chromatin immunoprecipitation

Summary

Summary: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.

Top Publications

  1. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
  2. pmc ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    Stephen G Landt
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1813-31. 2012
  3. pmc ChIP-seq: advantages and challenges of a maturing technology
    Peter J Park
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Nat Rev Genet 10:669-80. 2009
  4. pmc GREAT improves functional interpretation of cis-regulatory regions
    Cory Y McLean
    Department of Computer Science, Stanford University, Stanford, California, USA
    Nat Biotechnol 28:495-501. 2010
  5. pmc A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    Chongzhi Zang
    Department of Physics, The George Washington University, Washington, DC 20052, USA
    Bioinformatics 25:1952-8. 2009
  6. pmc Computation for ChIP-seq and RNA-seq studies
    Shirley Pepke
    Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA
    Nat Methods 6:S22-32. 2009
  7. pmc An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
  8. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
  9. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
  10. pmc Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    Erez Lieberman-Aiden
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, MA 02139, USA
    Science 326:289-93. 2009

Research Grants

  1. Yun Fai Chris Lau; Fiscal Year: 2014
  2. Carole R Mendelson; Fiscal Year: 2016
  3. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
  4. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
  5. BIOSYNTHESIS OF TRACHEAL MUCOUS GLYCOPROTEINS
    Pi Wan Cheng; Fiscal Year: 2010
  6. Schahram Akbarian; Fiscal Year: 2014
  7. Hepatic Steatosis Modulation by Apo B Gene Transcription
    JANET DEHOFF SPARKS; Fiscal Year: 2010
  8. Balakuntalam S Kasinath; Fiscal Year: 2016
  9. DAVID MATTHEW KELLER; Fiscal Year: 2016
  10. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2013

Detail Information

Publications367 found, 100 shown here

  1. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
    ..MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available...
  2. pmc ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    Stephen G Landt
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1813-31. 2012
    b>Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in ..
  3. pmc ChIP-seq: advantages and challenges of a maturing technology
    Peter J Park
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Nat Rev Genet 10:669-80. 2009
    b>Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes...
  4. pmc GREAT improves functional interpretation of cis-regulatory regions
    Cory Y McLean
    Department of Computer Science, Stanford University, Stanford, California, USA
    Nat Biotechnol 28:495-501. 2010
    ..Applying GREAT to data sets from chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) of multiple transcription-associated factors, ..
  5. pmc A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    Chongzhi Zang
    Department of Physics, The George Washington University, Washington, DC 20052, USA
    Bioinformatics 25:1952-8. 2009
    Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse ..
  6. pmc Computation for ChIP-seq and RNA-seq studies
    Shirley Pepke
    Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA
    Nat Methods 6:S22-32. 2009
    ....
  7. pmc An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
    ..We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes...
  8. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
    We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data...
  9. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    b>Chromatin immunoprecipitation (ChIP) followed by tag sequencing (ChIP-seq) using high-throughput next-generation instrumentation is fast, replacing chromatin immunoprecipitation followed by genome tiling array analysis (ChIP-chip) as the ..
  10. pmc Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    Erez Lieberman-Aiden
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, MA 02139, USA
    Science 326:289-93. 2009
    ..The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes...
  11. pmc A unique chromatin signature uncovers early developmental enhancers in humans
    Alvaro Rada-Iglesias
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nature 470:279-83. 2011
    ..Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis...
  12. pmc Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    Jie Wang
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 22:1798-812. 2012
    b>Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide...
  13. doi Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
    ..To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of 13 sequence-..
  14. pmc High-resolution DNA-binding specificity analysis of yeast transcription factors
    Cong Zhu
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:556-66. 2009
    ..However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many ..
  15. pmc c-Myc regulates transcriptional pause release
    Peter B Rahl
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 141:432-45. 2010
    ..We discuss the implications of these results for the role of c-Myc amplification in human cancer...
  16. pmc ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
    Willem Jan Welboren
    Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
    EMBO J 28:1418-28. 2009
    ..Furthermore, our data identify genes preferentially regulated by tamoxifen but not by E2 or fulvestrant. Thus (partial) antagonist loaded ERalpha acts mechanistically different on E2-activated and E2-repressed genes...
  17. pmc An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression
    Jindan Yu
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Cancer Cell 17:443-54. 2010
    ..Using chromatin immunoprecipitation coupled with massively parallel sequencing, we found that ERG disrupts androgen receptor (AR) ..
  18. pmc DREME: motif discovery in transcription factor ChIP-seq data
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 27:1653-9. 2011
    ..Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF...
  19. pmc Evaluation of algorithm performance in ChIP-seq peak detection
    Elizabeth G Wilbanks
    Graduate Group in Microbiology, University of California Davis, Davis, California, United States of America
    PLoS ONE 5:e11471. 2010
    Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions...
  20. pmc Systematic evaluation of factors influencing ChIP-seq fidelity
    Yiwen Chen
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Methods 9:609-14. 2012
    We evaluated how variations in sequencing depth and other parameters influence interpretation of chromatin immunoprecipitation-sequencing (ChIP-seq) experiments...
  21. pmc Long noncoding RNA as modular scaffold of histone modification complexes
    Miao Chih Tsai
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 329:689-93. 2010
    ..Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes...
  22. pmc Chromatin structure analyses identify miRNA promoters
    Fatih Ozsolak
    Department of Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Genes Dev 22:3172-83. 2008
    ..The high-throughput identification of miRNA promoter and enhancer regulatory elements sheds light on evolution of miRNA transcription and permits rapid identification of transcriptional networks of miRNAs...
  23. ncbi c-Myc-regulated microRNAs modulate E2F1 expression
    Kathryn A O'Donnell
    Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 435:839-43. 2005
    ....
  24. pmc Discovering motifs in ranked lists of DNA sequences
    Eran Eden
    Computer Science Department, Technion, Haifa, Israel
    PLoS Comput Biol 3:e39. 2007
    ..DRIM is publicly available at http://bioinfo.cs.technion.ac.il/drim...
  25. pmc ChIP-seq accurately predicts tissue-specific activity of enhancers
    Axel Visel
    Genomics Division, MS 84 171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    Nature 457:854-8. 2009
    ..Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several ..
  26. pmc RNA polymerase is poised for activation across the genome
    Ginger W Muse
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Nat Genet 39:1507-11. 2007
    ..This finding indicates a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues...
  27. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
    ..protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing...
  28. pmc JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
    Elodie Portales-Casamar
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
    Nucleic Acids Res 38:D105-10. 2010
    ..Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches...
  29. pmc A cis-regulatory map of the Drosophila genome
    Nicolas Negre
    Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, Illinois 60637, USA
    Nature 471:527-31. 2011
    ..We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific ..
  30. pmc Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation
    Lai Wei
    Molecular Immunology and Inflammation Branch, NIAMS, National Institutes of Health, Bethesda MD 20892, USA
    Immunity 32:840-51. 2010
    ..Using chromatin immunoprecipitation and massive parallel sequencing, we quantitated the full complement of STAT-bound genes, concurrently ..
  31. pmc Chromatin immunoprecipitation and microarray-based analysis of protein location
    Tong Ihn Lee
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Protoc 1:729-48. 2006
    Genome-wide location analysis, also known as ChIP-Chip, combines chromatin immunoprecipitation and DNA microarray analysis to identify protein-DNA interactions that occur in living cells...
  32. pmc Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    Ho Sung Rhee
    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Cell 147:1408-19. 2011
    b>Chromatin immunoprecipitation (ChIP-chip and ChIP-seq) assays identify where proteins bind throughout a genome...
  33. doi Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation
    Yutaka Kondo
    Department of Leukemia, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
    Nat Genet 40:741-50. 2008
    ..Using chromatin immunoprecipitation microarrays (ChIP-chip) in prostate cancer cells compared to normal prostate, we found that up to 5% ..
  34. pmc ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
    Zhengqing Ouyang
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 106:21521-6. 2009
    ..In the absence of binding by the first group, the binding of the second group is associated with genes that are repressed in ESCs and derepressed upon early differentiation...
  35. pmc Cistrome: an integrative platform for transcriptional regulation studies
    Tao Liu
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
    Genome Biol 12:R83. 2011
    ..Cistrome is available at http://cistrome.org/ap/...
  36. ncbi Protocol for the fast chromatin immunoprecipitation (ChIP) method
    Joel D Nelson
    Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98109, USA
    Nat Protoc 1:179-85. 2006
    ..This method is particularly useful in kinetic studies where multiple samples are processed at the same time. Starting with sheared chromatin, PCR-ready DNA can be isolated from 16-24 ChIP samples in 4-6 h using the fast method...
  37. pmc Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
    Stewart MacArthur
    Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
    Genome Biol 10:R80. 2009
    ....
  38. pmc HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, 48109 2029, USA
    BMC Bioinformatics 11:369. 2010
    ..A powerful technique has recently emerged that couples chromatin immunoprecipitation (ChIP) with next-generation sequencing, (ChIP-Seq)...
  39. pmc Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:447-55. 2011
    ..We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions...
  40. pmc Forkhead box M1 regulates the transcriptional network of genes essential for mitotic progression and genes encoding the SCF (Skp2-Cks1) ubiquitin ligase
    I Ching Wang
    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, College of Medicine, 60607 7170, USA
    Mol Cell Biol 25:10875-94. 2005
    ..Using quantitative chromatin immunoprecipitation and expression assays, we show that FoxM1 is essential for transcription of the mitotic regulatory ..
  41. pmc seqMINER: an integrated ChIP-seq data interpretation platform
    Tao Ye
    Department of Functional Genomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS UMR 7104, INSERM U 596, Universite de Strasbourg, BP 10142 67404 Illkirch Cedex, CU de Strasbourg, France
    Nucleic Acids Res 39:e35. 2011
    In a single experiment, chromatin immunoprecipitation combined with high throughput sequencing (ChIP-seq) provides genome-wide information about a given covalent histone modification or transcription factor occupancy...
  42. pmc ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions
    Terrence S Furey
    Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, CB 7264, Chapel Hill, North Carolina 27599, USA
    Nat Rev Genet 13:840-52. 2012
    b>Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins...
  43. ncbi Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    Gordon Robertson
    British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada
    Nat Methods 4:651-7. 2007
    We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo...
  44. pmc Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
    Kimberly R Blahnik
    Department of Computer Science, University of California Davis, Davis, CA 95616, USA
    Nucleic Acids Res 38:e13. 2010
    ..However, the bioinformatics analysis of large datasets collected using chromatin immunoprecipitation and high-throughput sequencing is often a roadblock that impedes researchers in their attempts to gain ..
  45. pmc Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis
    Deepti Malhotra
    Department of Environmental Health Sciences Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
    Nucleic Acids Res 38:5718-34. 2010
    ..Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response...
  46. pmc MicroRNA cluster 221-222 and estrogen receptor alpha interactions in breast cancer
    Gianpiero Di Leva
    Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, 460 West, 12th Ave, Columbus, OH 43210, USA
    J Natl Cancer Inst 102:706-21. 2010
    ..Because microRNAs (miRNAs) modulate gene expression, we hypothesized that they may have a role in ER-negative tumor formation...
  47. pmc A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth
    Qianben Wang
    Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 27:380-92. 2007
    ..We have mapped the AR binding regions on two chromosomes in human prostate cancer cells by combining chromatin immunoprecipitation (ChIP) with tiled oligonucleotide microarrays...
  48. ncbi Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7
    Rob D Chapman
    Institute of Clinical Molecular Biology and Tumour Genetics, GSF Research Center of Environment and Health, Munich Center for Integrated Protein Science CIPSM, Marchioninistrasse 25, 81377 Munich, Germany
    Science 318:1780-2. 2007
    ..Our results indicate that restriction of serine-7 epitopes to the Linker-proximal region limits CTD phosphorylation patterns and is a requirement for optimal gene expression...
  49. pmc Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos
    Bernd Schuettengruber
    Institut de Genetique Humaine, CNRS, Montpellier, France
    PLoS Biol 7:e13. 2009
    ..Here, we used chromatin immunoprecipitation (ChIP) on chip assays to map the chromosomal distribution of Drosophila PcG proteins, the N- and C-..
  50. doi Cyclical DNA methylation of a transcriptionally active promoter
    Raphaël Métivier
    Universite de Rennes I, CNRS, UMR 6026 Equipe SPARTE, IFR 140 GFAS, Campus de Beaulieu, 35042 Rennes Cedex, France
    Nature 452:45-50. 2008
    ..Cyclical changes in the methylation status of promoter CpGs may thus represent a critical event in transcriptional achievement...
  51. pmc Next-generation genomics: an integrative approach
    R David Hawkins
    Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nat Rev Genet 11:476-86. 2010
    ..With the advent of high-throughput methods--including genome-wide association (GWA) studies, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and RNA sequencing (RNA-seq)--acquisition of genome-scale data has ..
  52. pmc Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
    Manching Ku
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
    PLoS Genet 4:e1000242. 2008
    ..of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing...
  53. pmc An extended transcriptional network for pluripotency of embryonic stem cells
    Jonghwan Kim
    Department of Pediatric Oncology, Boston, MA 02115, USA
    Cell 132:1049-61. 2008
    ..Furthermore, we propose a transcriptional hierarchy for reprogramming factors and broadly distinguish targets of c-Myc versus other factors. Our data provide a resource for exploration of the complex network maintaining pluripotency...
  54. doi Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites
    Jose Juan Lopez-Rubio
    Unité de Biologie des Interactions Hôte Parasite, CNRS URA2581, Institut Pasteur, Paris, France
    Cell Host Microbe 5:179-90. 2009
    ..Our data point to the existence of perinuclear repressive centers associated with control of expression of malaria parasite genes involved in phenotypic variation and pathogenesis...
  55. pmc Distinguishing direct versus indirect transcription factor-DNA interactions
    Raluca Gordân
    Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
    Genome Res 19:2090-100. 2009
    ..Our method is not restricted to yeast or to ChIP-chip data, but can be applied in any system for which both in vivo binding data and in vitro DNA binding motifs are available...
  56. pmc Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy
    Tohru Fujiwara
    University of Wisconsin School of Medicine and Public Health, Wisconsin Institutes for Medical Research, Madison, 53705, USA
    Mol Cell 36:667-81. 2009
    ..These results establish fundamental principles underlying GATA factor mechanisms in chromatin and illustrate a complex network of considerable importance for the control of hematopoiesis...
  57. pmc Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis
    Esmeralda Casas
    Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, California 92093 0636, USA
    Cancer Res 71:245-54. 2011
    ..Together, our results show that Twist1 needs to induce Snail2 to suppress the epithelial branch of the EMT program and that Twist1 and Snail2 act together to promote EMT and tumor metastasis...
  58. pmc A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
    Teemu D Laajala
    Turku Centre for Biotechnology, FI 20521 Turku, Finland
    BMC Genomics 10:618. 2009
    b>Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study transcriptional regulation on a genome-wide scale...
  59. pmc Inferring direct DNA binding from ChIP-seq
    Timothy L Bailey
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Nucleic Acids Res 40:e128. 2012
    ..CentriMo is now part of the MEME Suite software package available at http://meme.nbcr.net. All data and output files presented here are available at: http://research.imb.uq.edu.au/t.bailey/sd/Bailey2011a...
  60. pmc A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
    ..Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions...
  61. pmc Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci
    Steven J Petesch
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Cell 134:74-84. 2008
    ..An RNAi screen of 28 transcription and chromatin-related factors reveals that depletion of heat shock factor, GAGA Factor, or Poly(ADP)-Ribose Polymerase or its activity abolishes the loss of nucleosomes upon Hsp70 activation...
  62. pmc Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts
    David R Mole
    Henry Wellcome Building of Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
    J Biol Chem 284:16767-75. 2009
    ..To better understand this transcriptional cascade we performed genome-wide chromatin immunoprecipitation using antibodies to two major HIF-alpha subunits, and correlated the results with genome-wide ..
  63. pmc PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci
    Mali Salmon-Divon
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    BMC Bioinformatics 11:415. 2010
    ....
  64. pmc Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
    Julia Zeitlinger
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Genes Dev 21:385-90. 2007
    ..of the dorsoventral (DV) determinants Dorsal, Twist, and Snail in the Drosophila embryo using chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip)...
  65. pmc Structure and function of a transcriptional network activated by the MAPK Hog1
    Andrew P Capaldi
    Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Department of Molecular and Cellular Biology, Cambridge, Massachusetts 02138, USA
    Nat Genet 40:1300-6. 2008
    ..This study lays out a path to identifying and characterizing the role of signal integration and processing in other gene regulatory networks...
  66. pmc A chromatin landmark and transcription initiation at most promoters in human cells
    Matthew G Guenther
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 130:77-88. 2007
    ..These observations extend to differentiated cells, suggesting that transcription initiation at most genes is a general phenomenon in human cells...
  67. pmc Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    Tae Hoon Kim
    Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093 0653, USA
    Cell 128:1231-45. 2007
    ..In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites...
  68. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010
    b>Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein ..
  69. ncbi Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
    Jason S Carroll
    Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
    Cell 122:33-43. 2005
    ..receptor (ER) with the complete nonrepetitive sequence of human chromosomes 21 and 22 by combining chromatin immunoprecipitation (ChIP) with tiled microarrays...
  70. doi A signal-noise model for significance analysis of ChIP-seq with negative control
    Han Xu
    Genome Institute of Singapore, Singapore
    Bioinformatics 26:1199-204. 2010
    ....
  71. pmc Identifying dispersed epigenomic domains from ChIP-Seq data
    Qiang Song
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 27:870-1. 2011
    ..While high-throughput methods like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains, there remain important analysis problems that are not adequately solved by current analysis tools...
  72. pmc ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
    Matthew D Young
    Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
    Nucleic Acids Res 39:7415-27. 2011
    ..The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation...
  73. pmc ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions
    Dominic Schmidt
    Department of Oncology, Hutchison MRC Research Centre, Hills Road, Cambridge CB20XZ, UK
    Methods 48:240-8. 2009
    b>Chromatin immunoprecipitation (ChIP) allows specific protein-DNA interactions to be isolated. Combining ChIP with high-throughput sequencing reveals the DNA sequence involved in these interactions...
  74. pmc Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus
    Evelyn N Kouwenhoven
    Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    PLoS Genet 6:e1001065. 2010
    ..We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP), followed by deep sequencing (ChIP-seq) in primary human keratinocytes, and identified ..
  75. doi Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses
    Masaki Fujisawa
    National Food Research Institute, 2 1 12 Kannondai, Tsukuba, Ibaraki 305 8642, Japan
    Planta 235:1107-22. 2012
    ..Here, we report the identification of novel RIN targets by transcriptome and chromatin immunoprecipitation (ChIP) analyses...
  76. ncbi The Polycomb group protein EZH2 directly controls DNA methylation
    Emmanuelle Viré
    Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, 808 Route de Lennik, 1070 Brussels, Belgium
    Nature 439:871-4. 2006
    ..Our results suggest that EZH2 serves as a recruitment platform for DNA methyltransferases, thus highlighting a previously unrecognized direct connection between two key epigenetic repression systems...
  77. pmc NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Genes Dev 22:1921-33. 2008
    ..These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure...
  78. pmc RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
    Morgane Thomas-Chollier
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
    Nucleic Acids Res 40:e31. 2012
    ..To our knowledge, peak-motifs is the only tool that performs a complete motif analysis and offers a user-friendly web interface without any restriction on sequence size or number of peaks...
  79. ncbi Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription
    Michael J Carrozza
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Cell 123:581-92. 2005
    ..This erases transcription elongation-associated acetylation to suppress intragenic transcription initiation...
  80. pmc Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts
    Joern Toedling
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:221. 2007
    b>Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is a high-throughput assay for DNA-protein-binding or post-translational chromatin/histone modifications...
  81. 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
    ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein-DNA interactions in-vivo on a genome scale...
  82. pmc Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
    Anton Valouev
    Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305, USA
    Nat Methods 5:829-34. 2008
    ..Uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) has recently become the focus of intense ..
  83. pmc Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data
    David L Corcoran
    Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
    PLoS ONE 4:e5279. 2009
    ..However, the length of the primary transcripts and promoter organization is currently unknown...
  84. pmc Cse4 is part of an octameric nucleosome in budding yeast
    Raymond Camahort
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Mol Cell 35:794-805. 2009
    ..Taken together, our experimental evidence supports the model that the Cse4 nucleosome is an octamer, containing two copies each of Cse4, H2A, H2B, and H4...
  85. pmc A unique H3K4me2 profile marks tissue-specific gene regulation
    Aleksandra Pekowska
    Centre d immunologie de Marseille Luminy, Universite Aix Marseille, Marseille 13009, France
    Genome Res 20:1493-502. 2010
    ..We propose that this epigenetic feature reflects the activity of an as yet unrecognized, intragenic cis-regulatory platform dedicated to refining tissue-specificity in gene expression...
  86. pmc ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome
    Gary Hon
    Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 4:e1000201. 2008
    ..The utility of this approach in uncovering novel, functionally significant genomic elements will aid future efforts of genome annotation via chromatin modifications...
  87. pmc On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    Ming Hu
    Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nucleic Acids Res 38:2154-67. 2010
    Coupling chromatin immunoprecipitation (ChIP) with recently developed massively parallel sequencing technologies has enabled genome-wide detection of protein-DNA interactions with unprecedented sensitivity and specificity...
  88. ncbi Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella
    William Wiley Navarre
    Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
    Science 313:236-8. 2006
    ..Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA...
  89. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In conjunction with expression, motif, and chromatin immunoprecipitation data, we find evidence of cell-type-specific characteristics, including the ability to identify ..
  90. pmc Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
    Dominic Schmidt
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Science 328:1036-40. 2010
    ..To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of ..
  91. doi Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
    Brian T Wilhelm
    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    Nature 453:1239-43. 2008
    ..Splicing efficiency was largely coordinated with transcript levels, and increased transcription led to increased splicing in test genes. Hundreds of introns showed such regulated splicing during cellular proliferation or differentiation...
  92. pmc A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb
    Steven A Vokes
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genes Dev 22:2651-63. 2008
    ..We characterized the Gli-dependent cis-regulatory network through a combination of whole-genome chromatin immunoprecipitation (ChIP)-on-chip and transcriptional profiling of the developing mouse limb...
  93. pmc Scm3, an essential Saccharomyces cerevisiae centromere protein required for G2/M progression and Cse4 localization
    Sam Stoler
    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
    Proc Natl Acad Sci U S A 104:10571-6. 2007
    ..Copurification and two-hybrid studies showed that Scm3 and Cse4 interact in vivo, and chromatin immunoprecipitation revealed that Scm3, like Cse4, is found associated with centromere DNA...
  94. pmc FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    Anthony P Fejes
    Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada
    Bioinformatics 24:1729-30. 2008
    ..Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads...
  95. pmc Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells
    Benjamin L Kidder
    EMD Serono Research Institute, Inc, Rockland, Massachusetts, United States of America
    PLoS ONE 3:e3932. 2008
    ..Therefore, to further understand ES cell transcriptional networks, we used genome-wide chromatin immunoprecipitation and microarray analysis (ChIP-chip) to map Stat3 and c-Myc binding targets in ES cells...
  96. pmc The polycomb group protein Suz12 is required for embryonic stem cell differentiation
    Diego Pasini
    Centre for Epigenetics and BRIC, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
    Mol Cell Biol 27:3769-79. 2007
    ..Furthermore, we provide evidence that PcGs have different mechanisms to regulate transcription during cellular differentiation...
  97. pmc The PurR regulon in Escherichia coli K-12 MG1655
    Byung Kwan Cho
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
    Nucleic Acids Res 39:6456-64. 2011
    ..the role of PurR under exogenous adenine stimulation at the genome-scale using high-resolution chromatin immunoprecipitation (ChIP)-chip and gene expression data obtained under in vivo conditions...
  98. pmc CEAS: cis-regulatory element annotation system
    Xuwo Ji
    Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, People s Republic China 100871
    Nucleic Acids Res 34:W551-4. 2006
    ..CEAS helps the adoption of ChIP-chip in mammalian systems and provides insights towards a more comprehensive understanding of transcriptional regulatory mechanisms. The URL of the server is http://ceas.cbi.pku.edu.cn...
  99. pmc Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
    Elizabeth D Wederell
    Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
    Nucleic Acids Res 36:4549-64. 2008
    ..We have used chromatin immunoprecipitation and massively parallel Illumina 1G sequencing (ChIP-Seq) to create a genome-wide profile of in vivo ..
  100. pmc Chromatin immunoprecipitation on microarray analysis of Smad2/3 binding sites reveals roles of ETS1 and TFAP2A in transforming growth factor beta signaling
    Daizo Koinuma
    Department of Biochemistry, The Cancer Institute of the Japanese Foundation for Cancer Research, Koto ku, Tokyo 135 8550, Japan
    Mol Cell Biol 29:172-86. 2009
    ..Here we identified 1,787 Smad2/3 binding sites in the promoter regions of over 25,500 genes by chromatin immunoprecipitation on microarray in HaCaT keratinocytes...
  101. pmc Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen
    Antoni Hurtado
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Nature 456:663-6. 2008
    ..These data provide mechanistic insight into the molecular basis of endocrine resistance in breast cancer...

Research Grants71

  1. Yun Fai Chris Lau; Fiscal Year: 2014
    ..we plan to identify and confirm the target genes of a TSPY-AR transcription complex using advanced chromatin immunoprecipitation and promoter tiling microarray (ChIP-Chip) approach...
  2. Carole R Mendelson; Fiscal Year: 2016
    ..Using chromatin immunoprecipitation, we will analyze temporal changes in in vivo recruitment of key transcription factors and coregulators ..
  3. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
    ..and control mice will be analyzed by identifying proteins binding the endogenous Fli1 promoter using chromatin immunoprecipitation (IP) and analyses of expression levels, post-translational modifications and interactions with co-..
  4. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..Methodology will include genomics and chromatin immunoprecipitation (ChIP) assays to scan for candidate VDREs, plus DNA gel mobility shift, real time PCR and promoter ..
  5. BIOSYNTHESIS OF TRACHEAL MUCOUS GLYCOPROTEINS
    Pi Wan Cheng; Fiscal Year: 2010
    ..They will be characterized by electrophoresis mobility shift assay and chromatin immunoprecipitation assay...
  6. Schahram Akbarian; Fiscal Year: 2014
    ..methylation in neuronal chromatin, (b) procedures to isolate neuronal chromatin from brain tissue, (c) chromatin immunoprecipitation followed by genome-wide profiling, (d) behavioral assays measuring despair and learned helplessness, ..
  7. Hepatic Steatosis Modulation by Apo B Gene Transcription
    JANET DEHOFF SPARKS; Fiscal Year: 2010
    ..the transcription factors (TF) that mediate transactivation of the apob gene using gel shift assays, chromatin immunoprecipitation, and in vitro loss and gain of function studies in rodent hepatocytes...
  8. Balakuntalam S Kasinath; Fiscal Year: 2016
    ..b>Chromatin immunoprecipitation (ChIP) assays will be performed to study GSK 3beta regulation of binding of Groucho, TCF/LEF1 to the ..
  9. DAVID MATTHEW KELLER; Fiscal Year: 2016
    ..Two experiments will be used to test for transcriptional repression, nuclear run-on assay and chromatin immunoprecipitation, and one experiment will be used to test for post-transcriptional degradation, pulse-chase RNA ..
  10. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2013
    ..b>Chromatin immunoprecipitation (ChIP) approaches with anti-methylated deoxy-cytosine and various anti-modified histone antibodies ..
  11. John W Wiley; Fiscal Year: 2016
    ..to identify putative regulatory CpG methylation sites at the promoters of stress response genes and chromatin immunoprecipitation (ChIP) analysis of relevant histone modification targets...
  12. Regulation of the Vibrio cholerae intestinal exit plan
    ANISIA J SILVA BENITEZ; Fiscal Year: 2010
    ..to rigorously test this hypothesis by integrating a variety of approaches such as bacterial genetics, chromatin immunoprecipitation (ChIP), ChiP-sequencing, confocal microscopy and animal models...
  13. FOXP3-microRNA146-NFkB Axis in Tumor Suppression
    Lizhong Wang; Fiscal Year: 2013
    ..We will use chromatin immunoprecipitation, electrophoretic mobility shift assay and luciferase reporter assays as well as site-directed ..
  14. Alvaro Puga; Fiscal Year: 2015
    ..5, AHR and dioxin exposure and use global gene expression analyses and chromatin immunoprecipitation to identify genetic and epigenetic signatures characteristic of TCDD effects during differentiation...
  15. An Aldosterone-Endothelin Feedback Mechanism on Sodium Homeostasis
    Charles S Wingo; Fiscal Year: 2012
    ..The in vitro work will be extended by using DNase I hypersensitivity, chromatin immunoprecipitation, and DNA affinity purification assays to study the role of chromatin structure and transcription ..
  16. Bioflavonoid Effects on EGF Signaling and Cell Cycle Pathways in Prostate Cancer
    BARRY MATTHEW MARKAVERICH; Fiscal Year: 2013
    ..b>Chromatin immunoprecipitation (ChIP) studies revealed that L reduced the acetylation state of histone H4 (at Lys 5, 8, 12, 16) ..
  17. Regulation of NFkappaB activity by the Estrogen Receptor
    Kendall W Nettles; Fiscal Year: 2012
    ..of NF-B, we will measure their recruitment to the MCP-1, IL-6, IL-8, MIP-1 and TNF-a genes by chromatin immunoprecipitation, and assay the effects of RNA interference targeting CBP and Grip1 on expression of the same genes...
  18. Iris Z Jaffe; Fiscal Year: 2016
    ..pathways in aldo-stimulated injury and atherosclerosis will also be investigated using chromatin immunoprecipitation in vessels from these mouse models...
  19. Molecular Biology of Human Erythrocyte Alpha Spectrin
    Patrick G Gallagher; Fiscal Year: 2013
    ..Techniques to be utilized include chromatin immunoprecipitation experiments followed by array hybridization (ChIP-chip) or whole genome sequencing (ChIP-seq), high ..
  20. Epigenetic effects of developmental endocrine disruptor exposure in the ovary
    Mehmet Uzumcu; Fiscal Year: 2010
    ..bisulfite sequencing and how these changes may interfere with the transcription factor binding using chromatin immunoprecipitation assay...
  21. RONALD JAY KOENIG; Fiscal Year: 2014
    ..In the first Specific Aim, chromatin immunoprecipitation - deep sequencing (ChIP-Seq) will be used to identify PPFP binding sites on a genome wide level...
  22. Epithelial differentiation in cornea
    Bogi Andersen; Fiscal Year: 2012
    ..In the second Aim, we will use chromatin immunoprecipitation and transcription assays to define the molecular mechanisms whereby Clim regulate the expression of ..
  23. Neuropeptide regulation of neurohypophyseal function
    Francis W Flynn; Fiscal Year: 2012
    ..Co-immunoprecipitation and chromatin immunoprecipitation will be used to identify the nuclear targets of nuclear NK3R...
  24. Epigenetic Analysis of iPS Cell Models of Aging and Alzheimer's Disease
    Bruce A Yankner; Fiscal Year: 2010
    ..iPS neurons will be performed using microarrays and by applying recent innovations in deep sequencing chromatin immunoprecipitation (ChIP- seq)...
  25. Regulation of apoptosis by PI 3-kinase/Akt signaling
    Geoffrey M Cooper; Fiscal Year: 2012
    ..Computational analysis of upstream regulatory regions combined with chromatin immunoprecipitation assays indicate that FOXO, NF[unreadable]B and Myc/Mad/Max transcription factors play major roles in ..
  26. Mechanisms of innate immune response modulation by mechanical ventilation
    William A Altemeier; Fiscal Year: 2012
    ..the role of AP-1 activation in ventilator-augmentation of LPS-induced inflammation by (a) using chromatin immunoprecipitation assay to identify which protein subunits of AP-1 are recruited to target gene promoters by mechanical ..
  27. Cellular and Molecular Regulation of Thrombopoiesis
    Ramesh A Shivdasani; Fiscal Year: 2012
    ..We have combined chromatin immunoprecipitation with hybridization to tiled genome arrays (ChIP-chip) to identify the complete complement of genes ..
  28. Peter B Dervan; Fiscal Year: 2014
    ..transcription factor-DNA interactions on a genome-wide scale;most notably through the coupling of chromatin immunoprecipitation to massively parallel sequencing (ChIP-Seq)...
  29. Regulation of Bile Acid Synthesis by Nuclear Receptors
    John Y L Chiang; Fiscal Year: 2010
    ..HepG2 and primary human hepatocytes will be used for chromatin immunoprecipitation (ChIP), co-IP and mammalian two-hybrid assays to study DNA-protein and protein-protein interaction...
  30. Mechanisms of Early Growth Response Factor 1 (Egr-1) Induction by HSV-1 Lytic Inf
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2010
    ..b>Chromatin Immunoprecipitation (ChIP) assays demonstrated that NFkB and cAMP response element binding protein (CREB) was induced by ..
  31. Regulation of IFN-beta induction by P2X7 purinergic receptor signaling
    JUDITH ANNE SMITH; Fiscal Year: 2011
    ..we will examine the recruitment of transcription factors to the IFN- [unreadable] gene promoter by chromatin immunoprecipitation to test our underlying hypothesis that P2X7 ligation leads to increased transcription factor occupancy ..
  32. SATB1-dependent epigenetic regulation of leukemia initiating cells
    Britta Will; Fiscal Year: 2011
    ..We will utilize global chromatin immunoprecipitation analysis (ChIP-seq) in combination with gene expression and DNA methylation pattern analysis...
  33. Paul M Lieberman; Fiscal Year: 2016
    ..To understand EBNA1 interactions with the host-chromosome, we used chromatin immunoprecipitation combined with next generation DNA sequencing (ChIP-Seq) and functional genomic methods to identify and ..
  34. AKAP Regulation of PKA Targeting in the Heart
    Meredith Bond; Fiscal Year: 2009
    ..In (new) Specific Aim 4.1, we will use Chromatin Immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) to: (i) identify genes whose upstream ..
  35. Erythropoietin in Non-Erythroid Cells: Function and Regulation
    Josef T Prchal; Fiscal Year: 2013
    ..We have studied the mechanism of HIF regulation of Epo transcription using chromatin immunoprecipitation (ChIP) and have found multiple HREs of the Epo gene...
  36. Arsenic, Histone Modification, and Transcription
    LYNN SHELDON; Fiscal Year: 2009
    ..mouse mammary tumor virus (MMTV) promoter in the presence and absence of sodium arsenite in vivo by chromatin immunoprecipitation (ChIP) analysis (Specific Aim I)...
  37. ALBERT HONG JAE KIM; Fiscal Year: 2016
    ..neurons will be identified through a genome-wide search for cohesion binding sites through chromatin immunoprecipitation coupled with next generation sequencing and correlated cohesion- dependent microarray analyses...
  38. PAULA GOODMAN FRAENKEL; Fiscal Year: 2015
    ..in the screen, we will characterize the modulators'effects on mammalian cellular iron transport, chromatin immunoprecipitation, RNA expression, and signaling pathways...
  39. Mechanisms of Astrocyte Development
    Teri L Belecky Adams; Fiscal Year: 2010
    ..BMP and SHH pathway members with other regulatory DNA-binding proteins such as co-immunoprecipitation, chromatin immunoprecipitation, and luciferase assays, 2) in vitro and in vivo manipulations of BMP pathways, 3) characterization of ..
  40. Role of estrogen-related receptors in cardiac and skeletal muscle
    Janice M Huss; Fiscal Year: 2010
    ..We will analyze these models with gene expression profiling coupled with chromatin immunoprecipitation to identify target genes for ERRs...
  41. VEGF Regulation of Hepatic Erythropoietin Synthesis
    Calvin Kuo; Fiscal Year: 2009
    ..Candidate factors (HIF proteins, HNF4, RXRalpha, GATA factors) will be directly tested by chromatin immunoprecipitation assays and functionally by adenoviral and transgenic expression of Cre to delete floxed alleles of ..
  42. A Cis-regulatory Model for Neural Border Induction
    Daniel Meulemans Medeiros; Fiscal Year: 2013
    ..The proposed work will test this model using mRNA injections, mutagenesis, and chromatin immunoprecipitation (ChIP)...
  43. Excessive Copper Levels Disrupt Hepatic Nuclear Receptor Function
    Clavia Ruth Wooton-Kee; Fiscal Year: 2011
    ..We will utilize the Atp7b-/- mouse to determine nuclear receptor DNA-binding activity via chromatin immunoprecipitation (ChIP) assays and to measure parameters of liver function, such as bile flow, biliary secretion of ..
  44. Peter L Freddolino; Fiscal Year: 2014
    ..IPODHR is superficially similar to chromatin immunoprecipitation (ChIP) experiments, but instead of isolating a single protein (and any DNA bound to it), IPODHR ..
  45. PROMOTER SPECIFICITY OF TRANSCRIPTION FACTORS
    David J Stillman; Fiscal Year: 2010
    ..b>Chromatin immunoprecipitation (ChIP) experiments show that there are two distinct mechanisms operative to prevent these factors from ..
  46. Maha Abdellatif; Fiscal Year: 2016
    ..More significantly, chromatin immunoprecipitation-deep sequencing analysis (ChIP-Seq) reveals that supplementing cardiac myocytes with miR-1 suppresses ..
  47. James F George; Fiscal Year: 2016
    ..sequences in the HO-1 promoter will be examined using the 3C (Chromosome Conformation Capture) and chromatin immunoprecipitation assays...
  48. Michael R Stallcup; Fiscal Year: 2016
    ..RNA interference to systematically deplete the endogenous levels of selected coregulators, followed by chromatin immunoprecipitation assays to examine the effects of coregulator depletion on the stepwise modification of histones and ..
  49. Transcriptional regulation of proteinuria
    SUMANT SINGH CHUGH; Fiscal Year: 2011
    ..factors that influence the binding of ZHX3 to the COL4A3 promoter will be studied by a combination of chromatin immunoprecipitation and site directed mutagenesis...
  50. The Role of the Nuclear Lamina in Chromatin Organization and Gene Expression in N
    Marcos Estecio; Fiscal Year: 2012
    ..Our method employs a modified chromatin immunoprecipitation protocol coupled with massively parallel Solexa 1G sequencing technology...
  51. Marcus P Cooper; Fiscal Year: 2014
    ..We will use genetic studies, reporter assays and chromatin immunoprecipitation to test this hypothesis...
  52. The role of NLRP7 and related genes in hydatidiform moles and reproductive failur
    Ignatia Van den Veyver; Fiscal Year: 2009
    ..In specific aim 1 we will investigate by two complementary methods, electromobility shift assays and chromatin immunoprecipitation, whether NLRP7 associates with methylated and unmethylated CpG sequences at ICRs...
  53. Is symmetrical dimethylation of Arginine 2 of Histone H3 used as an epigenetic si
    Marjorie A Oettinger; Fiscal Year: 2010
    ..H3R2me2s/K4me3 in mammalian cells in depth, using a combination of immunofluorescence and genome-wide chromatin immunoprecipitation on a range of cell types under various conditions...
  54. Pbx Homeodomain Proteins in Skeletal Muscle Differentiation
    LISA A MAVES; Fiscal Year: 2011
    ..a subset of, muscle gene promoters, genome-wide Pbx binding sites will be determined using a global chromatin immunoprecipitation approach...
  55. Astrocyte Development and Reactive Gliosis
    Teri L Belecky-Adams; Fiscal Year: 2012
    ..BMP and SHH pathway members with other regulatory DNA-binding proteins such as co-immunoprecipitation, chromatin immunoprecipitation, and luciferase assays, 2) in vitro and in vivo manipulations of BMP pathways following optic nerve ..
  56. Amit Berson; Fiscal Year: 2015
    ..Second, using a recently developed in- vivo, cell type-specific chromatin immunoprecipitation and deep-sequencing (ChIP-Seq) technique, chromatin landscape alterations induced by TDP-43 will be ..
  57. TRANSCRIPTION FACTORS IN CONTROL OF BRAIN DEVELOPMENT
    Eric E Turner; Fiscal Year: 2010
    ..4) Use locus-wide, real-time PCR-based chromatin immunoprecipitation assays, as well as database analysis and conventional protein-DNA interaction methodology, to define ..
  58. Genomic actions of progesterone receptors in human myometrial cells
    Sam Mesiano; Fiscal Year: 2010
    ..The gene promoters to which PR- A and PR-B bind in hTERT-HMA/B cells will be identified by nPR-chromatin immunoprecipitation (ChIP) followed by microarray-based genome-wide DNA location analysis (ChIP-on-chip)...
  59. DEVELOPMENT OF SPLIT DAMID AS AN ALTERNATIVE METHODOLOGY TO CHROMATIN IMMUNOPRECI
    Raphael Kopan; Fiscal Year: 2010
    ..research (06-MH-103) Project Title: Development of Split-DamID as an alternative methodology to chromatin immunoprecipitation Project Abstract A wide variety of genetic or drug-induced mental health disorders have been linked to ..
  60. Michael Freitag; Fiscal Year: 2015
    ..Biochemical methods (chromatin immunoprecipitation, chromosome conformation capture, affinity purification of centromere proteins) will complement ..
  61. Bogi Andersen; Fiscal Year: 2016
    ..We will use chromatin immunoprecipitation sequencing (ChIP-seq) and chromosome conformation capture (3C) assays to test the hypothesis that ..
  62. Steven F Ziegler; Fiscal Year: 2015
    ..Chromatin remodeling at the TSLPR locus will be assessed in DCs by chromatin immunoprecipitation and DNase hypersensitivity assays...
  63. Thomas M Vondriska; Fiscal Year: 2016
    ..approaches combined with super resolution STED microscopy (image chromatin packing), chromatin immunoprecipitation and DNA sequencing (localize proteins across the genome) and proteomics (determine proteins necessary ..
  64. Reading the histone code:nanoscale morphology of Epigneomic Histone Modifications
    M Mitchell Smith; Fiscal Year: 2010
    ..Biochemical techniques including mass spectroscopy, chromatin immunoprecipitation, and chromosome conformation capture, are making great strides in defining the functional combinations ..
  65. Transcriptional Regulation of Matrix Metalloproteinase-3 (MMP-3)
    RUTH BORGHAEI; Fiscal Year: 2007
    ..The chromatin immunoprecipitation (ChIP) assay will be used to determine which transcription factor(s) bind in vivo at the 5T and 6T ..
  66. High-Throughput Low Cost Production of Chromatin-Immunoprecipitation-Grade Antib
    KEITH ELLIOTT KROPP; Fiscal Year: 2010
    ..b>Chromatin immunoprecipitation (ChIP) coupled with microarray (ChIP-chip) or sequencing (ChIP- seq) is a widely used technique for ..
  67. GATA Factor Regulation of Vascular Endothelium
    EMERY BRESNICK; Fiscal Year: 2009
    ..b>Chromatin immunoprecipitation (ChIP) and ChIP coupled to microarray chip (ChIP-chip) assays will be conducted to determine which ..
  68. Elucidating the Rickettsia prowazekii EnvZ/OmpR Regulon
    JONATHON AUDIA; Fiscal Year: 2007
    ..of this R21 proposal is to use this two-component network as a relevant biological model to adapt the Chromatin Immunoprecipitation (ChIP) technique for use on an obligate intracellular, cytosol-limited pathogen...
  69. CYTOKINE REGULATION OF HUMAN EOSINOPHIL GENES
    Steven Ackerman; Fiscal Year: 2006
    ..mechanisms that regulate eosinophil IL-5Ralpha gene expression during eosinophil development? Chromatin immunoprecipitation (CHIP) and analyses of chromatin remodeling including DNAse I hypersensitivity mapping and DNase I in ..
  70. TRANSCRIPTION ACTIVATION BY HIV, TAT, HTLV TAX & HBV PX
    Michael Green; Fiscal Year: 2004
    ..The rationale for the proposal relies heavily on two relatively new technologies. First, the chromatin immunoprecipitation (ChIP) assay, which allows for the detection of specific proteins that are physically associated with ..