Genomes and Genes
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.
Publications326 found, 100 shown here
- The accessible chromatin landscape of the human genomeRobert 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...
- High-resolution profiling of histone methylations in the human genomeArtem 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...
- Mapping and analysis of chromatin state dynamics in nine human cell typesJason Ernst
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 473:43-9. 2011b>Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity...
- Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasisRajnish 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...
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan 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...
- Role of histone H3 lysine 27 methylation in Polycomb-group silencingRu 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 ..
- Topological domains in mammalian genomes identified by analysis of chromatin interactionsJesse 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...
- CTCF: master weaver of the genomeJennifer 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 ..
- HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variantsLucas 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...
- Translating the histone codeT Jenuwein
Research Institute of Molecular Pathology IMP at the Vienna Biocenter, Dr Bohrgasse 7, A 1030 Vienna, Austria
Science 293:1074-80. 2001b>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...
- Capturing chromosome conformationJob 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...
- Regulation of chromatin by histone modificationsAndrew J Bannister
The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK
Cell Res 21:381-95. 2011b>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...
- CpG islands and the regulation of transcriptionAimée 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...
- Systematic localization of common disease-associated variation in regulatory DNAMatthew 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...
- An oestrogen-receptor-alpha-bound human chromatin interactomeMelissa 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 ..
- Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammalsMitchell 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...
- Systematic protein location mapping reveals five principal chromatin types in Drosophila cellsGuillaume J Filion
Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
Cell 143:212-24. 2010b>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...
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controlsJoel Rozowsky
Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
Nat Biotechnol 27:66-75. 2009b>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 ..
- DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139E 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...
- Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domainsManching Ku
Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
PLoS Genet 4:e1000242. 2008In 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...
- Comprehensive analysis of the chromatin landscape in Drosophila melanogasterPeter V Kharchenko
Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 471:480-5. 2011b>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...
- Identification of functional elements and regulatory circuits by Drosophila modENCODESushmita 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...
- A map of the cis-regulatory sequences in the mouse genomeYin 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...
- Mechanisms of polycomb gene silencing: knowns and unknownsJeffrey A Simon
Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis 55455, USA
Nat Rev Mol Cell Biol 10:697-708. 2009Polycomb proteins form chromatin-modifying complexes that implement transcriptional silencing in higher eukaryotes...
- A unique chromatin signature uncovers early developmental enhancers in humansAlvaro 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 ..
- Comprehensive mapping of long-range interactions reveals folding principles of the human genomeErez 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...
- CTCF-mediated functional chromatin interactome in pluripotent cellsLusy 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...
- Mediator and cohesin connect gene expression and chromatin architectureMichael 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...
- Megabase chromatin domains involved in DNA double-strand breaks in vivoE 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.
- Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAsJohn 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...
- Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastomaJeremy 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)...
- Release of chromatin protein HMGB1 by necrotic cells triggers inflammationPaola 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...
- Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectMark 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...
- Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readersMichiel Vermeulen
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
Cell 142:967-80. 2010Trimethyl-lysine (me3) modifications on histones are the most stable epigenetic marks and they control chromatin-mediated regulation of gene expression...
- Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expressionAhmad 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...
- The role of chromatin during transcriptionBing Li
Stowers Medical Research Institute, 1000 East 50 th Street, Kansas City, MO 64110, USA
Cell 128:707-19. 2007b>Chromatin structure imposes significant obstacles on all aspects of transcription that are mediated by RNA polymerase II...
- The complex language of chromatin regulation during transcriptionShelley L Berger
The Wistar Institute, 3601 Spruce Street, Room 201, Philadelphia, Pennsylvania 19104, USA
Nature 447:407-12. 2007An 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 ..
- A high-resolution map of the three-dimensional chromatin interactome in human cellsFulai 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...
- Genome-wide maps of chromatin state in pluripotent and lineage-committed cellsTarjei 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 ..
- 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.
- Regulation of alternative splicing by histone modificationsReini 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...
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genomeMichael 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.
- CpG islands influence chromatin structure via the CpG-binding protein Cfp1John 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...
- Selective inhibition of BET bromodomainsPanagis 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'...
- Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domainA 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...
- High-resolution mapping and characterization of open chromatin across the genomeAlan 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...
- Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysisF 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 ..
- Differential chromatin marking of introns and expressed exons by H3K36me3Paulina Kolasinska-Zwierz
The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
Nat Genet 41:376-81. 2009Variation in patterns of methylations of histone tails reflects and modulates chromatin structure and function...
- A bivalent chromatin structure marks key developmental genes in embryonic stem cellsBradley 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.
- Functional and mechanistic diversity of distal transcription enhancersMichael 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...
- Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cellsOren Ram
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Cell 147:1628-39. 2011Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure...
- Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cellsYoshimasa 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...
- Histone acetylation in chromatin structure and transcriptionM 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...
- Chromatin-IgG complexes activate B cells by dual engagement of IgM and Toll-like receptorsElizabeth 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-..
- Activating RNAs associate with Mediator to enhance chromatin architecture and transcriptionFan 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...
- Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopyLothar 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 ..
- The dynamic architecture of Hox gene clustersDaan 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 ..
- The language of histone crosstalkJung 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.
- Genomic instability and aging-like phenotype in the absence of mammalian SIRT6Raul 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. 2006The Sir2 histone deacetylase functions as a chromatin silencer to regulate recombination, genomic stability, and aging in budding yeast...
- Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying putJeffrey A Simon
Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
Mol Cell 49:808-24. 2013b>Chromatin modification by Polycomb proteins provides an essential strategy for gene silencing in higher eukaryotes...
- Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulatorsAkihiro 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...
- Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulationRadha 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 ..
- The biology of chromatin remodeling complexesCedric 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, ..
- Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genesGillian 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...
- The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatinTakashi 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...
- Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotesMaya 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....
- Transcriptional architecture and chromatin landscape of the core circadian clock in mammalsNobuya 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...
- A map of open chromatin in human pancreatic isletsKyle 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)...
- Histones: annotating chromatinEric 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. 2009b>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...
- MicroRNA genes are transcribed by RNA polymerase IIYoontae 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...
- Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulationGuoliang 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 ..
- Heritable individual-specific and allele-specific chromatin signatures in humansRyan 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. 2010The 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...
- In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like stateMarius 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...
- Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicityChristine 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...
- Extensive variation in chromatin states across humansMaya 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 ..
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genomeNathaniel 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 ..
- LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcriptionEric Metzger
Universitäts Frauenklinik und Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, 79106 Freiburg, Germany
Nature 437:436-9. 2005Gene regulation in eukaryotes requires the coordinate interaction of chromatin-modulating proteins with specific transcription factors such as the androgen receptor...
- Long noncoding RNA as modular scaffold of histone modification complexesMiao Chih Tsai
Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Science 329:689-93. 2010Long 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...
- A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulationsSreenath 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...
- Histone H4-K16 acetylation controls chromatin structure and protein interactionsMichael Shogren-Knaak
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Science 311:844-7. 2006Acetylation of histone H4 on lysine 16 (H4-K16Ac) is a prevalent and reversible posttranslational chromatin modification in eukaryotes...
- Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant actionNadia 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 ..
- Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domainsSuresh 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...
- Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domainsVardhman 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...
- Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemiaMark 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...
- Chromatin accessibility pre-determines glucocorticoid receptor binding patternsSam 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...
- Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cellsMatthew G Guenther
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
Cell Stem Cell 7:249-57. 2010Knowledge 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 ..
- How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickersSean D Taverna
Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
Nat Struct Mol Biol 14:1025-40. 2007Histones 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...
- Regulation of nucleosome dynamics by histone modificationsGabriel E Zentner
Fred Hutchinson Cancer Research Center, Basic Sciences Division, Seattle, Washington, USA
Nat Struct Mol Biol 20:259-66. 2013b>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...
- Chromatin signatures of pluripotent cell linesVeronique 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...
- DNase I sensitivity QTLs are a major determinant of human expression variationJacob 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 ..
- A cis-regulatory map of the Drosophila genomeNicolas 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. 2011Systematic 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 ..
- Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associationsYuBo 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...
- Chromatin-Remodeling Components of the BAF Complex Facilitate ReprogrammingNishant 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 ..
- Biased chromatin signatures around polyadenylation sites and exonsNoah Spies
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
Mol Cell 36:245-54. 2009Core 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...
- Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2Aditi 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...
- Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identityLingyun 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 ..
- Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicingRobert 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...
- Chromatin structure analyses identify miRNA promotersFatih 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...
- Dissecting the regulatory circuitry of a eukaryotic genomeF 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...
- Distinct epigenomic landscapes of pluripotent and lineage-committed human cellsR 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 ..
- Genetic variation and regulatory networks: Mechanisms and complexityDANA PE ER; Fiscal Year: 2009..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
- Transcription factors regulating sensory gene expression and pain pathwaysEric E Turner; Fiscal Year: 2011..We will also examine chromatin modifications at the Islet1 target gene loci. Aim 3...
- Regulation of HSV-1 Gene Expression and Replication by Nuclear Hormone ReceptorsSHAOCHUNG 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 ..
- Role of the Y-Located TSPY Gene in Human OncogenesisYun 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...
- MECHANISMS IN THE REGULATION OF SP-A GENE EXPRESSIONCarole R Mendelson; Fiscal Year: 2013..modifications in histone phosphorylation, acetylation and methylation that likely cause profound changes in chromatin structure...
- Vitamin D3, Interference with Androgen Signal and Inhibition of Prostate CancerBandana Chatterjee; Fiscal Year: 2013..Transcription factors WSTF and E47 occupied regulated chromatin in response to androgen...
- Discovery of Small Molecule MBT Domain AntagonistsSTEPHEN 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 ..
- The role of Fli1 in T cell function and the pathogenesis of lupusTamara 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 ..
- 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 ..
- Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C FamilyJohn 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 (..
- Vitamin D Hormone Signaling in Bone Mineral HomeostasisMark 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...
- Genistein, microRNAs and kidney cancerRajvir Dahiya; Fiscal Year: 2013..the mechanisms of activation of these tumor suppressor miRNAs are through modulation of histone acetylation and chromatin remodeling...
- Remodeling Neuronal Chromatin in Mouse Models for DepressionSchahram Akbarian; Fiscal Year: 2013..It has been suggested that chromatin remodeling mechanisms, including histone modification changes, play an important role for the neurobiology of ..
- Epigenetics of Sex Differences in Brain and BehaviorBRIDGET 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...
- BIOSYNTHESIS OF TRACHEAL MUCOUS GLYCOPROTEINSPi Wan Cheng; Fiscal Year: 2010..They will be characterized by electrophoresis mobility shift assay and chromatin immunoprecipitation assay...
- Regulation of Airway Mucin Gene Expression by Epigenetic MechanismReen Wu; Fiscal Year: 2013..NHBE cells is regulated by epigenetic mechanisms, including changes in CpG island DNA methylation status and chromatin structure...
- Hepatic Steatosis Modulation by Apo B Gene TranscriptionJANET 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...
- ICSBP Function During Myeloid DifferentiationELIZABETH 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 ..
- New insights in mechanisms of renal injuryBalakuntalam S Kasinath; Fiscal Year: 2013..b>Chromatin immunoprecipitation (ChIP) assays will be performed to study GSK 3beta regulation of binding of Groucho, TCF/..
- Regulation of microRNA-375 by cyclic-AMP in pancreatic beta-cellsDAVID 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 ..
- MOLECULAR MECHANISMS OF COMPLEX MIXTURE TOXICITYAlvaro Puga; Fiscal Year: 2013..DNMT1 complexes to promoter chromatin and inhibiting phosphorylation, acetylation and methylation epigenetic marks established by BaP-induced gene ..
- Chronic Stress and Abdominal Pain: Novel MechanismsJohn W Wiley; Fiscal Year: 2013..changes in gene function without changes in the DNA sequence via DNA methylation, histone modification and chromatin remodeling...
- Regulation of the Vibrio cholerae intestinal exit planANISIA 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...
- FOXP3-microRNA146-NFkB Axis in Tumor SuppressionLizhong Wang; Fiscal Year: 2013..We will use chromatin immunoprecipitation, electrophoretic mobility shift assay and luciferase reporter assays as well as site-..
- Epigenomic Events in Development of the Locus Coeruleus Noradrenergic NeuronsJan 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...
- An Aldosterone-Endothelin Feedback Mechanism on Sodium HomeostasisCharles 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 ..
- MOLECULAR MECHANISMS OF DIOXIN ACTIONAlvaro 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 ..
- Bioflavonoid Effects on EGF Signaling and Cell Cycle Pathways in Prostate CancerBARRY 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, ..
- Interplay Between Tissue Architecture and Nuclear Organization in the DNA DamagePierre 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...
- MECHANISMS OF RADIORESISTANCE AND CELL CYCLE PROGRESSIONHoward 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 ..
- Novel genomic effects of Y-linked polymorphismsDaniel 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...
- PTEN TUMOR SUPPRESSOR AND SIGNAL TRANSDUCTIONRAMON E PARSONS; Fiscal Year: 2012..A combination of overexpression, RNAi, and chromatin immuno- precipitation experiments are planned to identify the mechanism of activation...
- ROLE OF SIRTUIN IN CIGARETTE SMOKE-INDUCED LUNG INFLAMMATION AND INJURYIrfan 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...
- Regulation of NFkappaB activity by the Estrogen ReceptorKendall 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 ..
- The Role of Vascular MR-Regulated Genes in Vascular Function and DiseaseIris 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...
- Molecular Biology of Human Erythrocyte Alpha SpectrinPatrick 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...
- Epigenetic effects of developmental endocrine disruptor exposure in the ovaryMehmet Uzumcu; Fiscal Year: 2010..changes by bisulfite sequencing and how these changes may interfere with the transcription factor binding using chromatin immunoprecipitation assay...
- Histone Chaperones in AngiogenesisSoumen 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...
- Pax8-PPARgamma regulation of transcription and metabolism in thyroid cancerRONALD 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 ..
- Improving Epigenetic-based Cell Reprogramming with Proteasome InhibitionJaroslaw 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...
- Transplacental Arsenic Induced Hepatic Dysfunction and Vascular DiseaseJ 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...
- Epigenetic Analysis of iPS Cell Models of Aging and Alzheimer's DiseaseBruce 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...
- Epithelial differentiation in corneaBogi 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 ..
- Neuropeptide regulation of neurohypophyseal functionFrancis W Flynn; Fiscal Year: 2012..Co-immunoprecipitation and chromatin immunoprecipitation will be used to identify the nuclear targets of nuclear NK3R...
- Intermediary Metabolism, Histone Acetylation, and Transcriptional RegulationAles 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...
- The Role of MYST Histone Acetyltransferase in Genome StabilityM Mitchell Smith; Fiscal Year: 2013..specifically expose its essential function, and characterize phenotypes, gene expression patterns, and promoter chromatin structure under nonpermissive conditions...
- Regulation of Genomic and Epigenomic Stability at CpG SitesAlfonso Bellacosa; Fiscal Year: 2013..Organisms also establish and regulate the proper chromatin states/DNA methylation patterns at CpG sites (epigenomic stability)...
- Mechanism(s) of Hepatocyte Transformation by the Hepatitis B Virus X ProteinOurania 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...
- Abnormal Bladder Epithelial Cell Gene Expression in BPS/ICSUSAN 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 ..
- Analysis of epigenetic regulation in early mammalian embryos via RNA interferenceCharles 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...
- Roles of RNA Polymerases IV and V in siRNA-mediated gene silencingCRAIG 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 ..
- Mechanisms of TGFB Signal TransductionAkiko 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"...
- Protein composition and interactions of telemeric chromatinMichael 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...
- Mechanisms of innate immune response modulation by mechanical ventilationWilliam 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 ..
- Regulation of apoptosis by PI 3-kinase/Akt signalingGeoffrey 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 ..
- 14th International Workshop on Ataxia-Telangiectasia and ATMRichard 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 ..
- Cellular and Molecular Regulation of ThrombopoiesisRamesh A Shivdasani; Fiscal Year: 2012..We have combined chromatin immunoprecipitation with hybridization to tiled genome arrays (ChIP-chip) to identify the complete complement of ..
- Regulation of Bile Acid Synthesis by Nuclear ReceptorsJohn 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 ..
- B Cell Development in AgingJohn C Cambier; Fiscal Year: 2010..This sequence of events is controlled, in part, by chromatin accessibility of the genes involved in these processes...
- REGULATION OF GENE EXPRESSION BY DNA BINDING LIGANDSPeter 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)...
- SATB1-dependent epigenetic regulation of leukemia initiating cellsBritta 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 ..
- Chromatin Modifications and Vulnerability to Glutamate ToxicityALEXEI 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. ..
- Reading the histone code:nanoscale morphology of Epigneomic Histone ModificationsM 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 ..
- DNA Topology In TBP/DNA Complexes: Chromatin ConnectionsJason Kahn; Fiscal Year: 2004..In eukaryotes, DNA packaging into chromatin generally represses transcription...
- Heterochromatin on the human inactive X chromosomeBrian P Chadwick; Fiscal Year: 2012..Unexpectedly, the X-linked macrosatellite DXZ4 is packaged into the opposite chromatin arrangement than that of the surrounding chromosome...
- CHROMATIN HISTONE MODIFICATIONS AND HMG PROTEINSEDWIN BRADBURY; Fiscal Year: 1992The 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...
- Effect of chromatin remodelers/modifiers on HIV-1 Tat activated transcriptionFatah 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...
- Novel Epigenetic Marks in MitosisKENNETH 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 ..
- Chromatin and Coactivators in HSV-1 gene regulationSTEVEN TRIEZENBERG; Fiscal Year: 2009Eukaryotic genomes are packaged in chromatin, a nucleoprotein complex containing DNA, histones, and nonhistone chromosomal proteins...
- The Role of PARP-1 in Hormone-Regulated TranscriptionWilliam 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...
- In Vitro Reconstitution of Alpha Fetroprotein RegulationMichelle 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 ..
- ANALYSIS OF CHROMATIN REMODELING IN MAMMARY GLAND DEVELOPMENT USING TILING ARRAYSMonique Rijnkels; Fiscal Year: 2009The interplay between chromatin structure and transcriptional regulators has an important role in gene regulation throughout development and differentiation...
- HNF3-mediated chromatin remodeling: A role in liver gene regulationSARAH 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...
- Regulation of DNA Metabolism During Herpes Simplex Virus-1 InfectionKEVIN FRANCIS BRYANT; Fiscal Year: 2010The goal of the research in this application is to understand the mechanisms involved in chromatin-mediated regulation of gene expression...