Gene Regulation: Methods and Protocols by Minou BinaGene Regulation: Methods and Protocols by Minou Bina

Gene Regulation: Methods and Protocols

EditorMinou Bina

Hardcover | February 23, 2013

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This volume offers cutting-edge technologies for studies of gene regulation. The chapters include introductions to their respective topics, lists of the necessary materials and reagents, and step-by-step, readily reproducible laboratory protocols.
Title:Gene Regulation: Methods and ProtocolsFormat:HardcoverDimensions:416 pages, 10 × 7.01 × 0.01 inPublished:February 23, 2013Publisher:Humana PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:1627032835

ISBN - 13:9781627032834

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Table of Contents

1. Gene RegulationMinou Bina  2. Isolation of Nuclei for use in Genome-wide DNase Hypersensitivity Assays to Probe Chromatin StructureGuoyu Ling and David J. Waxman 3. DNase I Digestion of Isolated Nulcei for Genome-Wide Mapping of DNase Hypersensitivity Sites in ChromatinGuoyu Ling and David J. Waxman  4. Isolation and Analysis of DNA Derived from Nucleosome-Free RegionsMatthew Murtha, Yatong Wang, Claudio Basilico, and Lisa Dailey 5. Acquisition of High Quality DNA for Massive Parallel Sequencing by in vivo Chromatin ImmunoprecipitationM. van den Boogaard, L.Y.E. Wong, V.M. Christoffels and P. Barnett 6. Luciferase Assay to Study the Activity of a Cloned Promoter DNA FragmentNina Solberg and Stefan Krauss 7. Promoter Deletion Analysis using a Dual-luciferase Reporter System Yong Zhong Xu, Cynthia Kanagaratham, Sylwia Jancik and Danuta Radzioch 8. Application of mRNA Display for in vitro Selection of DNA-binding Transcription Factor Complexes Seiji Tateyama and Hiroshi Yanagawa 9. Isolation of Intracellular Protein:DNA Complexes using HaloCHIP; An Antibody Free Alternative to Chromatin ImmunoprecipitationDanette L. Daniels and Marjeta Urh 10. A Modified Yeast One-Hybrid System for Genome Wide Identification of Transcription Factor Binding SitesKazuyuki Yanai 11. Identifying Specific Protein--DNA Interactions using SILAC--based Quantitative ProteomicsCornelia G. Spruijt, H. Irem Baymaz and Michiel Vermeulen 12. Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein-DNA ComplexesElsie I. Parés-Matos13. Combination of Native and Denaturing PAGE for the Detection of Protein Binding Regions in Long Fragments of Genomic DNAKristel Kaer and Mart Speek 14. Quantitative NanoProteomics Approach for Protein Complex (QNanoPX) using Gold Nanoparticle-based DNA ProbeShu-Hui Chen and Mei-Yin Lin 15. Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multicomponent Transcriptional ComplexesTakayuki Furumatsu and Hiroshi Asahara  16. Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model SystemRebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel 17. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA PolymeraseSimone C. Wiesler, Finn Werner and Robert O. J. Weinzierl 18. Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living CellsHisayo Sadamoto and Hideki Muto 19. Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian CellsC.J.J. Boogerd, V.M. Christoffels and P. Barnett 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation DynamicsIlona U. Rafalska-Metcalf and Susan M. Janicki 21. Peptide Microarrays for Profiling of Serine/threonine Kinase Activity of Recombinant Kinases and Lysates of Cells and Tissue SamplesRiet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adriënne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian CellsChieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex CompositionJeong-Heon Lee and David Skalnik 24. Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-resolution Mass Spectrometry to Study the Dynamics of Site-specific Histone MethylationXing-Jun Cao, Barry M. Zee and Benjamin A. Garcia 25. Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation Melanie Le May and Qiao Li 26. Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription FactorsDaniela B. Mendonça, Gustavo Mendonça, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid ReceptorsChen Zhang, Steven K. Nordeen and David J. Shapiro 28. Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-dependent Gene ExpressionJihong Chen and Qiao Li 29. Histone Deacetylases Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells  Jihong Chen, Natascha Lacroix and Qiao Li 30. Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress TranscriptionPing Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA MethyltransferasesJianchang Yang 11. Identifying Specific Protein--DNA Interactions using SILAC--based Quantitative ProteomicsCornelia G. Spruijt, H. Irem Baymaz and Michiel Vermeulen 12. Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein-DNA ComplexesElsie I. Parés-Matos13. Combination of Native and Denaturing PAGE for the Detection of Protein Binding Regions in Long Fragments of Genomic DNAKristel Kaer and Mart Speek 14. Quantitative NanoProteomics Approach for Protein Complex (QNanoPX) using Gold Nanoparticle-based DNA ProbeShu-Hui Chen and Mei-Yin Lin 15. Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multicomponent Transcriptional ComplexesTakayuki Furumatsu and Hiroshi Asahara  16. Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model SystemRebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel 17. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA PolymeraseSimone C. Wiesler, Finn Werner and Robert O. J. Weinzierl 18. Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living CellsHisayo Sadamoto and Hideki Muto 19. Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian CellsC.J.J. Boogerd, V.M. Christoffels and P. Barnett 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation DynamicsIlona U. Rafalska-Metcalf and Susan M. Janicki 21. Peptide Microarrays for Profiling of Serine/threonine Kinase Activity of Recombinant Kinases and Lysates of Cells and Tissue SamplesRiet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adriënne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian CellsChieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex CompositionJeong-Heon Lee and David Skalnik 24. Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-resolution Mass Spectrometry to Study the Dynamics of Site-specific Histone MethylationXing-Jun Cao, Barry M. Zee and Benjamin A. Garcia 25. Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation Melanie Le May and Qiao Li 26. Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription FactorsDaniela B. Mendonça, Gustavo Mendonça, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid ReceptorsChen Zhang, Steven K. Nordeen and David J. Shapiro 28. Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-dependent Gene ExpressionJihong Chen and Qiao Li 29. Histone Deacetylases Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells  Jihong Chen, Natascha Lacroix and Qiao Li 30. Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress TranscriptionPing Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA MethyltransferasesJianchang Yang 16. Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model SystemRebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel 17. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA PolymeraseSimone C. Wiesler, Finn Werner and Robert O. J. Weinzierl 18. Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living CellsHisayo Sadamoto and Hideki Muto 19. Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian CellsC.J.J. Boogerd, V.M. Christoffels and P. Barnett 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation DynamicsIlona U. Rafalska-Metcalf and Susan M. Janicki 21. Peptide Microarrays for Profiling of Serine/threonine Kinase Activity of Recombinant Kinases and Lysates of Cells and Tissue SamplesRiet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adriënne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian CellsChieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex CompositionJeong-Heon Lee and David Skalnik 24. Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-resolution Mass Spectrometry to Study the Dynamics of Site-specific Histone MethylationXing-Jun Cao, Barry M. Zee and Benjamin A. Garcia 25. Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation Melanie Le May and Qiao Li 26. Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription FactorsDaniela B. Mendonça, Gustavo Mendonça, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid ReceptorsChen Zhang, Steven K. Nordeen and David J. Shapiro 28. Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-dependent Gene ExpressionJihong Chen and Qiao Li 29. Histone Deacetylases Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells  Jihong Chen, Natascha Lacroix and Qiao Li 30. Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress TranscriptionPing Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA MethyltransferasesJianchang Yang 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation DynamicsIlona U. Rafalska-Metcalf and Susan M. Janicki 21. Peptide Microarrays for Profiling of Serine/threonine Kinase Activity of Recombinant Kinases and Lysates of Cells and Tissue SamplesRiet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adriënne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian CellsChieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex CompositionJeong-Heon Lee and David Skalnik 24. Heavy Methyl-SILAC Labeling Coupled with Liquid Chromatography and High-resolution Mass Spectrometry to Study the Dynamics of Site-specific Histone MethylationXing-Jun Cao, Barry M. Zee and Benjamin A. Garcia 25. Analysis of p300 Occupancy at the Early Stage of Stem Cell Differentiation by Chromatin Immunoprecipitation Melanie Le May and Qiao Li 26. Mammalian Two-Hybrid Assays for Studies of Interaction of p300 with Transcription FactorsDaniela B. Mendonça, Gustavo Mendonça, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid ReceptorsChen Zhang, Steven K. Nordeen and David J. Shapiro 28. Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-dependent Gene ExpressionJihong Chen and Qiao Li 29. Histone Deacetylases Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells  Jihong Chen, Natascha Lacroix and Qiao Li 30. Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress TranscriptionPing Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA MethyltransferasesJianchang Yang