Gene regulation : methods and protocols / edited by Minou Bina.

Includes bibliographical references and index.

Gene regulation / Minou Bina -- Isolation of nuclei for use in genome-wide DNase hypersensitivity assays to probe chromatin structure / Guoyu Ling and David J. Waxman -- DNase I digestion of isolated nulcei for genome-wide mapping of DNase hypersensitivity sites in chromatin / Guoyu Ling and David J. Waxman -- Isolation and analysis of DNA derived from nucleosome-free regions / Matthew Murtha ... [et al.] -- Acquisition of high quality DNA for massive parallel sequencing by in vivo chromatin immunoprecipitation / M. van den Boogaard ... [et al.] -- Luciferase assay to study the activity of a cloned promoter DNA fragment / Nina Solberg and Stefan Krauss -- Promoter deletion analysis using a dual-luciferase reporter system / Yong Zhong Xu ... [et al.] -- Application of mRNA display for in vitro selection of DNA-binding transcription factor complexes / Seiji Tateyama and Hiroshi Yanagawa -- Isolation of intracellular protein - DNA complexes using HaloCHIP an antibody-free alternative to chromatin immunoprecipitation / Danette L. Daniels and Marjeta Urh -- Modified yeast one-hybrid system for genome-wide identification of transcription factor binding sites / Kazuyuki Yanai -- Identifying specific protein-DNA interactions using SILAC-based quantitative proteomics / Cornelia G. Spruijt, H. Irem Baymaz, and Michiel Vermeulen -- Electrophoretic mobility-shift and super-shift assays for studies and characterization of protein-DNA complexes / Elsie I. Pares-Matos -- Combination of native and denaturing PAGE for the detection of protein binding regions in long fragments of genomic DNA / Kristel Kaer and Mart Speek -- Quantitative nanoproteomics approach for protein complex (QNanoPX) using gold nanoparticle-based DNA probe / Shu-Hui Chen and Mei-Yin Lin -- Chromatin assembly and in vitro transcription analyses for evaluation of individual protein activities in multicomponent transcriptional complexes / Takayuki Furumatsu and Hiroshi Asahara -- 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 -- Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase / Simone C. Wiesler, Finn Werner, and Robert O.J. Weinzierl -- Fluorescence cross-correlation spectroscopy (FCCS) to observe dimerization of transcription factors in living cells / Hisayo Sadamoto and Hideki Muto --- Nuclear recruitment assay as a tool to validate transcription factor interactions in mammalian cells / C.J.J. Boogerd, V.M. Christoffels, and P. Barnett -- Preparation of cell lines for single-cell analysis of transcriptional activation dynamics / Ilona U. Rafalska-Metcalf and Susan M. Janicki -- Peptide microarrays for profiling of serine/threonine kinase activity of recombinant kinases and lysates of cells and tissue samples / Riet Hilhorst ... [et al.] -- Immunoaffinity purification of protein complexes from mammalian cells / Chieri Tomomori-Sato ... [et al.] -- Simple and efficient identification of chromatin modifying complexes and characterization of complex composition / Jeong-Heon Lee and David Skalnik -- 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 -- Analysis of p300 occupancy at the early stage of stem cell differentiation by chromatin immunoprecipitation / Melanie Le May and Qiao Li -- Mammalian two-hybrid assays for studies of interaction of p300 with transcription factors / Daniela B. Mendonca, Gustavo Mendonca, and Lyndon F. Cooper -- 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 -- Use of histone deacetylase inhibitors to examine the roles of bromodomain and histone acetylation in p300-dependent gene expression / Jihong Chen and Qiao Li -- 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 -- Sedimentation and immunoprecipitation assays for analyzing complexes that repress transcription / Ping Lu ... [et al.] -- Methods for studies of protein interactions with different DNA methyltransferases / Jianchang Yang.