Description
In this volume of Methods in Molecular Biology(TM), expert investigators offer comprehensive, complementary, and cutting-edge technologies for studies of gene regulation. The chapters of Gene Regulation: Methods and Protocols are organized to provide an integrated and a coherent view of control systems and their associated components. The protocols are broad in their scope. They include molecular, biochemical, spectroscopic techniques as well as high throughput strategies. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and broad in their scope, the protocols are useful to researchers in many disciplines including molecular biology, genomics, biochemistry, biomedicine, nutrition, and agricultural sciences. 1. Gene Regulation Minou Bina 2. Isolation of Nuclei for use in Genome-wide DNase Hypersensitivity Assays to Probe Chromatin Structure Guoyu Ling and David J. Waxman 3. DNase I Digestion of Isolated Nulcei for Genome-Wide Mapping of DNase Hypersensitivity Sites in Chromatin Guoyu Ling and David J. Waxman 4. Isolation and Analysis of DNA Derived from Nucleosome-Free Regions Matthew Murtha, Yatong Wang, Claudio Basilico, and Lisa Dailey 5. Acquisition of High Quality DNA for Massive Parallel Sequencing by in vivo Chromatin Immunoprecipitation M. 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 Fragment Nina 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 Immunoprecipitation Danette L. Daniels and Marjeta Urh 10. A Modified Yeast One-Hybrid System for Genome Wide Identification of Transcription Factor Binding Sites Kazuyuki Yanai 11. Identifying Specific Protein–DNA Interactions using SILAC–based Quantitative Proteomics Cornelia G. Spruijt, H. Irem Baymaz and Michiel Vermeulen 12. Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein-DNA Complexes Elsie I. Pars-Matos 13. 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 Probe Shu-Hui Chen and Mei-Yin Lin 15. Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multicomponent Transcriptional Complexes Takayuki Furumatsu and Hiroshi Asahara 16. Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model System Rebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel 17. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase Simone C. Wiesler, Finn Werner and Robert O. J. Weinzierl 18. Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living Cells Hisayo Sadamoto and Hideki Muto 19. Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian Cells C.J.J. Boogerd, V.M. Christoffels and P. Barnett 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation Dynamics Ilona 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 Samples Riet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adrinne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian Cells Chieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition Jeong-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 Methylation Xing-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 Factors Daniela B. Mendona, Gustavo Mendona, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid Receptors Chen 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 Expression Jihong 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 Transcription Ping Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA Methyltransferases Jianchang Yang 11. Identifying Specific Protein–DNA Interactions using SILAC–based Quantitative Proteomics Cornelia G. Spruijt, H. Irem Baymaz and Michiel Vermeulen 12. Electrophoretic Mobility-Shift and Super-Shift Assays for Studies and Characterization of Protein-DNA Complexes Elsie I. Pars-Matos 13. 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 Probe Shu-Hui Chen and Mei-Yin Lin 15. Chromatin Assembly and In Vitro Transcription Analyses for Evaluation of Individual Protein Activities in Multicomponent Transcriptional Complexes Takayuki Furumatsu and Hiroshi Asahara 16. Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model System Rebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel 17. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase Simone C. Wiesler, Finn Werner and Robert O. J. Weinzierl 18. Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living Cells Hisayo Sadamoto and Hideki Muto 19. Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian Cells C.J.J. Boogerd, V.M. Christoffels and P. Barnett 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation Dynamics Ilona 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 Samples Riet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adrinne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian Cells Chieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition Jeong-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 Methylation Xing-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 Factors Daniela B. Mendona, Gustavo Mendona, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid Receptors Chen 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 Expression Jihong 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 Transcription Ping Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA Methyltransferases Jianchang Yang 16. Using FRET to Monitor Protein-induced DNA Bending: The TBP-TATA Complex as a Model System Rebecca H. Blair, James A. Goodrich, and Jennifer F. Kugel 17. Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase Simone C. Wiesler, Finn Werner and Robert O. J. Weinzierl 18. Fluorescence Cross-correlation Spectroscopy (FCCS) to Observe Dimerization of Transcription Factors in Living Cells Hisayo Sadamoto and Hideki Muto 19. Nuclear Recruitment Assay as a Tool to validate Transcription Factor Interactions in Mammalian Cells C.J.J. Boogerd, V.M. Christoffels and P. Barnett 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation Dynamics Ilona 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 Samples Riet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adrinne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian Cells Chieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition Jeong-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 Methylation Xing-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 Factors Daniela B. Mendona, Gustavo Mendona, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid Receptors Chen 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 Expression Jihong 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 Transcription Ping Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA Methyltransferases Jianchang Yang 20. Preparation of Cell Lines for Single-Cell Analysis of Transcriptional Activation Dynamics Ilona 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 Samples Riet Hilhorst, Liesbeth Houkes, Monique Mommersteeg, Joyce Musch, Adrinne van den Berg and Rob Ruijtenbeek 22. Immunoaffinity Purification of Protein Complexes from Mammalian Cells Chieri Tomomori-Sato, Shigeo Sato, Ronald C. Conaway, and Joan W. Conaway 23. Simple and Efficient Identification of Chromatin Modifying Complexes and Characterization of Complex Composition Jeong-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 Methylation Xing-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 Factors Daniela B. Mendona, Gustavo Mendona, Lyndon F. Cooper 27. Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-length Steroid Receptor Coactivator-1a with Steroid Receptors Chen 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 Expression Jihong 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 Transcription Ping Lu, Bruce S. Hostager, Paul B. Rothman and John D. Colgan 31. Methods for Studies of Protein Interactions with Different DNA Methyltransferases Jianchang Yang
