Gene Regulation: Methods and Protocols - Rilegato

Rilegato

ISBN 10: 1627032835 ISBN 13: 9781627032834

Casa editrice: Humana Pr Inc, 2013

Riassunto

In this volume of Methods in Molecular Biology™, 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™ 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.

Su questo libro

Contenuti:

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. Parés-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, Adriënne 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. Mendonça, Gustavo Mendonça, 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. Parés-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, Adriënne 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. Mendonça, Gustavo Mendonça, 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, Adriënne 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. Mendonça, Gustavo Mendonça, 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, Adriënne 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. Mendonça, Gustavo Mendonça, 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

Su questa edizione

• Editore: Humana Pr Inc
• Data di pubblicazione: 2013
• ISBN 10: 1627032835
• ISBN 13: 9781627032834
• Rilegatura: Copertina rigida
• Numero edizione: 1
• Numero di pagine: 401
• Redattore: Bina Minou