chromatin

Summary

Summary: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.

Top Publications

  1. pmc The accessible chromatin landscape of the human genome
    Robert E Thurman
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 489:75-82. 2012
  2. ncbi 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
  3. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
  4. pmc Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
    Rajnish A Gupta
    Howard Hughes Medical Institute and Program in Epithelial Biology, California 94305, USA
    Nature 464:1071-6. 2010
  5. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
  6. ncbi Role of histone H3 lysine 27 methylation in Polycomb-group silencing
    Ru Cao
    Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Science 298:1039-43. 2002
  7. pmc Topological domains in mammalian genomes identified by analysis of chromatin interactions
    Jesse R Dixon
    Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
    Nature 485:376-80. 2012
  8. pmc CTCF: master weaver of the genome
    Jennifer E Phillips
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Cell 137:1194-211. 2009
  9. pmc HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    Lucas D Ward
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology and The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
    Nucleic Acids Res 40:D930-4. 2012
  10. ncbi Translating the histone code
    T Jenuwein
    Research Institute of Molecular Pathology IMP at the Vienna Biocenter, Dr Bohrgasse 7, A 1030 Vienna, Austria
    Science 293:1074-80. 2001

Detail Information

Publications326 found, 100 shown here

  1. pmc The accessible chromatin landscape of the human genome
    Robert E Thurman
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 489:75-82. 2012
    ..Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns...
  2. ncbi 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
    ..Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations...
  3. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
    b>Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity...
  4. pmc Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
    Rajnish A Gupta
    Howard Hughes Medical Institute and Program in Epithelial Biology, California 94305, USA
    Nature 464:1071-6. 2010
    ..homeotic gene expression suggest that individual lincRNAs can function as the interface between DNA and specific chromatin remodelling activities...
  5. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification...
  6. ncbi Role of histone H3 lysine 27 methylation in Polycomb-group silencing
    Ru Cao
    Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Science 298:1039-43. 2002
    ..We demonstrate that the complex specifically methylates nucleosomal histone H3 at lysine 27 (H3-K27). Using chromatin immunoprecipitation assays, we show that H3-K27 methylation colocalizes with, and is dependent on, E(Z) binding ..
  7. pmc Topological domains in mammalian genomes identified by analysis of chromatin interactions
    Jesse R Dixon
    Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
    Nature 485:376-80. 2012
    ..These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function...
  8. pmc CTCF: master weaver of the genome
    Jennifer E Phillips
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Cell 137:1194-211. 2009
    ..These analyses support a primary role for CTCF in the global organization of chromatin architecture and suggest that CTCF may be a heritable component of an epigenetic system regulating the interplay ..
  9. pmc HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
    Lucas D Ward
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology and The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
    Nucleic Acids Res 40:D930-4. 2012
    ..from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals and their effect on regulatory motifs...
  10. ncbi Translating the histone code
    T Jenuwein
    Research Institute of Molecular Pathology IMP at the Vienna Biocenter, Dr Bohrgasse 7, A 1030 Vienna, Austria
    Science 293:1074-80. 2001
    b>Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA...
  11. ncbi Capturing chromosome conformation
    Job Dekker
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Science 295:1306-11. 2002
    ..reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber...
  12. pmc Regulation of chromatin by histone modifications
    Andrew J Bannister
    The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK
    Cell Res 21:381-95. 2011
    b>Chromatin is not an inert structure, but rather an instructive DNA scaffold that can respond to external cues to regulate the many uses of DNA...
  13. pmc CpG islands and the regulation of transcription
    Aimée M Deaton
    The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
    Genes Dev 25:1010-22. 2011
    ..function by destabilizing nucleosomes and attracting proteins that create a transcriptionally permissive chromatin state...
  14. pmc Systematic localization of common disease-associated variation in regulatory DNA
    Matthew T Maurano
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Science 337:1190-5. 2012
    ..variants systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks...
  15. 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
    ..Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been ..
  16. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci...
  17. pmc Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
    Guillaume J Filion
    Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Cell 143:212-24. 2010
    b>Chromatin is important for the regulation of transcription and other functions, yet the diversity of chromatin composition and the distribution along chromosomes are still poorly characterized...
  18. 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 ..
  19. ncbi DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139
    E P Rogakou
    Laboratory of Molecular Pharmacology, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 273:5858-68. 1998
    ..10(9) base pairs of a mammalian G1 genome, leads to the gamma-phosphorylation of H2AX distributed over 1% of the chromatin. Thus, about 0.03% of the chromatin appears to be involved per DNA double-stranded break...
  20. 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
    In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes...
  21. pmc Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
    Peter V Kharchenko
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 471:480-5. 2011
    b>Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes...
  22. pmc Identification of functional elements and regulatory circuits by Drosophila modENCODE
    Sushmita Roy
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 330:1787-97. 2010
    ..generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome...
  23. pmc A map of the cis-regulatory sequences in the mouse genome
    Yin Shen
    Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093 0653, USA
    Nature 488:116-20. 2012
    ..Our results provide a resource for the annotation of functional elements in the mammalian genome and for the study of mechanisms regulating tissue-specific gene expression...
  24. doi Mechanisms of polycomb gene silencing: knowns and unknowns
    Jeffrey A Simon
    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis 55455, USA
    Nat Rev Mol Cell Biol 10:697-708. 2009
    Polycomb proteins form chromatin-modifying complexes that implement transcriptional silencing in higher eukaryotes...
  25. 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
    ..Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of ..
  26. 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
    ..an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments...
  27. pmc CTCF-mediated functional chromatin interactome in pluripotent cells
    Lusy Handoko
    Genome Institute of Singapore, Singapore
    Nat Genet 43:630-8. 2011
    ..However, little is known about CTCF-associated higher-order chromatin structures at a global scale...
  28. pmc Mediator and cohesin connect gene expression and chromatin architecture
    Michael H Kagey
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 467:430-5. 2010
    ..Mediator and cohesin co-occupy different promoters in different cells, thus generating cell-type-specific DNA loops linked to the gene expression program of each cell...
  29. pmc Megabase chromatin domains involved in DNA double-strand breaks in vivo
    E P Rogakou
    Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Cell Biol 146:905-16. 1999
    ..The results further suggest the possible existence of units of higher order chromatin structure involved in monitoring DNA integrity.
  30. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John L Rinn
    Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 129:1311-23. 2007
    ..Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states...
  31. doi Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma
    Jeremy Schwartzentruber
    McGill University and Genome Quebec Innovation Centre, Montreal, Quebec H3A 1A4, Canada
    Nature 482:226-31. 2012
    ..Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48)...
  32. ncbi Release of chromatin protein HMGB1 by necrotic cells triggers inflammation
    Paola Scaffidi
    DIBIT, Istituto Scientifico San Raffaele, 20132 Milano, Italy
    Nature 418:191-5. 2002
    ..In the cell nucleus it acts as an architectural chromatin-binding factor that bends DNA and promotes protein assembly on specific DNA targets...
  33. pmc Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    Mark B Gerstein
    Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA
    Science 330:1775-87. 2010
    ..a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization...
  34. doi Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
    Michiel Vermeulen
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Cell 142:967-80. 2010
    Trimethyl-lysine (me3) modifications on histones are the most stable epigenetic marks and they control chromatin-mediated regulation of gene expression...
  35. pmc Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    Ahmad M Khalil
    The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:11667-72. 2009
    ..Here, we expand the catalog of human lincRNAs to approximately 3,300 by analyzing chromatin-state maps of various human cell types...
  36. ncbi The role of chromatin during transcription
    Bing Li
    Stowers Medical Research Institute, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Cell 128:707-19. 2007
    b>Chromatin structure imposes significant obstacles on all aspects of transcription that are mediated by RNA polymerase II...
  37. ncbi The complex language of chromatin regulation during transcription
    Shelley L Berger
    The Wistar Institute, 3601 Spruce Street, Room 201, Philadelphia, Pennsylvania 19104, USA
    Nature 447:407-12. 2007
    An important development in understanding the influence of chromatin on gene regulation has been the finding that DNA methylation and histone post-translational modifications lead to the recruitment of protein complexes that regulate ..
  38. pmc A high-resolution map of the three-dimensional chromatin interactome in human cells
    Fulai Jin
    1 Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA 2
    Nature 503:290-4. 2013
    ..However, previous studies lack either the resolution or coverage to permit a whole-genome, unbiased view of chromatin interactions...
  39. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural ..
  40. ncbi Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    Marieke Simonis
    Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
    Nat Genet 38:1348-54. 2006
    ..Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.
  41. pmc Regulation of alternative splicing by histone modifications
    Reini F Luco
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Science 327:996-1000. 2010
    ..Histone marks affect splicing outcome by influencing the recruitment of splicing regulators via a chromatin-binding protein...
  42. ncbi Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    Michael Weber
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
    Nat Genet 39:457-66. 2007
    ..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation.
  43. pmc CpG islands influence chromatin structure via the CpG-binding protein Cfp1
    John P Thomson
    Wellcome Trust Centre for Cell Biology, Michael Swann Building, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
    Nature 464:1082-6. 2010
    ..of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown...
  44. pmc Selective inhibition of BET bromodomains
    Panagis Filippakopoulos
    Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
    Nature 468:1067-73. 2010
    ..So far, successful efforts have been limited to chromatin modifying enzymes, or so-called epigenetic 'writers' and 'erasers'...
  45. ncbi Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain
    A J Bannister
    Wellcome CRC Institute and Department of Pathology, University of Cambridge, UK
    Nature 410:120-4. 2001
    ..This model may also explain the stable inheritance of the heterochromatic state...
  46. 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
    ..Combining these two technologies, we have created a comprehensive and accurate genome-wide open chromatin map...
  47. pmc Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis
    F Nikulenkov
    Department of Microbiology, Tumor and Cell Biology MTC, Karolinska Institutet, Stockholm, Sweden
    Cell Death Differ 19:1992-2002. 2012
    ..Our analysis of genome-wide chromatin occupancy by p53 using chromatin immunoprecipitation (ChIP)-seq revealed 'p53 default program', that is, the ..
  48. pmc Differential chromatin marking of introns and expressed exons by H3K36me3
    Paulina Kolasinska-Zwierz
    The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nat Genet 41:376-81. 2009
    Variation in patterns of methylations of histone tails reflects and modulates chromatin structure and function...
  49. ncbi A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
    ..These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency.
  50. pmc Functional and mechanistic diversity of distal transcription enhancers
    Michael Bulger
    Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester, NY 14627, USA
    Cell 144:327-39. 2011
    ..However, mechanisms for enhancer function are emerging that do not fit solely within such a model, suggesting that enhancers as a class of DNA regulatory element may be functionally and mechanistically diverse...
  51. pmc Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    Oren Ram
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 147:1628-39. 2011
    Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure...
  52. ncbi Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells
    Yoshimasa Saito
    Department of Urology, Biochemistry, and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, USA
    Cancer Cell 9:435-43. 2006
    ..revealed that 17 out of 313 human miRNAs were upregulated more than 3-fold by simultaneous treatment with the chromatin-modifying drugs 5-aza-2'-deoxycytidine and 4-phenylbutyric acid...
  53. ncbi Histone acetylation in chromatin structure and transcription
    M Grunstein
    Department of Biological Chemistry, UCLA School of Medicine and the Molecular Biology Institute, University of California, Los Angeles 90095, USA
    Nature 389:349-52. 1997
    ..These acetylation patterns may direct histone assembly and help regulate the unfolding and activity of genes...
  54. ncbi Chromatin-IgG complexes activate B cells by dual engagement of IgM and Toll-like receptors
    Elizabeth A Leadbetter
    Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
    Nature 416:603-7. 2002
    ..Here we show that effective activation of RF+ B cells is mediated by IgG2a-chromatin immune complexes and requires the synergistic engagement of the antigen receptor and a member of the MyD88-..
  55. pmc Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
    Fan Lai
    The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
    Nature 494:497-501. 2013
    ..We show that ncRNA-a interact with Mediator to regulate its chromatin localization and kinase activity towards histone H3 serine 10...
  56. pmc Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy
    Lothar Schermelleh
    Center for Integrated Protein Science, Department of Biology, Ludwig Maximilians University Munich, 82152 Planegg Martinsried, Germany
    Science 320:1332-6. 2008
    ..By simultaneously imaging chromatin, nuclear lamina, and the nuclear pore complex (NPC), we observed several features that escape detection by ..
  57. doi The dynamic architecture of Hox gene clusters
    Daan Noordermeer
    National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Fédérale EPFL, Lausanne, Switzerland
    Science 334:222-5. 2011
    ..Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse ..
  58. pmc The language of histone crosstalk
    Jung Shin Lee
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Cell 142:682-5. 2010
    ..However, recent studies indicate that histone modifications have context-dependent effects, making their interplay more like a language within the chromatin signaling pathway than a code.
  59. ncbi Genomic instability and aging-like phenotype in the absence of mammalian SIRT6
    Raul Mostoslavsky
    Howard Hughes Medical Institute, The Children s Hospital, CBR Institute for Biomedical Research, Harvard University Medical School, Boston, MA 02115, USA
    Cell 124:315-29. 2006
    The Sir2 histone deacetylase functions as a chromatin silencer to regulate recombination, genomic stability, and aging in budding yeast...
  60. pmc Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put
    Jeffrey A Simon
    Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
    Mol Cell 49:808-24. 2013
    b>Chromatin modification by Polycomb proteins provides an essential strategy for gene silencing in higher eukaryotes...
  61. doi Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators
    Akihiro Fujimoto
    Center for Genomic Medicine, RIKEN, Yokohama, Japan
    Nat Genet 44:760-4. 2012
    ..Statistical and functional analyses yielded a list of recurrently mutated genes. Multiple chromatin regulators, including ARID1A, ARID1B, ARID2, MLL and MLL3, were mutated in ∼50% of the tumors...
  62. doi Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
    Radha Raman Pandey
    Department of Genetics and Pathology, Dag Hammarskjölds väg 20, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Mol Cell 32:232-46. 2008
    ..Kcnq1ot1 interacts with chromatin and with the H3K9- and H3K27-specific histone methyltransferases G9a and the PRC2 complex in a lineage-specific ..
  63. doi The biology of chromatin remodeling complexes
    Cedric R Clapier
    Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
    Annu Rev Biochem 78:273-304. 2009
    ..However, this constraint also allows nucleosomes and other chromatin components to actively participate in the regulation of transcription, chromosome segregation, DNA replication, ..
  64. pmc Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes
    Gillian L Dalgliesh
    Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
    Nature 463:360-3. 2010
    ..The results highlight the role of mutations in components of the chromatin modification machinery in human cancer...
  65. doi The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin
    Takashi Nagano
    Laboratory of Chromatin and Gene Expression, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
    Science 322:1717-20. 2008
    ..We show that Air interacts with the Slc22a3 promoter chromatin and the H3K9 histone methyltransferase G9a in placenta...
  66. pmc Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes
    Maya Capelson
    Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 140:372-83. 2010
    ....
  67. pmc Transcriptional architecture and chromatin landscape of the core circadian clock in mammals
    Nobuya Koike
    Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390 9111, USA
    Science 338:349-54. 2012
    ..pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression, and chromatin states...
  68. pmc A map of open chromatin in human pancreatic islets
    Kyle J Gaulton
    Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    Nat Genet 42:255-9. 2010
    ..To identify regulatory DNA active in human pancreatic islets, we profiled chromatin by formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq)...
  69. doi Histones: annotating chromatin
    Eric I Campos
    Department of Biochemistry, Howard Hughes Medical Institute, NYU School of Medicine, New York, New York 10016, USA
    Annu Rev Genet 43:559-99. 2009
    b>Chromatin is a highly regulated nucleoprotein complex through which genetic material is structured and maneuvered to elicit cellular processes, including transcription, cell division, differentiation, and DNA repair...
  70. pmc MicroRNA genes are transcribed by RNA polymerase II
    Yoontae Lee
    Institute of Molecular Biology and Genetics and School of Biological Science, Seoul National University, Seoul, Korea
    EMBO J 23:4051-60. 2004
    ..Furthermore, chromatin immunoprecipitation analyses show that pol II is physically associated with a miRNA promoter...
  71. pmc Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    Guoliang Li
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Cell 148:84-98. 2012
    ..Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions ..
  72. pmc Heritable individual-specific and allele-specific chromatin signatures in humans
    Ryan McDaniell
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
    Science 328:235-9. 2010
    The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown...
  73. ncbi In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state
    Marius Wernig
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 448:318-24. 2007
    ..Here we show that DNA methylation, gene expression and chromatin state of such induced reprogrammed stem cells are similar to those of ES cells...
  74. pmc Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicity
    Christine L Chaffer
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Cell 154:61-74. 2013
    ..We find that plastic non-CSCs maintain the ZEB1 promoter in a bivalent chromatin configuration, enabling them to respond readily to microenvironmental signals, such as TGFβ...
  75. pmc Extensive variation in chromatin states across humans
    Maya Kasowski
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 342:750-2. 2013
    ..We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of ..
  76. ncbi Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    Nathaniel D Heintzman
    Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
    Nat Genet 39:311-8. 2007
    ..We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are ..
  77. ncbi LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription
    Eric Metzger
    Universitäts Frauenklinik und Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
    Nature 437:436-9. 2005
    Gene regulation in eukaryotes requires the coordinate interaction of chromatin-modulating proteins with specific transcription factors such as the androgen receptor...
  78. 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
    Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here, we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes...
  79. pmc A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations
    Sreenath V Sharma
    Massachusetts General Hospital Cancer Center, 149 13th Street, Charlestown, MA 02129, USA
    Cell 141:69-80. 2010
    ..reduced drug sensitivity and maintain viability via engagement of IGF-1 receptor signaling and an altered chromatin state that requires the histone demethylase RBP2/KDM5A/Jarid1A...
  80. ncbi Histone H4-K16 acetylation controls chromatin structure and protein interactions
    Michael Shogren-Knaak
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 311:844-7. 2006
    Acetylation of histone H4 on lysine 16 (H4-K16Ac) is a prevalent and reversible posttranslational chromatin modification in eukaryotes...
  81. ncbi Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action
    Nadia M Tsankova
    The University of Texas Southwestern Medical Center, Department of Psychiatry and Center for Basic Neuroscience, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9070, USA
    Nat Neurosci 9:519-25. 2006
    ..imipramine (a tricyclic antidepressant) to mice and studied adaptations at the levels of gene expression and chromatin remodeling of five brain-derived neurotrophic factor (Bdnf) splice variant mRNAs (I-V) and their unique ..
  82. 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
    ..However, it is not clear whether it plays a role in chromatin domain barriers between active and repressive domains...
  83. pmc Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains
    Vardhman K Rakyan
    Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
    Genome Res 20:434-9. 2010
    ..Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoters...
  84. pmc Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia
    Mark A Dawson
    Department of Haematology, Cambridge Institute for Medical Research and Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0XY, UK
    Nature 478:529-33. 2011
    ..polymerase-associated factor complex (PAFc), are associated with the BET family of acetyl-lysine recognizing, chromatin 'adaptor' proteins...
  85. doi Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
    Sam John
    Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Nat Genet 43:264-8. 2011
    ..receptor, a paradigmatic ligand-activated transcription factor, is targeted to preexisting foci of accessible chromatin. Factor binding invariably potentiates chromatin accessibility...
  86. pmc Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells
    Matthew G Guenther
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell Stem Cell 7:249-57. 2010
    Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) should provide a robust means to assess whether the genomes of these cells ..
  87. pmc How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers
    Sean D Taverna
    Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
    Nat Struct Mol Biol 14:1025-40. 2007
    Histones comprise the major protein component of chromatin, the scaffold in which the eukaryotic genome is packaged, and are subject to many types of post-translational modifications (PTMs), especially on their flexible tails...
  88. doi Regulation of nucleosome dynamics by histone modifications
    Gabriel E Zentner
    Fred Hutchinson Cancer Research Center, Basic Sciences Division, Seattle, Washington, USA
    Nat Struct Mol Biol 20:259-66. 2013
    b>Chromatin is a dynamic structure that must respond to myriad stimuli to regulate access to DNA, and chemical modification of histones is a major means by which the cell modulates nucleosome mobility and turnover...
  89. ncbi Chromatin signatures of pluripotent cell lines
    Veronique Azuara
    Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
    Nat Cell Biol 8:532-8. 2006
    ..Unusually, in ES cells these markers of open chromatin were also combined with H3K27 trimethylation at some non-expressed genes...
  90. pmc DNase I sensitivity QTLs are a major determinant of human expression variation
    Jacob F Degner
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 482:390-4. 2012
    ..Here we show that genetic variants that modify chromatin accessibility and transcription factor binding are a major mechanism through which genetic variation leads to ..
  91. 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
    Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes ..
  92. pmc Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations
    YuBo Zhang
    1 Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA 2 3 Department of Life Sciences, Faculty of Natural Sciences, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel R Y B National Heart, Lung, and Blood Institute, National Institutes of Health, Systems Biology Center, 9000 Rockville Pike, Bethesda, Maryland 20892, USA Y Z
    Nature 504:306-10. 2013
    ..Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements...
  93. doi Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming
    Nishant Singhal
    Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, D 48149 Munster, Germany
    Cell 141:943-55. 2010
    ..Using proteomics, we identified components of the ATP-dependent BAF chromatin-remodeling complex, which significantly increases reprogramming efficiency when used together with the four ..
  94. pmc Biased chromatin signatures around polyadenylation sites and exons
    Noah Spies
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Mol Cell 36:245-54. 2009
    Core RNA-processing reactions in eukaryotic cells occur cotranscriptionally in a chromatin context, but the relationship between chromatin structure and pre-mRNA processing is poorly understood...
  95. pmc Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2
    Aditi Kanhere
    Division of Infection and Immunity, University College London, London W1T 4JF, UK
    Mol Cell 38:675-88. 2010
    ..We propose that short RNAs play a role in the association of PRC2 with its target genes...
  96. pmc Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    Lingyun Song
    Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    Genome Res 21:1757-67. 2011
    ..types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map "open chromatin." Over 870,000 DNaseI or FAIRE sites, which correspond tightly to nucleosome-depleted regions, were identified ..
  97. pmc Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing
    Robert J Sims
    Department of Biochemistry, New York University School of Medicine, New York, NY 10016, USA
    Mol Cell 28:665-76. 2007
    ..Knockdown of CHD1 and H3K4me3 levels by siRNA reduced association of U2 snRNP components with chromatin and, more importantly, altered the efficiency of pre-mRNA splicing on active genes in vivo...
  98. 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
    ..We identified the proximal promoters of 175 human miRNAs by combining nucleosome mapping with chromatin signatures for promoters...
  99. ncbi Dissecting the regulatory circuitry of a eukaryotic genome
    F C Holstege
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Cell 95:717-28. 1998
    ..Components of the RNA polymerase II holoenzyme, the general transcription factor TFIID, and the SAGA chromatin modification complex were found to have roles in expression of distinct sets of genes...
  100. pmc Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
    R David Hawkins
    Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
    Cell Stem Cell 6:479-91. 2010
    ..By comparing the chromatin-modification profiles and DNA methylomes in hESCs and primary fibroblasts, we find that nearly one-third of the ..

Research Grants74

  1. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  2. Transcription factors regulating sensory gene expression and pain pathways
    Eric E Turner; Fiscal Year: 2011
    ..We will also examine chromatin modifications at the Islet1 target gene loci. Aim 3...
  3. Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone Receptors
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2013
    ..Specific Aim 1. To test the hypothesis that T3/TR control the transcription of thymidine kinase (TK) by chromatin regulation using silencing mediator of retinoid and thyroid receptors (SMRT) recruited by Nuclear Orphan ..
  4. Role of the Y-Located TSPY Gene in Human Oncogenesis
    Yun Fai Chris Lau; Fiscal Year: 2013
    ..Third, 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...
  5. MECHANISMS IN THE REGULATION OF SP-A GENE EXPRESSION
    Carole R Mendelson; Fiscal Year: 2013
    ..modifications in histone phosphorylation, acetylation and methylation that likely cause profound changes in chromatin structure...
  6. Vitamin D3, Interference with Androgen Signal and Inhibition of Prostate Cancer
    Bandana Chatterjee; Fiscal Year: 2013
    ..Transcription factors WSTF and E47 occupied regulated chromatin in response to androgen...
  7. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..1] The template upon which the epigenome is written is chromatin - the complex of histone proteins, RNA and DNA that efficiently package the genome in an appropriately ..
  8. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
    ..lupus prone 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 ..
  9. Collagen X and heparan sulfate proteoglycan in the hematopoietic stem cell niche.
    ELIZABETH G SWEENEY; Fiscal Year: 2012
    ..hematopoiesis, transgenesis and spermatogonial transplanation, cloning, mitochondria, pattern formation, chromatin structure, angiogenesis, arginylation as a posttranslational modification, transcriptional regulation of ..
  10. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2013
    ..participant in the synchronized expression of a single gene product by way of regulating, in succession, chromatin remodeling (ssDNA binding), transcription (dsDNA binding), splicing (ssDNA and ssRNA binding) and microRNA (..
  11. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..attracting comodulator protein/enzyme complexes that either repress or induce DNA transcription by chromatin remodeling and linkage to RNA polymerase II...
  12. Genistein, microRNAs and kidney cancer
    Rajvir Dahiya; Fiscal Year: 2013
    ..the mechanisms of activation of these tumor suppressor miRNAs are through modulation of histone acetylation and chromatin remodeling...
  13. Remodeling Neuronal Chromatin in Mouse Models for Depression
    Schahram Akbarian; Fiscal Year: 2013
    ..It has been suggested that chromatin remodeling mechanisms, including histone modification changes, play an important role for the neurobiology of ..
  14. Epigenetics of Sex Differences in Brain and Behavior
    BRIDGET NUGENT; Fiscal Year: 2012
    ..dinucleotides within a gene's promoter region via addition of a methyl group, resulting in changes in chromatin conformation and gene silencing...
  15. BIOSYNTHESIS OF TRACHEAL MUCOUS GLYCOPROTEINS
    Pi Wan Cheng; Fiscal Year: 2010
    ..They will be characterized by electrophoresis mobility shift assay and chromatin immunoprecipitation assay...
  16. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2013
    ..NHBE cells is regulated by epigenetic mechanisms, including changes in CpG island DNA methylation status and chromatin structure...
  17. Hepatic Steatosis Modulation by Apo B Gene Transcription
    JANET DEHOFF SPARKS; Fiscal Year: 2010
    ..will define 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...
  18. ICSBP Function During Myeloid Differentiation
    ELIZABETH ANN EKLUND; Fiscal Year: 2011
    ..During the previous funding period, we pursued identification of such target-genes. Using chromatin immuno-precipitation and CpG island microarray screening, we identified ICSBP- target-genes which encode ..
  19. New insights in mechanisms of renal injury
    Balakuntalam S Kasinath; Fiscal Year: 2013
    ..b>Chromatin immunoprecipitation (ChIP) assays will be performed to study GSK 3beta regulation of binding of Groucho, TCF/..
  20. Regulation of microRNA-375 by cyclic-AMP in pancreatic beta-cells
    DAVID MATTHEW KELLER; Fiscal Year: 2010
    ..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 ..
  21. MOLECULAR MECHANISMS OF COMPLEX MIXTURE TOXICITY
    Alvaro Puga; Fiscal Year: 2013
    ..DNMT1 complexes to promoter chromatin and inhibiting phosphorylation, acetylation and methylation epigenetic marks established by BaP-induced gene ..
  22. Chronic Stress and Abdominal Pain: Novel Mechanisms
    John W Wiley; Fiscal Year: 2013
    ..changes in gene function without changes in the DNA sequence via DNA methylation, histone modification and chromatin remodeling...
  23. Regulation of the Vibrio cholerae intestinal exit plan
    ANISIA J SILVA BENITEZ; Fiscal Year: 2010
    ..we propose 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...
  24. 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-..
  25. Epigenomic Events in Development of the Locus Coeruleus Noradrenergic Neurons
    Jan Krzysztof Blusztajn; Fiscal Year: 2012
    ..We will integrate this novel information into a framework defined by chromatin state maps and developmental gene expression profiles of LCNN...
  26. 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 ..
  27. MOLECULAR MECHANISMS OF DIOXIN ACTION
    Alvaro Puga; Fiscal Year: 2013
    ..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 ..
  28. Bioflavonoid Effects on EGF Signaling and Cell Cycle Pathways in Prostate Cancer
    BARRY MATTHEW MARKAVERICH; Fiscal Year: 2013
    ..L modulation of EGF Signaling and Cell Cycle Pathway genes was also confirmed in DU-145 prostate cancer cells. Chromatin immunoprecipitation (ChIP) studies revealed that L reduced the acetylation state of histone H4 (at Lys 5, 8, 12, ..
  29. Interplay Between Tissue Architecture and Nuclear Organization in the DNA Damage
    Pierre Alexandre Vidi; Fiscal Year: 2013
    ..NuMA is rapidly phosphorylated upon DNA damage, is necessary for the maintenance of H2AX phosphorylation (a chromatin mark at DSBs), and interacts with the WICH chromatin remodeling complex that functions in the DDR...
  30. MECHANISMS OF RADIORESISTANCE AND CELL CYCLE PROGRESSION
    Howard B Lieberman; Fiscal Year: 2013
    ..on three hypotheses: 1) DNMT1 and DNMT3b are highly expressed in certain prostate cancer cell lines because of chromatin structure, promoter methylation abnormalities or mutation, and bind more tightly to Rad9 only in DU145, AVLA31 ..
  31. Novel genomic effects of Y-linked polymorphisms
    Daniel L Hartl; Fiscal Year: 2012
    ..of Y-linked sequences that compete with the autosomal and X-linked genes for binding with limiting amounts of chromatin-associated proteins that affect levels of gene expression...
  32. PTEN TUMOR SUPPRESSOR AND SIGNAL TRANSDUCTION
    RAMON E PARSONS; Fiscal Year: 2012
    ..A combination of overexpression, RNAi, and chromatin immuno- precipitation experiments are planned to identify the mechanism of activation...
  33. ROLE OF SIRTUIN IN CIGARETTE SMOKE-INDUCED LUNG INFLAMMATION AND INJURY
    Irfan Rahman; Fiscal Year: 2013
    ..information regulator 2) which is equivalent to human sirtuin1 (SIRT1) is essential for maintaining silent chromatin via the deacetylation of histones and non-histone proteins...
  34. Regulation of NFkappaB activity by the Estrogen Receptor
    Kendall W Nettles; Fiscal Year: 2012
    ..suppression 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 ..
  35. The Role of Vascular MR-Regulated Genes in Vascular Function and Disease
    Iris Z Jaffe; Fiscal Year: 2013
    ..pathways in aldo-stimulated injury and atherosclerosis will also be investigated using chromatin immunoprecipitation in vessels from these mouse models...
  36. Molecular Biology of Human Erythrocyte Alpha Spectrin
    Patrick G Gallagher; Fiscal Year: 2013
    ..this proposal is to identify and characterize the cis-sequences, trans-factors, and epigenetic state, including chromatin architecture, across the ?-spectrin gene locus that regulate its expression in erythroid and nonerythroid cells...
  37. Epigenetic effects of developmental endocrine disruptor exposure in the ovary
    Mehmet Uzumcu; Fiscal Year: 2010
    ..changes by bisulfite sequencing and how these changes may interfere with the transcription factor binding using chromatin immunoprecipitation assay...
  38. Histone Chaperones in Angiogenesis
    Soumen Paul; Fiscal Year: 2012
    ..cells, we examined molecular mechanisms that mediate alteration of the nucleoprotein structure at the Vegfr1 chromatin domain. In particular, we were interested about the alteration of histone modification patterns...
  39. Pax8-PPARgamma regulation of transcription and metabolism in thyroid cancer
    RONALD JAY KOENIG; Fiscal Year: 2013
    ..In the first Specific Aim, chromatin immunoprecipitation - deep sequencing (ChIP-Seq) will be used to identify PPFP binding sites on a genome wide ..
  40. Improving Epigenetic-based Cell Reprogramming with Proteasome Inhibition
    Jaroslaw Staszkiewicz; Fiscal Year: 2011
    ..NuPotential has developed several methods to reprogram somatic cells to a pluripotent state by * modifying chromatin structure to induce expression of silenced pluripotency genes...
  41. Transplacental Arsenic Induced Hepatic Dysfunction and Vascular Disease
    J Christopher States; Fiscal Year: 2010
    ..for the arsenic effect, and molecular studies of arsenic exposure induced changes in DNA methylation, chromatin structure, gene expression and genetic imprinting...
  42. Epigenetic Analysis of iPS Cell Models of Aging and Alzheimer's Disease
    Bruce A Yankner; Fiscal Year: 2010
    ..of cell death genes, synaptic genes and genes encoding proteins involved in epigenetic modification of chromatin. Moreover, some of these changes also appear in the expression profile of the prefrontal cortex in AD...
  43. 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 ..
  44. 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...
  45. Intermediary Metabolism, Histone Acetylation, and Transcriptional Regulation
    Ales Vancura; Fiscal Year: 2013
    ..Histone acetylation is a dynamic modification that affects chromatin structure and regulates diverse cellular functions, such as gene expression, DNA repair, and cell proliferation...
  46. The Role of MYST Histone Acetyltransferase in Genome Stability
    M Mitchell Smith; Fiscal Year: 2013
    ..specifically expose its essential function, and characterize phenotypes, gene expression patterns, and promoter chromatin structure under nonpermissive conditions...
  47. Regulation of Genomic and Epigenomic Stability at CpG Sites
    Alfonso Bellacosa; Fiscal Year: 2013
    ..Organisms also establish and regulate the proper chromatin states/DNA methylation patterns at CpG sites (epigenomic stability)...
  48. Mechanism(s) of Hepatocyte Transformation by the Hepatitis B Virus X Protein
    Ourania M Andrisani; Fiscal Year: 2013
    ..SUZ12 and ZNF198 mediate chromatin remodeling and associate with PML nuclear bodies (NBs) that regulate DNA repair, apoptosis and viral replication...
  49. Abnormal Bladder Epithelial Cell Gene Expression in BPS/IC
    SUSAN F KEAY; Fiscal Year: 2013
    ..experiments showed abnormal BPS/IC bladder epithelial cell expression of several differentiation proteins plus a chromatin remodeling protein, recent studies were performed which determined that BPS/IC cells indeed display an abnormal ..
  50. Analysis of epigenetic regulation in early mammalian embryos via RNA interference
    Charles R Long; Fiscal Year: 2010
    ..refers to differential patterns of gene expression based solely on the physical and biochemical properties of chromatin, without a change in DNA sequence...
  51. Roles of RNA Polymerases IV and V in siRNA-mediated gene silencing
    CRAIG STUART PIKAARD; Fiscal Year: 2013
    ..siRNA-AGO4 complexes bind to these Pol V transcripts, facilitating recruitment of AGO4 to the adjacent chromatin. In subsequent steps that are not understood, the de novo DNA methyltransferase, DRM2 and histone modifying ..
  52. Mechanisms of TGFB Signal Transduction
    Akiko Hata; Fiscal Year: 2013
    ..of proteins composed of serum response factor (SRF) and coactivators, such as MRTFs (MRTF-A or MRTF-B), and chromatin remodeling factor Brg1, which binds to a DNA element named "CArG box"...
  53. Protein composition and interactions of telemeric chromatin
    Michael P Killoran; Fiscal Year: 2010
    ..Protection of telomeres and regulation of telomerase relies on a specialized, but still poorly understood, chromatin structure at the chromosome terminus...
  54. Mechanisms of innate immune response modulation by mechanical ventilation
    William A Altemeier; Fiscal Year: 2012
    ..3) Determine 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 ..
  55. 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 ..
  56. 14th International Workshop on Ataxia-Telangiectasia and ATM
    Richard A Gatti; Fiscal Year: 2010
    ..of the meeting will include the role of ATM and related proteins in the DNA damage response, the importance of chromatin and genomic instability in the activation of ATM, the role of ATM in the developing nervous system and in ..
  57. 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 ..
  58. Regulation of Bile Acid Synthesis by Nuclear Receptors
    John Y L Chiang; Fiscal Year: 2010
    ..The specific aim 1 will study nuclear receptor and co-regulator modulation of CYP7A1 and CYP8B1 chromatin. The roles of HNF4? and FTP, and their co-regulators Prox1, PGC-1?, histone deacetylase (HDAC) and silencing ..
  59. B Cell Development in Aging
    John C Cambier; Fiscal Year: 2010
    ..This sequence of events is controlled, in part, by chromatin accessibility of the genes involved in these processes...
  60. REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDS
    Peter B Dervan; Fiscal Year: 2013
    ..determining transcription factor-DNA interactions on a genome-wide scale;most notably through the coupling of chromatin immunoprecipitation to massively parallel sequencing (ChIP-Seq)...
  61. SATB1-dependent epigenetic regulation of leukemia initiating cells
    Britta Will; Fiscal Year: 2011
    ..We and others have identified a particular chromatin remodeling factor, special AT-rich sequence-binding protein 1 (SATB1) as an important epigenetic factor ..
  62. Chromatin Modifications and Vulnerability to Glutamate Toxicity
    ALEXEI D KONDRATYEV; Fiscal Year: 2010
    ..This proposal will examine these mechanisms and will lay the foundation for identification of new targets for therapy of a broad variety of neurological conditions relevant to excitotoxicity. ..
  63. Reading the histone code:nanoscale morphology of Epigneomic Histone Modifications
    M Mitchell Smith; Fiscal Year: 2010
    ..Specific Challenge Topic: 06-GM-101 Structural Analysis of Macromolecular Complexes. A major challenge in chromatin biology and molecular cytology is how to study the macromolecular structures of specific epigenetic chromatin ..
  64. DNA Topology In TBP/DNA Complexes: Chromatin Connections
    Jason Kahn; Fiscal Year: 2004
    ..In eukaryotes, DNA packaging into chromatin generally represses transcription...
  65. Heterochromatin on the human inactive X chromosome
    Brian P Chadwick; Fiscal Year: 2012
    ..Unexpectedly, the X-linked macrosatellite DXZ4 is packaged into the opposite chromatin arrangement than that of the surrounding chromosome...
  66. CHROMATIN HISTONE MODIFICATIONS AND HMG PROTEINS
    EDWIN BRADBURY; Fiscal Year: 1992
    The chromatin loop or domain model suggests that loops have structural roles in the organization of chromosomes and functional roles in determining the units of eukaryotic gene expression and their functional states...
  67. Effect of chromatin remodelers/modifiers on HIV-1 Tat activated transcription
    Fatah Kashanchi; Fiscal Year: 2010
    ..The long-term goal of our research is to understand how the chromatin environment, Tat, and chromatin remodelers/modifiers cooperate to influence HIV-1 transcription...
  68. Novel Epigenetic Marks in Mitosis
    KENNETH S contact ZARET; Fiscal Year: 2010
    ..to determine how different kinds of new epigenetic marks are distributed and stabilized specifically in mitotic chromatin. While many transcription factors, co-regulators, and histone modifications exist in interphase chromatin and ..
  69. Chromatin and Coactivators in HSV-1 gene regulation
    STEVEN TRIEZENBERG; Fiscal Year: 2009
    Eukaryotic genomes are packaged in chromatin, a nucleoprotein complex containing DNA, histones, and nonhistone chromosomal proteins...
  70. The Role of PARP-1 in Hormone-Regulated Transcription
    William Kraus; Fiscal Year: 2007
    ..we are interested how the activity of ERa is modulated by its associated coregulatory proteins in the chromatin environment of the nucleus...
  71. In Vitro Reconstitution of Alpha Fetroprotein Regulation
    Michelle Barton; Fiscal Year: 2007
    ..test the hypotheses that (Specific Aim I) aberrant loss of regulated AFP repression is the result of altered chromatin structure, (Specific Aim II) multiple proteins interact to establish specific chromatin structures that preclude ..
  72. ANALYSIS OF CHROMATIN REMODELING IN MAMMARY GLAND DEVELOPMENT USING TILING ARRAYS
    Monique Rijnkels; Fiscal Year: 2009
    The interplay between chromatin structure and transcriptional regulators has an important role in gene regulation throughout development and differentiation...
  73. HNF3-mediated chromatin remodeling: A role in liver gene regulation
    SARAH E KOHLER; Fiscal Year: 2010
    ..For these genes to be turned on, chromatin must be de-compacted to allow transcription factors access to the DNA template...
  74. Regulation of DNA Metabolism During Herpes Simplex Virus-1 Infection
    KEVIN FRANCIS BRYANT; Fiscal Year: 2010
    The goal of the research in this application is to understand the mechanisms involved in chromatin-mediated regulation of gene expression...