Summary: The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.

Top Publications

  1. ncbi Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex
    D D Sarbassov
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 307:1098-101. 2005
  2. ncbi ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    Shuhei Matsuoka
    Department of Genetics and Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Science 316:1160-6. 2007
  3. pmc iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
    Julian König
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 17:909-15. 2010
  4. pmc HITS-CLIP yields genome-wide insights into brain alternative RNA processing
    Donny D Licatalosi
    Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 456:464-9. 2008
  5. pmc Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1
    Dragana Ahel
    DNA Damage Response Laboratory, Clare Hall, London Research Institute, South Mimms EN6 3LD, UK
    Science 325:1240-3. 2009
  6. pmc MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action
    Jiayu Wen
    The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
    RNA 17:820-34. 2011
  7. pmc Experimental strategies for microRNA target identification
    Daniel W Thomson
    Centre for Cancer Biology, SA Pathology, Frome Road Adelaide, South Australia 5000, Australia
    Nucleic Acids Res 39:6845-53. 2011
  8. pmc Proteolytic cleavage in an endolysosomal compartment is required for activation of Toll-like receptor 9
    Boyoun Park
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02115, USA
    Nat Immunol 9:1407-14. 2008
  9. ncbi Inhibition of MDM2-mediated p53 ubiquitination and degradation by ribosomal protein L5
    Mu Shui Dai
    Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon 97201, USA
    J Biol Chem 279:44475-82. 2004
  10. pmc Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing
    Yoshinao Ruike
    Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 20 Yoshida Shimoadachi cho Sakyo ku, Kyoto 606 8501, Japan
    BMC Genomics 11:137. 2010

Detail Information

Publications418 found, 100 shown here

  1. ncbi Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex
    D D Sarbassov
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 307:1098-101. 2005
    ..Rictor-mTOR may serve as a drug target in tumors that have lost the expression of PTEN, a tumor suppressor that opposes Akt/PKB activation...
  2. ncbi ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    Shuhei Matsuoka
    Department of Genetics and Center for Genetics and Genomics, Brigham and Women s Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Science 316:1160-6. 2007
    ..This database paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals...
  3. pmc iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
    Julian König
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 17:909-15. 2010
    ..Here, we developed individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) to study the role of hnRNP C in splicing regulation...
  4. pmc HITS-CLIP yields genome-wide insights into brain alternative RNA processing
    Donny D Licatalosi
    Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 456:464-9. 2008
    ..of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP)...
  5. pmc Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1
    Dragana Ahel
    DNA Damage Response Laboratory, Clare Hall, London Research Institute, South Mimms EN6 3LD, UK
    Science 325:1240-3. 2009
    ..Furthermore, we show that depletion or overexpression of ALC1 results in sensitivity to DNA-damaging agents. Collectively, these results provide new insights into the mechanisms by which poly(ADP-ribose) regulates DNA repair...
  6. pmc MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action
    Jiayu Wen
    The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
    RNA 17:820-34. 2011
    ..expression analyses following miRNA transfection/inhibition and, more recently, Argonaute cross-linked immunoprecipitation (CLIP)-seq assays have been used to detect miRNA target sites...
  7. pmc Experimental strategies for microRNA target identification
    Daniel W Thomson
    Centre for Cancer Biology, SA Pathology, Frome Road Adelaide, South Australia 5000, Australia
    Nucleic Acids Res 39:6845-53. 2011
    ..This review summarizes and critiques the existing experimental techniques for miRNA target identification...
  8. pmc Proteolytic cleavage in an endolysosomal compartment is required for activation of Toll-like receptor 9
    Boyoun Park
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02115, USA
    Nat Immunol 9:1407-14. 2008
    ..Lysosomal proteolysis thus contributes to innate immunity by facilitating specific cleavage of TLR9...
  9. ncbi Inhibition of MDM2-mediated p53 ubiquitination and degradation by ribosomal protein L5
    Mu Shui Dai
    Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon 97201, USA
    J Biol Chem 279:44475-82. 2004
    ..Actinomycin D-induced p53 was inhibited by small interference RNA against L5. By reciprocal co-immunoprecipitation, we further showed that there were at least two MDM2-ribosomal protein complexes in cells: MDM2-L5-L11-L23 ..
  10. pmc Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing
    Yoshinao Ruike
    Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46 20 Yoshida Shimoadachi cho Sakyo ku, Kyoto 606 8501, Japan
    BMC Genomics 11:137. 2010
    ..However, the mechanisms that underlie methylome changes are not well understood nor is the genomic distribution of DNA methylation changes well characterized...
  11. pmc Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    Sung Wook Chi
    Laboratory of Molecular Neuro Oncology and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 460:479-86. 2009
    ..Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites...
  12. doi A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
    Shivendra Kishore
    Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
    Nat Methods 8:559-64. 2011
    Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins...
  13. pmc Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
    Lukas Chavez
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, D 14195 Berlin, Germany
    Genome Res 20:1441-50. 2010
    The generation of genome-wide data derived from methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) has become a major tool for epigenetic studies in health and disease...
  14. doi Experimental identification of microRNA targets by immunoprecipitation of Argonaute protein complexes
    Michaela Beitzinger
    Laboratory for RNA Biology, Center for Integrated Protein Science Munich CIPSM, Max Planck Institute of Biochemistry, Martinsried, Germany
    Methods Mol Biol 732:153-67. 2011
    ..Here we provide a detailed protocol for isolation and identification of miRNA target mRNAs from immunoprecipitated human Ago protein complexes...
  15. ncbi GINS maintains association of Cdc45 with MCM in replisome progression complexes at eukaryotic DNA replication forks
    Agnieszka Gambus
    Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
    Nat Cell Biol 8:358-66. 2006
    ..GINS is also important for the normal progression of DNA replication forks, and we show that it is required after initiation to maintain the association between MCM and Cdc45 within RPCs...
  16. ncbi RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
    Jack D Keene
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    Nat Protoc 1:302-7. 2006
    ..The approach outlined here, termed RNP immunoprecipitation-microarray (RIP-Chip), allows the identification of discrete subsets of RNAs associated with multi-targeted ..
  17. ncbi c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I
    Carla Grandori
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Nat Cell Biol 7:311-8. 2005
    ..We propose that stimulation of rRNA synthesis by c-Myc is a key pathway driving cell growth and tumorigenesis...
  18. doi A molecular determinant for the establishment of sister chromatid cohesion
    Elcin Unal
    Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218, USA
    Science 321:566-9. 2008
    ..Smc3 head acetylation and its cell cycle regulation provide important insights into the biology and mechanism of cohesion establishment...
  19. ncbi CLIP: a method for identifying protein-RNA interaction sites in living cells
    Jernej Ule
    Howard Hughes Medical Institute and the Laboratory of Molecular Neuro Oncology, The Rockefeller University, New York, USA
    Methods 37:376-86. 2005
    ..We have developed the cross-linking and immunoprecipitation assay, which exploits the covalent protein-nucleic acid cross-linking to stringently purify a specific ..
  20. doi Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
    Shalima S Nair
    Epigenetics Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
    Epigenetics 6:34-44. 2011
    ..compared two commonly used approaches to enrich for methylated DNA regions of the genome, namely methyl-DNA immunoprecipitation (MeDIP) that is based on enrichment with antibodies specific for 5'-methylcytosine (5MeC), and capture of ..
  21. ncbi The Mad1/Mad2 complex as a template for Mad2 activation in the spindle assembly checkpoint
    Anna De Antoni
    Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano, Italy
    Curr Biol 15:214-25. 2005
    ..These events are linked to the existence of two distinct conformers of Mad2: a closed conformer bound to its kinetochore receptor Mad1 or its target in the checkpoint Cdc20 and an open conformer unbound to these ligands...
  22. pmc 14-3-3 binding to LRRK2 is disrupted by multiple Parkinson's disease-associated mutations and regulates cytoplasmic localization
    R Jeremy Nichols
    University of Dundee, Scotland, UK
    Biochem J 430:393-404. 2010
    ..These results provide the first evidence suggesting that 14-3-3 regulates LRRK2 and that disruption of the interaction of LRRK2 with 14-3-3 may be linked to Parkinson's disease...
  23. ncbi A critical role of cavin (polymerase I and transcript release factor) in caveolae formation and organization
    Libin Liu
    Department of Biochemistry, Boston University Medical School, Boston, Massachusetts 02118, USA
    J Biol Chem 283:4314-22. 2008
    ..We propose that the presence of cavin on the inside surface of caveolae stabilizes these structures, probably through interaction with the cytoskeleton, and cavin therefore plays an important role in caveolae formation and organization...
  24. pmc Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development
    Gunnar R Mair
    Leiden Malaria Research Group, Department of Parasitology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
    PLoS Pathog 6:e1000767. 2010
    ..Through RNA-immunoprecipitation and global expression profiling of CITH-KO mutants we highlight CITH as a crucial repressor of maternally ..
  25. pmc PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
    David L Corcoran
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Genome Biol 12:R79. 2011
    Crosslinking and immunoprecipitation (CLIP) protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular, PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking...
  26. pmc Sec24b selectively sorts Vangl2 to regulate planar cell polarity during neural tube closure
    Janna Merte
    The Solomon H Snyder Department of Neuroscience and Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205, USA
    Nat Cell Biol 12:41-6; sup pp 1-8. 2010
    ..Thus, during COPII vesicle formation, Sec24b shows cargo specificity for a core PCP component, Vangl2, of which proper ER-to-Golgi transport is essential for the establishment of PCP, convergent extension and closure of the neural tube...
  27. ncbi High-throughput mapping of a dynamic signaling network in mammalian cells
    Miriam Barrios-Rodiles
    Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
    Science 307:1621-5. 2005
    ..We show that Occludin regulates TGFbeta type I receptor localization for efficient TGFbeta-dependent dissolution of tight junctions during epithelial-to-mesenchymal transitions...
  28. pmc GxxxG motifs within the amyloid precursor protein transmembrane sequence are critical for the etiology of Abeta42
    Lisa Marie Munter
    Institut fur Chemie und Biochemie, Freie Universitat Berlin, Berlin, Germany
    EMBO J 26:1702-12. 2007
    ..The results demonstrate that dimerization of APP TMS is a risk factor for AD due to facilitating Abeta42 production...
  29. pmc Dysregulation of mTOR signaling in fragile X syndrome
    Ali Sharma
    Dominick P Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, New York 10461, USA
    J Neurosci 30:694-702. 2010
    ..Elevated mTOR signaling may provide a functional link between overactivation of group I mGluRs and aberrant synaptic plasticity in the fragile X mouse, mechanisms relevant to impaired cognition in fragile X syndrome...
  30. doi Methylated DNA immunoprecipitation (MeDIP)
    Fabio Mohn
    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
    Methods Mol Biol 507:55-64. 2009
    Methylated DNA immunoprecipitation (MeDIP) is a versatile immunocapturing approach for unbiased detection of methylated DNA...
  31. pmc The Plasmodium circumsporozoite protein is proteolytically processed during cell invasion
    Alida Coppi
    Department of Medical and Molecular Parasitology, New York University School of Medicine, New York, NY 10010, USA
    J Exp Med 201:27-33. 2005
    ..Inhibitors of CSP processing inhibit cell invasion in vitro, and treatment of mice with E-64, a highly specific cysteine protease inhibitor, completely inhibits sporozoite infectivity in vivo...
  32. pmc VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases
    Takumi Kamura
    Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi ku, Fukuoka, Fukuoka 812 8582, Japan
    Genes Dev 18:3055-65. 2004
    ..These data suggest that the functions of the Cul2-Rbx1 and Cul5-Rbx2 modules are distinct...
  33. pmc HITS-CLIP: panoramic views of protein-RNA regulation in living cells
    Robert B Darnell
    Laboratory of Neuro Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, NY 10065, USA
    Wiley Interdiscip Rev RNA 1:266-86. 2010
    ..Examples of the successes, limitations, and future of the technique will be discussed...
  34. pmc Persistently activated Stat3 maintains constitutive NF-kappaB activity in tumors
    Heehyoung Lee
    Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
    Cancer Cell 15:283-93. 2009
    ..Both murine and human cancers display highly acetylated RelA, which is associated with Stat3 activity. This Stat3/NF-kappaB interaction is thus central to both the transformed and nontransformed elements in tumors...
  35. pmc Profiling of UV-induced ATM/ATR signaling pathways
    Matthew P Stokes
    Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA
    Proc Natl Acad Sci U S A 104:19855-60. 2007
    ..differentially phosphorylated upon UV damage, some of which were confirmed by SILAC, Western blotting, and immunoprecipitation/Western blotting...
  36. pmc Negative regulation of the deacetylase SIRT1 by DBC1
    Wenhui Zhao
    Institute for Cancer Genetics, and Department of Pathology College of Physicians and Surgeons, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA
    Nature 451:587-90. 2008
    ..Notably, these effects can be reversed in cells by concomitant knockdown of endogenous SIRT1. Our study demonstrates that DBC1 promotes p53-mediated apoptosis through specific inhibition of SIRT1...
  37. ncbi Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation
    David E Nowak
    The University of Texas Medical Branch, Galveston 77555 1060, USA
    Biotechniques 39:715-25. 2005
    The chromatin immunoprecipitation (ChIP) assay has recently been exploited as a powerful and versatile technique for probing protein-DNA interactions within the chromatin environment...
  38. doi Arabidopsis RNA immunoprecipitation
    Lionel C Terzi
    Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee DD25EH, UK
    Plant J 59:163-8. 2009
    ..In order to facilitate the functional characterization of RNA-binding proteins, we have applied the RNA immunoprecipitation assay to Arabidopsis...
  39. pmc Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps
    Chyi Ying A Chen
    Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas, USA
    Nat Struct Mol Biol 16:1160-6. 2009
    ..These findings indicate that promotion of biphasic deadenylation to trigger mRNA decay is an intrinsic property of miRISCs...
  40. pmc Large-scale mapping of human protein-protein interactions by mass spectrometry
    Rob M Ewing
    Protana, Toronto, Ontario, Canada
    Mol Syst Biol 3:89. 2007
    ..Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification ..
  41. doi Protein kinase CK2 regulates the formation and clearance of aggresomes in response to stress
    Masahiko Watabe
    Department of Pharmacology, Teikyo University School of Medicine, Tokyo 173 8605, Japan
    J Cell Sci 124:1519-32. 2011
    ..These findings identify CK2 as a crucial protein involved in the formation and clearance of aggresomes, and hence in cell viability in response to misfolded protein stress...
  42. pmc Quantitative evaluation of siRNA delivery in vivo
    Yi Pei
    Department of RNA Therapeutics, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
    RNA 16:2553-63. 2010
    ..This is achieved by specific immunoprecipitation of the RISC from tissue lysates and quantification of small RNAs in the immunoprecipitates by stem-loop PCR...
  43. pmc Excess phosphoinositide 3-kinase subunit synthesis and activity as a novel therapeutic target in fragile X syndrome
    Christina Gross
    Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
    J Neurosci 30:10624-38. 2010
    ..Targeting excessive PI3K activity might thus be a potent therapeutic strategy for FXS...
  44. ncbi AHNAK, a novel component of the dysferlin protein complex, redistributes to the cytoplasm with dysferlin during skeletal muscle regeneration
    Yanchao Huang
    Center for Human and Clinical Genetics, Leiden Univesity Medical Center, Leiden, The Netherlands
    FASEB J 21:732-42. 2007
    ..It may also have significant implications for understanding the biology of AHNAK-containing exocytotic vesicles, "enlargosomes," in plasma membrane remodeling and repair...
  45. pmc A luciferase immunoprecipitation systems assay enhances the sensitivity and specificity of diagnosis of Strongyloides stercoralis infection
    Roshan Ramanathan
    Clinical Parasitology Unit and Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Infect Dis 198:444-51. 2008
    We investigated whether luciferase immunoprecipitation systems (LIPS) can be the basis for a more rapid, specific, and standardized assay for the diagnosis of Strongyloides stercoralis infection.
  46. pmc Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors
    Loyal A Goff
    Rutgers Stem Cell Research Center, Rutgers University, Piscataway, New Jersey, United States of America
    PLoS ONE 4:e7192. 2009
  47. pmc A multifunctional human Argonaute2-specific monoclonal antibody
    Sabine Rüdel
    Center for Integrated Protein Science Munich, Laboratory of RNA Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
    RNA 14:1244-53. 2008
    ..We show that anti-Ago2(11A9) is specific for human Ago2 and detects Ago2 in Western blots as well as in immunoprecipitation experiments...
  48. ncbi Chromatin immunoprecipitation in postmortem brain
    Hsien Sung Huang
    Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA 01604, USA
    J Neurosci Methods 156:284-92. 2006
    ..Furthermore, chromatin immunoprecipitation protocols applicable to postmortem tissue are lacking, and the impact of potential confounds such as ..
  49. ncbi Immunoprecipitation of mRNA-protein complexes
    Tiina Peritz
    Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
    Nat Protoc 1:577-80. 2006
    b>Immunoprecipitation of mRNA-protein complexes is a method that can be used to study RNA binding protein (RBP)-RNA interactions...
  50. pmc CHOP induces death by promoting protein synthesis and oxidation in the stressed endoplasmic reticulum
    Stefan J Marciniak
    Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
    Genes Dev 18:3066-77. 2004
    ..CHOP deletion thus protects cells from ER stress by decreasing ER client protein load and changing redox conditions within the organelle...
  51. ncbi Baf60c is essential for function of BAF chromatin remodelling complexes in heart development
    Heiko Lickert
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
    Nature 432:107-12. 2004
  52. pmc Multiple repeat elements within the FAM21 tail link the WASH actin regulatory complex to the retromer
    Da Jia
    Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
    Mol Biol Cell 23:2352-61. 2012
    ..We propose that multivalency enables FAM21 to sense the density of retromer on membranes, allowing coordination of SHRC recruitment, and consequent actin polymerization, with retromer sorting domain organization/maturation...
  53. pmc ATR and ATM differently regulate WRN to prevent DSBs at stalled replication forks and promote replication fork recovery
    Francesca Ammazzalorso
    Department of Environment and Primary Prevention, Section of Experimental and Computational Carcinogenesis and Section of Molecular Epidemiology, Istituto Superiore di Sanita, Rome, Italy
    EMBO J 29:3156-69. 2010
    ..Altogether, our findings indicate that ATR and ATM promote recovery from perturbed replication by differently regulating WRN at defined moments of the response to replication fork arrest...
  54. pmc BLOC-1 interacts with BLOC-2 and the AP-3 complex to facilitate protein trafficking on endosomes
    Santiago M Di Pietro
    Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
    Mol Biol Cell 17:4027-38. 2006
    ..These findings support the idea that BLOC-1 and -2 represent hitherto unknown components of the endosomal protein trafficking machinery...
  55. pmc Two PABPC1-binding sites in GW182 proteins promote miRNA-mediated gene silencing
    Eric Huntzinger
    Department of Biochemistry, Max Planck Institute for Developmental Biology, Tubingen, Germany
    EMBO J 29:4146-60. 2010
    ..Our findings reveal that despite species-specific differences in the relative strength of the PABPC1-binding sites, the interaction between GW182 proteins and PABPC1 is critical for miRNA-mediated silencing in animal cells...
  56. pmc The novel cargo Alcadein induces vesicle association of kinesin-1 motor components and activates axonal transport
    Yoichi Araki
    Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
    EMBO J 26:1475-86. 2007
    ..Inappropriate interactions of Alc- and APP-containing vesicles with kinesin-1 may promote aberrant APP metabolism in Alzheimer's disease...
  57. ncbi Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation [corrected]
    Chuan Jin Wu
    Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nat Cell Biol 8:398-406. 2006
    ..These results provide a mechanism for NEMO's critical role in IKK activation, and a key to understanding the link between cytokine-receptor proximal signalling and IKK and NF-kappaB activation...
  58. pmc Kaposi's sarcoma-associated herpesvirus ORF57 promotes escape of viral and human interleukin-6 from microRNA-mediated suppression
    Jeong Gu Kang
    Tumor Virus RNA Biology Laboratory, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, 10 Center Dr, Rm 6N106, Bethesda, MD 20892 1868, USA
    J Virol 85:2620-30. 2011
    ..Here, we report genome-wide analysis of viral RNA targets of KSHV ORF57 by a novel UV-cross-linking and immunoprecipitation (CLIP) assay...
  59. ncbi Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms
    Rageen Rajendram
    Program in Biological Sciences, University of Toronto, Ontario, Canada
    Epigenetics 6:410-5. 2011
    In this study, we verified the accuracy of two array methods--methylated DNA immunoprecipitation coupled with CpG island microarrays (MeDIP-CGI-arrays) and sodium bisulfite conversion based microarrays (BC-arrays)--in predicting regional ..
  60. pmc Dysferlin interacts with histone deacetylase 6 and increases alpha-tubulin acetylation
    Sabrina Di Fulvio
    Neuromuscular Research Group, Departments of Neurology and Biomedicine, University, Hospital, Basel, Switzerland
    PLoS ONE 6:e28563. 2011
    ..This study suggests a novel role for dysferlin in myogenesis and identifies HDAC6 as a novel dysferlin-interacting protein...
  61. pmc The R1441C mutation of LRRK2 disrupts GTP hydrolysis
    Patrick A Lewis
    Laboratory of Neurogenetics, National Institute on Aging, 35 Convent Drive, Bethesda, MD 20892 3707, USA
    Biochem Biophys Res Commun 357:668-71. 2007
    ..We show that LRRK2 immunoprecipitated from cells has a detectable GTPase activity that is disrupted by a familial mutation associated with PD located within the GTPase domain, R1441C...
  62. ncbi Proteomics exploration reveals that actin is a signaling target of the kinase Akt
    Franck Vandermoere
    ERI 8 Inserm JE 2488, University of Sciences and Technologies Lille, Villeneuve d Ascq, France
    Mol Cell Proteomics 6:114-24. 2007
    ..The interaction between Akt and actin was further confirmed by reverse immunoprecipitation, and confocal microscopy demonstrated a co-localization specifically induced under growth factor ..
  63. doi NMDA receptor-mediated PIP5K activation to produce PI(4,5)P₂ is essential for AMPA receptor endocytosis during LTD
    Takamitsu Unoki
    Department of Physiological Chemistry, Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, 1 1 1 Ten nohdai, Tsukuba 305 8571, Japan
    Neuron 73:135-48. 2012
    ..Furthermore, knockdown of PIP5Kγ661 inhibited the NMDA-induced AMPA receptor endocytosis. Therefore, NMDA receptor activation controls AMPA receptor endocytosis during hippocampal LTD by regulating PIP5Kγ661 activity at postsynapses...
  64. pmc Functional analysis of the leading malaria vaccine candidate AMA-1 reveals an essential role for the cytoplasmic domain in the invasion process
    Moritz Treeck
    Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
    PLoS Pathog 5:e1000322. 2009
    ..We show that the cytoplasmic domain of AMA-1 is phosphorylated. Mutational analysis suggests an important role for the phosphorylation in the invasion process, which might translate into novel therapeutic strategies...
  65. pmc Tcl1 interacts with Atm and enhances NF-κB activation in hematologic malignancies
    Eugenio Gaudio
    Department of Molecular Immunology, Virology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
    Blood 119:180-7. 2012
    ..Our findings reveal functional cross-talk between Atm and Tcl1 and provide evidence for a novel pathway that could be targeted in leukemias and lymphomas...
  66. pmc An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
    Gene W Yeo
    Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Mol Biol 16:130-7. 2009 RNA map for the cell type-specific splicing regulator FOX2 (also known as RBM9) via cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells...
  67. ncbi Axonal transport, amyloid precursor protein, kinesin-1, and the processing apparatus: revisited
    Orly Lazarov
    Department of Neurobiology, Pharmacology, and Physiology, The University of Chicago, Chicago, Illinois 60637, USA
    J Neurosci 25:2386-95. 2005
  68. pmc TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing
    Astrid D Haase
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4508 Basel, Switzerland
    EMBO Rep 6:961-7. 2005
    ..The TRBP-Dicer interaction shown raises interesting questions about the potential interplay between RNAi and interferon-PKR pathways...
  69. pmc BLM and the FANC proteins collaborate in a common pathway in response to stalled replication forks
    Pietro Pichierri
    UPR2169 CNRS, Genetic Instability and Cancer, Institut Gustave Roussy, Pavillon de Recherche, rue Camille Desmoulins, Villejuif, France
    EMBO J 23:3154-63. 2004
  70. pmc The HtrA-like serine protease PepD interacts with and modulates the Mycobacterium tuberculosis 35-kDa antigen outer envelope protein
    Mark J White
    Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
    PLoS ONE 6:e18175. 2011
    ..We postulate that proteolytic cleavage of the 35-kDa antigen by PepD helps maintain cell wall homeostasis in Mycobacterium and regulates specific stress response pathways during periods of extracytoplasmic stress...
  71. doi LRP2 is an auxiliary SHH receptor required to condition the forebrain ventral midline for inductive signals
    Annabel Christ
    Max Delbruck Center for Molecular Medicine, Charite Universitatsmedizin, D 13125 Berlin, Germany
    Dev Cell 22:268-78. 2012
    ..Our data identify a critical role for LRP2 in SHH signaling and reveal the molecular mechanism underlying forebrain anomalies in mice and patients with Lrp2 defects...
  72. pmc Effective identification of Akt interacting proteins by two-step chemical crosslinking, co-immunoprecipitation and mass spectrometry
    Bill X Huang
    Laboratory of Molecular Signaling, National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 8:e61430. 2013
    ..Identification of Akt-interacting proteins has been customarily achieved by co-immunoprecipitation combined with western blot and/or MS analysis...
  73. doi Enrichment of methylated DNA by methyl-CpG immunoprecipitation
    Miriam Sonnet
    Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center DKFZ, Heidelberg, Germany
    Methods Mol Biol 971:201-12. 2013
    ..Methyl-CpG Immunoprecipitation (MCIp) employs an immobilized recombinant human methyl-CpG binding domain protein 2, MBD2, which binds ..
  74. pmc Entamoeba histolytica cysteine proteinase 5 binds integrin on colonic cells and stimulates NFkappaB-mediated pro-inflammatory responses
    YongZhong Hou
    Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Centre, Calgary, Alberta T2N 4N1, Canada
    J Biol Chem 285:35497-504. 2010
    ..histolytica trophozoites use to trigger an inflammatory response in the pathogenesis of intestinal amebiasis...
  75. doi The NMDA receptor subunit GluN3A protects against 3-nitroproprionic-induced striatal lesions via inhibition of calpain activation
    Rebeca Martinez-Turrillas
    Cellular Neurobiology Laboratory, Centro de Investigación Médica Aplicada CIMA, Pamplona, Spain
    Neurobiol Dis 48:290-8. 2012
  76. doi Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma
    Alex Cazes
    INSERM U830, Institut Curie, Centre de Recherche, Paris, France
    Cancer Res 73:195-204. 2013
    ..These results indicate that genomic rearrangements constitute an alternative mechanism to ALK point mutations resulting in receptor activation...
  77. pmc A handcuff model for the cohesin complex
    Nenggang Zhang
    Department of Pediatric Hematology Oncology, Texas Children s Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
    J Cell Biol 183:1019-31. 2008
    ..These data support a two-ring handcuff model for the cohesin complex, which is flexible enough to establish and maintain sister chromatid cohesion as well as ensure the fidelity of chromosome segregation in higher eukaryotes...
  78. pmc The adaptor function of TRAPPC2 in mammalian TRAPPs explains TRAPPC2-associated SEDT and TRAPPC9-associated congenital intellectual disability
    Min Zong
    School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People s Republic of China
    PLoS ONE 6:e23350. 2011
    ..Here, we reveal that the mammalian equivalent of the TRAPPII complex is structurally distinct from the yeast counterpart thus leading to insight into mechanism of disease...
  79. doi Physical and functional crosstalk between Fanconi anemia core components and the GINS replication complex
    Emanuela Tumini
    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
    DNA Repair (Amst) 10:149-58. 2011
    ..We found, by yeast two-hybrid assay and co-immunoprecipitation in human cells, that the core complex subunit FANCF physically interacts with PSF2, a member of the GINS ..
  80. pmc Critical role of PI3K signaling for NF-kappaB-dependent survival in a subset of activated B-cell-like diffuse large B-cell lymphoma cells
    Bernhard Kloo
    Department of Cellular Signal Integration, German Research Center for Environmental Health, Institute of Toxicology, 85764 Neuherberg, Germany
    Proc Natl Acad Sci U S A 108:272-7. 2011
    ..These results demonstrate a critical function of PI3K-PDK1 signaling upstream of MALT1 protease and NF-κB in distinct ABC DLBCL cells and provide a rationale for the pharmacologic use of PI3K inhibitors in DLBCL therapy...
  81. pmc Dynamic interactions of high Cdt1 and geminin levels regulate S phase in early Xenopus embryos
    Jolanta Kisielewska
    University of Newcastle, The Institute for Cell and Molecular Biosciences, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
    Development 139:63-74. 2012
    ..b>Immunoprecipitation of Cdt1 and geminin complexes, together with their cell cycle spatiotemporal dynamics, strongly supports ..
  82. pmc MUC1-C oncoprotein promotes STAT3 activation in an autoinductive regulatory loop
    Rehan Ahmad
    Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Sci Signal 4:ra9. 2011
    ..These findings indicate that MUC1-C promotes STAT3 activation and that MUC1-C and STAT3 function in an autoinductive loop that may play a role in cancer cell survival...
  83. pmc O-GlcNAcylation increases ChREBP protein content and transcriptional activity in the liver
    Céline Guinez
    INSERM, U1016, Institut Cochin, Paris, France
    Diabetes 60:1399-413. 2011
  84. pmc Toward an understanding of the protein interaction network of the human liver
    Jian Wang
    State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
    Mol Syst Biol 7:536. 2011
    ..Our data represent the first comprehensive description of a HLPN, which could be a valuable tool for understanding the functioning of the protein interaction network of the human liver...
  85. ncbi The Dbf4 motif C zinc finger promotes DNA replication and mediates resistance to genotoxic stress
    Darryl R Jones
    Department of Biology, University of Waterloo, Waterloo, ON, Canada
    Cell Cycle 9:2018-26. 2010
    ..These results support a model whereby DDK interaction with Mcm2 is important to stabilize and/or restart replication forks during conditions where a prolonged S-phase checkpoint is triggered...
  86. pmc The chaperone activity of heat shock protein 90 is critical for maintaining the stability of leucine-rich repeat kinase 2
    Lizhen Wang
    Unit of Transgenesis, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland 20892, USA
    J Neurosci 28:3384-91. 2008
    ..Therefore, inhibition of LRRK2 kinase activity can be achieved by blocking Hsp90-mediated chaperone activity and Hsp90 inhibitors may serve as potential anti-PD drugs...
  87. doi Methylation analysis by DNA immunoprecipitation
    Kelsie L Thu
    Department of Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
    J Cell Physiol 222:522-31. 2010
    ..b>Immunoprecipitation (IP)-based methods to evaluate methylation status of DNA have been instrumental in such genome-wide ..
  88. ncbi Involvement of Matrin 3 and SFPQ/NONO in the DNA damage response
    Maayan Salton
    Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
    Cell Cycle 9:1568-76. 2010
    ..Collectively the data suggest that SFPQ, NONO and MATR3 are involved in the early stage of the DSB response, setting the scene for DSB repair...
  89. pmc Individual microRNAs (miRNAs) display distinct mRNA targeting "rules"
    Wang Xia Wang
    Department of Pathology, University of Kentucky Medical Center, Lexington, KY, USA
    RNA Biol 7:373-80. 2010
    ..Here we isolated AGO- and miRNA-containing miRNPs from human H4 tumor cells by co-immunoprecipitation (co-IP) with anti-AGO antibody...
  90. pmc Optineurin negatively regulates the induction of IFNbeta in response to RNA virus infection
    Jamel Mankouri
    Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
    PLoS Pathog 6:e1000778. 2010
    ..b>Immunoprecipitation and immunofluorescence studies identified optineurin in a protein complex containing the antiviral protein ..
  91. pmc SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production
    Tadahiro Shimazu
    Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
    Cell Metab 12:654-61. 2010
    ..Our findings show SIRT3 regulates ketone body production during fasting and provide molecular insight into how protein acetylation can regulate enzymatic activity...
  92. 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
    ..Chromatin immunoprecipitation analyses demonstrate that androgen receptor and LSD1 form chromatin-associated complexes in a ligand-..
  93. doi Whole genome DNA methylation analysis based on high throughput sequencing technology
    Ning Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
    Methods 52:203-12. 2010
    ..two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq)...
  94. ncbi The DIX domain of Dishevelled confers Wnt signaling by dynamic polymerization
    Thomas Schwarz-Romond
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Struct Mol Biol 14:484-92. 2007
  95. pmc Prion disease blood test using immunoprecipitation and improved quaking-induced conversion
    Christina D Orru
    Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
    MBio 2:e00078-11. 2011
    ..Now we have integrated antibody 15B3-based immunoprecipitation with QuIC reactions to increase sensitivity and isolate prions from inhibitors such as those in plasma ..
  96. ncbi Bruton's tyrosine kinase and phospholipase Cgamma2 mediate chemokine-controlled B cell migration and homing
    David J J de Gorter
    Department of Pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
    Immunity 26:93-104. 2007
  97. pmc Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes
    Wang Xia Wang
    Department of Pathology and Laboratory Medicine, University of Kentucky Medical Center, Lexington, Kentucky, 40506 9983, USA
    RNA 16:394-404. 2010
    ..Here we employed a biochemical approach to isolate AGO-containing miRNPs from human H4 tumor cells by co-immunoprecipitation (co-IP) with a previously described anti-AGO antibody...
  98. ncbi The short apical membrane half-life of rescued {Delta}F508-cystic fibrosis transmembrane conductance regulator (CFTR) results from accelerated endocytosis of {Delta}F508-CFTR in polarized human airway epithelial cells
    Agnieszka Swiatecka-Urban
    Department of Physiology, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
    J Biol Chem 280:36762-72. 2005
  99. pmc Disulphide production by Ero1α-PDI relay is rapid and effectively regulated
    Christian Appenzeller-Herzog
    Department of Biology, University of Copenhagen, Copenhagen, Denmark
    EMBO J 29:3318-29. 2010
    ..Instead, our data suggest that a dynamic equilibrium between Ero1- and glutathione disulphide-mediated oxidation of PDIs constitutes an important element of ER redox homeostasis...
  100. doi MicroRNA122 is a key regulator of α-fetoprotein expression and influences the aggressiveness of hepatocellular carcinoma
    Kentaro Kojima
    Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo 113 8655, Japan
    Nat Commun 2:338. 2011
  101. pmc Breast cancer-specific mutations in CK1epsilon inhibit Wnt/beta-catenin and activate the Wnt/Rac1/JNK and NFAT pathways to decrease cell adhesion and promote cell migration
    Silvie Foldynová-Trantírková
    Biology Centre AS CR, V, V, I, and University of South Bohemia, Branisovska 31, Ceske Budejovice, Czech Republic
    Breast Cancer Res 12:R30. 2010
    ..Because CK1epsilon is a crucial regulator of the Wnt signaling cascades, we determined how these CK1epsilon mutations interfere with the Wnt pathway and affect the behavior of epithelial breast cancer cell lines...

Research Grants71

  1. Role of the Y-Located TSPY Gene in Human Oncogenesis
    Yun Fai Chris Lau; Fiscal Year: 2013
    ..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...
    Carole R Mendelson; Fiscal Year: 2013
    ..Using chromatin immunoprecipitation, we will analyze temporal changes in in vivo recruitment of key transcription factors and coregulators to ..
  3. Gamma-Synuclein-Mediated Regulation of Norepinephrine Transporter
    Anita Sidhu; Fiscal Year: 2010
    ..Co-immunoprecipitation studies will be conducted to measure interactions between -Syn and microtubule binding proteins [MAPs, tau] ..
  4. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
    ..control mice will be analyzed by identifying proteins binding the endogenous Fli1 promoter using chromatin immunoprecipitation (IP) and analyses of expression levels, post-translational modifications and interactions with co-factors ..
  5. Role of Polyamines in MYCN-Amplified Neuroblastoma
    ANDRE BACHMANN; Fiscal Year: 2009
    ..Northern blot, RT-PCR, nuclear run-ons, messenger RNA half-life studies, Western blot, yeast two-hybrid, co-immunoprecipitation, GST-pull down, site-directed mutagenesis, DNA cloning, confocal laser microscopy, enzyme and in vitro ..
  6. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2013
    ..on the cells responsible for 1,25- dihydroxyvitamin D and estradiol-driven bone growth;2) employ new RNA immunoprecipitation and micro- RNA methodology to study the versatility of these hnRNPS to control transcript splicing and ..
  7. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..Methodology will include genomics and chromatin immunoprecipitation (ChIP) assays to scan for candidate VDREs, plus DNA gel mobility shift, real time PCR and promoter ..
  8. Rac GTPase signaling during embryonic salivary gland branching morphogenesis
    Sharon Sequeira; Fiscal Year: 2012 factor;GTPase, guanosine triphosphate hydroxylase;IB, immunoblotting;IF, immunofluorescence;IP, immunoprecipitation;Par, partitioning-defective proteins;PLGA, polylactic-co-glycolic acid polymer;Rac1, Ras-related C3 ..
  9. Role and Regulation of INrf2
    ANIL KUMAR JAISWAL; Fiscal Year: 2013
    ..b>Immunoprecipitation and mass spectra analysis demonstrated interaction of INrf2 also with Phosphoglyerate mutase family member ..
  10. Remodeling Neuronal Chromatin in Mouse Models for Depression
    Schahram Akbarian; Fiscal Year: 2013 neuronal chromatin, (b) procedures to isolate neuronal chromatin from brain tissue, (c) chromatin immunoprecipitation followed by genome-wide profiling, (d) behavioral assays measuring despair and learned helplessness, ..
    Pi Wan Cheng; Fiscal Year: 2010
    ..They will be characterized by electrophoresis mobility shift assay and chromatin immunoprecipitation assay...
  12. Molecular Regulation of Progesterone Synthesis
    John S Davis; Fiscal Year: 2013
    ..liver receptor homolog-1) known to regulate StAR expression and progesterone synthesis we will perform co-immunoprecipitation and co-localization studies using mutant proteins...
  13. Hepatic Steatosis Modulation by Apo B Gene Transcription
    JANET DEHOFF SPARKS; Fiscal Year: 2010
    ..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...
  14. New insights in mechanisms of renal injury
    Balakuntalam S Kasinath; Fiscal Year: 2013
    ..Chromatin immunoprecipitation (ChIP) assays will be performed to study GSK 3beta regulation of binding of Groucho, TCF/LEF1 to the ..
  15. Regulation of Airway Mucin Gene Expression by Epigenetic Mechanism
    Reen Wu; Fiscal Year: 2013
    ..Chromatin immunoprecipitation (ChIP) approaches with anti-methylated deoxy-cytosine and various anti-modified histone antibodies will be ..
  16. 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 RNA labeling...
  17. Chronic Stress and Abdominal Pain: Novel Mechanisms
    John W Wiley; Fiscal Year: 2013
    ..identify putative regulatory CpG methylation sites at the promoters of stress response genes and chromatin immunoprecipitation (ChIP) analysis of relevant histone modification targets...
  18. Identification and Analysis of Flavivirus Protease and RNA Helicase Inhibitors
    Radhakrishnan Padmanabhan; Fiscal Year: 2009
    ..Inhibitors of interaction between NS3-RNA, NS3-NTP, NS3-NS5 will be analyzed by immunoprecipitation, surface plasmon resonance and gel shift assays...
  19. Regulation of the Vibrio cholerae intestinal exit plan
    ANISIA J SILVA BENITEZ; Fiscal Year: 2010
    ..test this hypothesis by integrating a variety of approaches such as bacterial genetics, chromatin immunoprecipitation (ChIP), ChiP-sequencing, confocal microscopy and animal models...
  20. Viral and Host Determinants of New World Alphaviral Entry
    ASIM AMINSHARIF AHMED; Fiscal Year: 2013
    ..through a series of binding and infection competitions, and identify specific cell surface receptors by immunoprecipitation with soluble alphaviral E2 receptor binding domains...
  21. FOXP3-microRNA146-NFkB Axis in Tumor Suppression
    Lizhong Wang; Fiscal Year: 2013
    ..We will use chromatin immunoprecipitation, electrophoretic mobility shift assay and luciferase reporter assays as well as site-directed mutagenesis ..
    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 differentiation...
  23. An Aldosterone-Endothelin Feedback Mechanism on Sodium Homeostasis
    Charles S Wingo; Fiscal Year: 2012
    ..The in vitro work will be extended by using DNase I hypersensitivity, chromatin immunoprecipitation, and DNA affinity purification assays to study the role of chromatin structure and transcription factor ..
  24. Bioflavonoid Effects on EGF Signaling and Cell Cycle Pathways in Prostate Cancer
    ..Chromatin immunoprecipitation (ChIP) studies revealed that L reduced the acetylation state of histone H4 (at Lys 5, 8, 12, 16) associated ..
  25. Nuclear-Cytoplasmic Shuttling of Foxc2 via 14-3-3 Determines Proximal Tubule Cell
    DIANA LYNNE GOLDEN; Fiscal Year: 2012
    ..will also be examined to determine if 14-3-3 modulates Foxc2 and [unreadable]-actinin interaction by co-immunoprecipitation. Inhibition of endogenous Foxc2 expression by siRNA transfection will be utilized to examine the effect of ..
  26. Characterization of epsilon-sarcoglycan interacting proteins in mouse brain
    Yuqing Li; Fiscal Year: 2012
    ..b>Immunoprecipitation of the ?-SG complex will be performed using specific monoclonal antibody against ?-SG followed by ..
  27. 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...
  28. Regulation of NFkappaB activity by the Estrogen Receptor
    Kendall W Nettles; Fiscal Year: 2012
    ..of NF-B, we will measure their recruitment to the MCP-1, IL-6, IL-8, MIP-1 and TNF-a genes by chromatin immunoprecipitation, and assay the effects of RNA interference targeting CBP and Grip1 on expression of the same genes...
  29. Diverse Roles for RIC8 During G Protein Signaling in Fungi
    Katherine A Borkovich; Fiscal Year: 2012
    ..Physical interactions between RIC8 and G proteins will be probed using co-immunoprecipitation. RIC8 will be tested for Ga GEF activity...
  30. Molecular Biology of Human Erythrocyte Alpha Spectrin
    Patrick G Gallagher; Fiscal Year: 2013
    ..Techniques to be utilized include chromatin immunoprecipitation experiments followed by array hybridization (ChIP-chip) or whole genome sequencing (ChIP-seq), high ..
  31. Epigenetic effects of developmental endocrine disruptor exposure in the ovary
    Mehmet Uzumcu; Fiscal Year: 2010
    ..sequencing and how these changes may interfere with the transcription factor binding using chromatin immunoprecipitation assay...
  32. 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 level...
  33. 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...
  34. Epithelial differentiation in cornea
    Bogi Andersen; Fiscal Year: 2012
    ..In the second Aim, we will use chromatin immunoprecipitation and transcription assays to define the molecular mechanisms whereby Clim regulate the expression of genes ..
    L Jeannine Brady; Fiscal Year: 2013
    ..translocation and its interaction with streptococcal ribosomes using chemical cross-linking and immunoprecipitation, and 3) to dissect the composition and interactions among the S. mutans secretion machinery components...
  36. Mechanisms of Angiogenesis in Retinopathy of Prematurity
    Mary Elizabeth Hartnett; Fiscal Year: 2009
    ..VEGF receptors 1 and 2, neuropilins;ELISA and Western blot to measure protein (VEGF; cleaved caspase-3);immunoprecipitation and probing to detect phosphorylated VEGF receptors, protein kinase [unreadable]II, JAKs, STATs;..
  37. Epigenetic Analysis of iPS Cell Models of Aging and Alzheimer's Disease
    Bruce A Yankner; Fiscal Year: 2010
    ..neurons will be performed using microarrays and by applying recent innovations in deep sequencing chromatin immunoprecipitation (ChIP- seq)...
  38. Hepatitis B virus replication and DDB1
    Betty L Slagle; Fiscal Year: 2013
    ..In Specific Aim 1, an immunoprecipitation/mass spectrometry (MS) approach will be used to identify the Cul4-DDB1-DCAF profile of uninfected human ..
  39. Mechanisms of Angiogenesis of Retinopathy of Prematurity
    ..VEGF receptors 1 and 2, neuropilins;ELISA and Western blot to measure protein (VEGF;cleaved caspase-3);immunoprecipitation and probing to detect phosphorylated VEGF receptors, protein kinase [unreadable]II, JAKs, STATs;..
  40. Regulation of apoptosis by PI 3-kinase/Akt signaling
    Geoffrey M Cooper; Fiscal Year: 2012
    ..Computational analysis of upstream regulatory regions combined with chromatin immunoprecipitation assays indicate that FOXO, NF[unreadable]B and Myc/Mad/Max transcription factors play major roles in ..
  41. Mechanisms of innate immune response modulation by mechanical ventilation
    William A Altemeier; Fiscal Year: 2012
    ..the role of AP-1 activation in ventilator-augmentation of LPS-induced inflammation by (a) using chromatin immunoprecipitation assay to identify which protein subunits of AP-1 are recruited to target gene promoters by mechanical ..
  42. KCNQ Channels and Vasoconstrictor Signal Transduction
    Kenneth L Byron; Fiscal Year: 2013
    ..Molecules associated with KCNQ channels in signaling complexes will be identified using co-immunoprecipitation with native or FLAG-tagged KCNQ channel proteins. 3...
  43. Cellular and Molecular Regulation of Thrombopoiesis
    Ramesh A Shivdasani; Fiscal Year: 2012
    ..We have combined chromatin immunoprecipitation with hybridization to tiled genome arrays (ChIP-chip) to identify the complete complement of genes that NF-..
  44. Regulation of Bile Acid Synthesis by Nuclear Receptors
    John Y L Chiang; Fiscal Year: 2010
    ..HepG2 and primary human hepatocytes will be used for chromatin immunoprecipitation (ChIP), co-IP and mammalian two-hybrid assays to study DNA-protein and protein-protein interaction...
    Peter B Dervan; Fiscal Year: 2013
    ..transcription factor-DNA interactions on a genome-wide scale;most notably through the coupling of chromatin immunoprecipitation to massively parallel sequencing (ChIP-Seq)...
  46. Structure and Function of the Hepatitis C Virus Genome
    Peter Sarnow; Fiscal Year: 2013
    ..Specifically, a cell-based crosslinking-immunoprecipitation (CLIP) assay will be employed to identify HCV and cellular RNA ligands for RIG-I...
  47. Mechanisms of Early Growth Response Factor 1 (Egr-1) Induction by HSV-1 Lytic Inf
    SHAOCHUNG VICTOR HSIA; Fiscal Year: 2010
    ..Chromatin Immunoprecipitation (ChIP) assays demonstrated that NFkB and cAMP response element binding protein (CREB) was induced by HSV-1 ..
  48. Regulation of IFN-beta induction by P2X7 purinergic receptor signaling
    JUDITH ANNE SMITH; Fiscal Year: 2011
    ..will examine the recruitment of transcription factors to the IFN- [unreadable] gene promoter by chromatin immunoprecipitation to test our underlying hypothesis that P2X7 ligation leads to increased transcription factor occupancy of ..
  49. Developing miRNA diagnostic methods and identifying tumor regulatory networks
    Thomas Tuschl; Fiscal Year: 2010
    ..of miRNA deregulation, we will apply our recently developed Photoreactive-Uridine-Enhanced Crosslinking and Immunoprecipitation (PURE- CLIP) method of miRNA-bound Argonaute protein complexes to identify the miRNA target sites in ..
  50. SATB1-dependent epigenetic regulation of leukemia initiating cells
    Britta Will; Fiscal Year: 2011
    ..We will utilize global chromatin immunoprecipitation analysis (ChIP-seq) in combination with gene expression and DNA methylation pattern analysis...
  51. AKAP Regulation of PKA Targeting in the Heart
    Meredith Bond; Fiscal Year: 2009
    ..cell cycle progression, apoptosis and survival, We identified Chd8 as an AKAP by phage display, by co- immunoprecipitation by the regulatory subunit RII of PKA;and disruption of RII binding by mutation of the RII binding site to ..
  52. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..To understand EBNA1 interactions with the host-chromosome, we used chromatin immunoprecipitation combined with next generation DNA sequencing (ChIP-Seq) and functional genomic methods to identify and ..
  53. Erythropoietin in Non-Erythroid Cells: Function and Regulation
    Josef T Prchal; Fiscal Year: 2013
    ..We have studied the mechanism of HIF regulation of Epo transcription using chromatin immunoprecipitation (ChIP) and have found multiple HREs of the Epo gene...
  54. Mechanisms of Astrocyte Development
    Teri L Belecky Adams; Fiscal Year: 2010
    ..determine interactions of BMP and SHH pathway members with other regulatory DNA-binding proteins such as co-immunoprecipitation, chromatin immunoprecipitation, and luciferase assays, 2) in vitro and in vivo manipulations of BMP ..
  55. Arsenic, Histone Modification, and Transcription
    LYNN SHELDON; Fiscal Year: 2009
    ..mammary tumor virus (MMTV) promoter in the presence and absence of sodium arsenite in vivo by chromatin immunoprecipitation (ChIP) analysis (Specific Aim I)...
  56. High-affinity RNA targets of Survival Motor Neuron Protein
    Ravindra N Singh; Fiscal Year: 2013
    ..analysis of transcriptome-wide interactions of SMN using powerful approaches of UV crosslinking and immunoprecipitation (CLIP) and high throughput sequencing...
  57. Modifiers of hepcidin expression as new therapies for iron overload
    PAULA GOODMAN FRAENKEL; Fiscal Year: 2013
    ..screen, we will characterize the modulators'effects on mammalian cellular iron transport, chromatin immunoprecipitation, RNA expression, and signaling pathways...
    ALBERT HONG JAE KIM; Fiscal Year: 2013
    ..neurons will be identified through a genome-wide search for cohesion binding sites through chromatin immunoprecipitation coupled with next generation sequencing and correlated cohesion- dependent microarray analyses...
  59. Mitochondrial Mechanisms of Programmed Necrosis in the Aged Female Heart
    Alexandra M Machikas; Fiscal Year: 2013
    ..The molecular basis of PN will be further analyzed using co- immunoprecipitation and co-localization methods...
  60. Role of estrogen-related receptors in cardiac and skeletal muscle
    Janice M Huss; Fiscal Year: 2010
    ..We will analyze these models with gene expression profiling coupled with chromatin immunoprecipitation to identify target genes for ERRs...
  61. VEGF Regulation of Hepatic Erythropoietin Synthesis
    Calvin Kuo; Fiscal Year: 2009
    ..Candidate factors (HIF proteins, HNF4, RXRalpha, GATA factors) will be directly tested by chromatin immunoprecipitation assays and functionally by adenoviral and transgenic expression of Cre to delete floxed alleles of relevant ..
  62. Regulation of the Endothelial Citrulline-Nitric Oxide Cycle
    Duane C Eichler; Fiscal Year: 2010
    ..To test this hypothesis, we will employ: 1) in vitro translation;2) RNA immunoprecipitation;3) RNA EMSA;4) polysome profiling analyses;5) stress granule formation and inhibition assays;and 6) ..
  63. A Cis-regulatory Model for Neural Border Induction
    Daniel Meulemans Medeiros; Fiscal Year: 2013
    ..The proposed work will test this model using mRNA injections, mutagenesis, and chromatin immunoprecipitation (ChIP)...
    Eseng Lai; Fiscal Year: 2001
    ..Co-immunoprecipitation/Western blot studies with tagged intermediates will be used to examine potential interactions between BF-1 ..
  65. Regulation of Epithelial Sodium Channel by CFTR chloride channel
    Bakhrom Berdiev; Fiscal Year: 2009
    ..determine the CFTR-ENaC interaction using Fluorescence Resonance Energy Transfer (FRET) microscopy and co-immunoprecipitation (co-IP)...
  66. Reading the histone code:nanoscale morphology of Epigneomic Histone Modifications
    M Mitchell Smith; Fiscal Year: 2010
    ..Biochemical techniques including mass spectroscopy, chromatin immunoprecipitation, and chromosome conformation capture, are making great strides in defining the functional combinations of ..
  67. 14 3 3 Implications in Topoisomerase II Pharmacology
    David Kroll; Fiscal Year: 2003
    ..Using reciprocal affinity chromatography and co-immunoprecipitation methods, we have shown that 14-3-3e, but NOT the G2 arrest protein 14-3-3E, directly binds human topo lla...
  68. Functional Characterization of Coxiella burnetii Dot/Icm Substrates
    Daniel E Voth; Fiscal Year: 2010
    ..These studies will involve the use of RT-PCR and co- immunoprecipitation approaches to elucidate effector activity during infection and intracellular growth...
    Raphael Kopan; Fiscal Year: 2010
    ..research (06-MH-103) Project Title: Development of Split-DamID as an alternative methodology to chromatin immunoprecipitation Project Abstract A wide variety of genetic or drug-induced mental health disorders have been linked to ..
  70. Role of p62 in Protein Aggregation and Neurodegeneration in ALS
    Haining Zhu; Fiscal Year: 2009
    ..Co-immunoprecipitation experiments showed that p62 specifically recognized mutant SOD1, but not the WT protein...
  71. High-Throughput Low Cost Production of Chromatin-Immunoprecipitation-Grade Antib
    KEITH ELLIOTT KROPP; Fiscal Year: 2010
    ..Chromatin immunoprecipitation (ChIP) coupled with microarray (ChIP-chip) or sequencing (ChIP- seq) is a widely used technique for ..