA- and protein-coding genes for expression
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 19:1742-51. 2009
    ..Our data suggest that miRNA- and protein-coding genes share similar mechanisms of regulation by chromatin modifications, which poise inducible genes for activation in response to environmental stimuli...
  23. pmc The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses
    Jinfang Zhu
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Immunity 37:660-73. 2012
    ..Our study revealed redundancy and synergy among several Th1 cell-inducing pathways in regulating the expression of T-bet and IFN-γ, and a critical role of T-bet in suppressing an endogenous Th2 cell-associated program...
  24. pmc IL-1 family members and STAT activators induce cytokine production by Th2, Th17, and Th1 cells
    Liying Guo
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 106:13463-8. 2009
    ....
  25. pmc Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns
    Tae Young Roh
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:74-81. 2007
    ..Therefore, by combining epigenetic modification and sequence data, we have established a novel genome-wide method for identifying regulatory elements not discernable by comparative genomics alone...
  26. pmc Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling
    Hong Liu
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 10, Room 7N311, 9000 Rockville Pike, Bethesda, Maryland 20892 1674, USA
    Mol Cell Biol 26:2550-9. 2006
    ..The data presented in this report establish that Z-DNA formation is an important mechanism in modulating chromatin structure, in similarity to the activities of ATP-dependent remodelers and posttranslational histone modifications...
  27. pmc Transcriptional enhancer factor 1 (TEF-1/TEAD1) mediates activation of IFITM3 gene by BRGl
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    FEBS Lett 582:391-7. 2008
    ..The regulation of IFITM3 by TEF-1 demonstrates that TEF-1 dependent regulation is more widespread than its previously established role in the expression of muscle specific genes...
  28. pmc H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
    Chunyuan Jin
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
    Nat Genet 41:941-5. 2009
    ..Other combinations of variants have different distributions, consistent with distinct roles for histone variants in the modulation of gene expression...
  29. pmc Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation
    Gangqing Hu
    1 Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA 2
    Nat Immunol 14:1190-8. 2013
    ..We found that the lincRNA LincR-Ccr2-5'AS, together with GATA-3, was an essential component of a regulatory circuit in gene expression specific to the TH2 subset of helper T cells and was important for the migration of TH2 cells. ..
  30. pmc Epigenetic control of the variable expression of a Plasmodium falciparum receptor protein for erythrocyte invasion
    Lubin Jiang
    Laboratory of Malaria Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
    Proc Natl Acad Sci U S A 107:2224-9. 2010
    ..Our data indicate that the failure of Dd2 to express the sialic acid-independent invasion receptor gene RH4 is associated with the epigenetic silencing mark H3K9 trimethylation present throughout the cycle...
  31. pmc Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Struct Mol Biol 17:629-34. 2010
    ..Our analysis also uncovered an entirely unexpected phenomenon: namely, that Pol II is present at the majority of genomic loci that are bound by Pol III...
  32. pmc H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
    Gangqing Hu
    Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell Stem Cell 12:180-92. 2013
    ..We propose that H2A.Z mediates such contrasting activities by acting as a general facilitator that generates access for a variety of complexes, both activating and repressive...
  33. pmc T-cell acute leukemia 1 (TAL1) regulation of erythropoietin receptor and association with excessive erythrocytosis
    Heather Rogers
    Molecular Medicine Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 1822, USA
    J Biol Chem 287:36720-31. 2012
    ..These data suggest that TAL1 binds to the EPO-R promoter to activate EPO-R expression and provides a potential link to elevated EPO-R expression leading to hypersensitivity to erythropoietin and the resultant excessive erythrocytosis...
  34. pmc Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells
    Yasuto Araki
    Laboratory of Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
    Immunity 30:912-25. 2009
    ..Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8(+) T cell function...
  35. pmc Extended self-renewal and accelerated reprogramming in the absence of Kdm5b
    Benjamin L Kidder
    Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
    Mol Cell Biol 33:4793-810. 2013
    ..These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process. ..
  36. pmc The genomic landscape of histone modifications in human T cells
    Tae Young Roh
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 103:15782-7. 2006
    ..Therefore, these regions have a distinctive chromatin modification pattern and thus may represent a distinct class of chromatin domains...
  37. pmc Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum
    María J López-Barragán
    Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
    BMC Genomics 12:587. 2011
    ..Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown...
  38. pmc Epigenome mapping in normal and disease States
    Alika K Maunakea
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
    Circ Res 107:327-39. 2010
    ....
  39. pmc Characterization of human epigenomes
    Zhibin Wang
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Curr Opin Genet Dev 19:127-34. 2009
    ....
  40. pmc The chromatin-remodeling BAF complex mediates cellular antiviral activities by promoter priming
    Kairong Cui
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Mol Cell Biol 24:4476-86. 2004
    ..We propose that constitutive binding of the BAF complex is an important mechanism for the IFN-inducible promoters to respond rapidly to IFN and virus stimulation...
  41. pmc The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells
    Ryoji Yagi
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Immunity 40:378-88. 2014
    ..Thus, GATA3 plays parallel roles in regulating the development and functions of CD4(+) T cells and IL-7Rα(+) ILCs...
  42. pmc Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation
    Liqi Li
    Section on Cellular and Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Blood 121:4575-85. 2013
    ..Together, these results provide a foundation for defining the mechanism and scope of Ldb1 complex activity during erythropoiesis...
  43. ncbi request reprint HMGA1 mediates the activation of the CRYAB promoter by BRG1
    Beverly Duncan
    Laboratory of Molecular Immunology, NHLBI, NIH, Bethesda, Maryland 20892, USA
    DNA Cell Biol 26:745-52. 2007
    ..Our data indicate that HMGA1 nonhistone chromatin proteins, the SWI/SNF chromatin remodeling complexes, and sequence-specific transcription factors act together to regulate the expression of the CRYAB gene...
  44. pmc Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
    Iouri Chepelev
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:e106. 2009
    ..Our results indicate that this is a cost-effective and efficient strategy to systematically identify SNVs in the expressed regions of the human genome...
  45. pmc Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells
    Gang Wei
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Immunity 30:155-67. 2009
    ..Our data suggest an epigenetic mechanism underlying the specificity and plasticity of effector and regulatory T cells and also provide a framework for understanding complexity of CD4(+) T helper cell differentiation...
  46. pmc Epigenomics of T cell activation, differentiation, and memory
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Curr Opin Immunol 22:341-7. 2010
    ..On the other hand, memory T cells are poised and do not require epigenetic changes for short-term activation...
  47. pmc Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
    Tae Young Roh
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genes Dev 19:542-52. 2005
    ..TCR signaling induces 4045 new acetylation loci that may mediate the global chromatin remodeling and gene activation. We propose that the acetylation islands are epigenetic marks that allow prediction of functional regulatory elements...
  48. pmc Interleukin-21 receptor gene induction in human T cells is mediated by T-cell receptor-induced Sp1 activity
    Zheng Wu
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood InstituteNational Institutes of Health, Building 10, Room 7N252, Bethesda, Maryland 20892 1674, USA
    Mol Cell Biol 25:9741-52. 2005
    ..These data indicate that TCR-induced IL-21R expression is driven by TCR-mediated augmentation of Sp1 protein levels and may partly depend on the dephosphorylation of Sp1...
  49. pmc c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells
    Zuqin Nie
    Laboratory of Pathology, NCI, Bethesda, MD 20892, USA
    Cell 151:68-79. 2012
    ..This rule of Myc action explains the vast majority of Myc biology observed in literature...
  50. pmc The transcription factors T-bet and Runx are required for the ontogeny of pathogenic interferon-γ-producing T helper 17 cells
    Yan Wang
    Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Immunity 40:355-66. 2014
    ..Thus, our studies identify a critical role for T-bet and Runx transcription factors in the generation of pathogenic IFN-γ-producing Th17 cells...
  51. doi request reprint Genome-wide approaches to studying chromatin modifications
    Dustin E Schones
    Laboratory of Molecular Immunology, The National Heart, Lung and Blood Institute, National Institutes of Health, Building 10, Room 7B05, 9, 000 Rockville Pike, Bethesda, Maryland 20892, USA
    Nat Rev Genet 9:179-91. 2008
    ..Here we review genome-wide approaches to studying epigenomic structure and the exciting findings that have been obtained using these technologies...
  52. pmc Native chromatin preparation and illumina/solexa library construction
    Suresh Cuddapah
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    CSH Protoc 2009:pdb.prot5237. 2009
    ....
  53. pmc The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression
    Juhong Liu
    Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892 1500, USA
    EMBO J 25:2119-30. 2006
    ..Engineering FUSE into episomal vectors predictably re-programmed metallothionein-promoter-driven reporter expression. The in vitro recruitment of FBP and FIR to dynamically stressed c-myc DNA paralleled the in vivo process...
  54. doi request reprint Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription
    Zhixiong Xu
    National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
    Nat Struct Mol Biol 18:372-8. 2011
    ..This suggests a function for the INS promoter in coordinating insulin transcription and secretion through long-range regulation of SYT8 expression in human islets...
  55. pmc Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression
    Wei Liao
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Immunol 9:1288-96. 2008
    ..Our results identify a previously unappreciated function for IL-2 in 'priming' T cells for T(H)2 differentiation and in maintaining the expression of Il4ra and other genes in T(H)2-committed cells...
  56. pmc Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq
    Kairong Cui
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 833:413-9. 2012
    ..This chapter outlines the reagents and experimental procedures of MNase-Seq for mapping nucleosome positions in the human genome...
  57. pmc Genomic location analysis by ChIP-Seq
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
    J Cell Biochem 107:11-8. 2009
    ..Now protein binding can be mapped in a truly genome-wide manner with extremely high resolution. This review discusses ChIP-Seq technology, its possible pitfalls, data analysis and several early applications...
  58. pmc Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle
    Haiqing Fu
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
    PLoS Genet 9:e1003542. 2013
    ..These data are consistent with the hypothesis that dimethylated H3K79 associates with some replication origins and marks replicated chromatin during S-phase to prevent re-replication and preserve genomic stability...
  59. pmc Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
    Iouri Chepelev
    Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
    Cell Res 22:490-503. 2012
    ..The Gene Expression Omnibus accession number for the raw and analyzed chromatin interaction data is GSE32677...
  60. pmc Marek's disease virus infection induces widespread differential chromatin marks in inbred chicken lines
    Apratim Mitra
    Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
    BMC Genomics 13:557. 2012
    ..Also, epigenetic factors are believed to be one of the major determinants of disease response...
  61. pmc PTIP promotes chromatin changes critical for immunoglobulin class switch recombination
    Jeremy A Daniel
    Experimental Immunology Branch, National Cancer Institute, National Institutes of Health NIH, Bethesda, MD 20892, USA
    Science 329:917-23. 2010
    ..These results demonstrate that PTIP promotes specific chromatin changes that control the accessibility of the Igh locus to CSR and suggest a nonredundant role for the MLL3-MLL4 complex in altering antibody effector function...
  62. pmc Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells
    Liqi Li
    Section on Cellular and Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
    Nat Immunol 12:129-36. 2011
    ..Our results identify a central role for Ldb1 in regulating the transcriptional program responsible for the maintenance of HSCs...
  63. pmc Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis
    Hong Hao
    Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 8:e1002649. 2012
    ..Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s) for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis...
  64. pmc Effect of PCR extension temperature on high-throughput sequencing
    María José López-Barragán
    Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, USA
    Mol Biochem Parasitol 176:64-7. 2011
    ..falciparum genome. Our method will improve the efficiency and coverage in sequencing an AT-rich genome...
  65. pmc DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts
    Natalia I Dmitrieva
    Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 108:20796-801. 2011
    ..We propose that the universal presence of NaCl around animal cells has directly influenced the evolution of the structure of their genomes...
  66. ncbi request reprint High-resolution genome-wide mapping of histone modifications
    Tae Young Roh
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
    Nat Biotechnol 22:1013-6. 2004
    ..These findings indicate that GMAT should find valuable applications in mapping target sites of chromatin-modifying enzymes...
  67. pmc GATA3 controls Foxp3⁺ regulatory T cell fate during inflammation in mice
    Elizabeth A Wohlfert
    Mucosal Immunology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
    J Clin Invest 121:4503-15. 2011
    ..Overall, our work reveals what we believe to be a new facet in the complex role of GATA3 in T cells and highlights what may be a fundamental role in controlling Treg physiology during inflammation...
  68. pmc Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing
    Baoyan Xu
    Hematology Branch, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 110:10264-9. 2013
    ..Although more work is needed to determine the etiologic role of NIH-CQV in human disease, our data indicate that a parvovirus-like virus is highly prevalent in a cohort of patients with non-A-E hepatitis...