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  • Book
    edited by Minou Bina.
    Digital : Springer2013
    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 nuclei for genome-wide mapping of Denise 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. 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. Pares-Matos -- 13. Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA / Kristel 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 Ruijtenbeck -- 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. Mendonnc̦a, Gustavo Mendonc̦a, and 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 deacetylase inhibitor 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.