Chromatin Immunoprecipitation: Methods and Protocols

Description

This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. The collection also includes protocols designed to improve the performance of ChIP for specific applications. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine. Front Matter ....Pages i-x ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance (Neus Visa, Antonio Jordán-Pla)....Pages 1-7 Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments (Antonio Jordán-Pla, Neus Visa)....Pages 9-28 How to Combine ChIP with qPCR (Patrik Asp)....Pages 29-42 Analysis of Protein–DNA Interaction by Chromatin Immunoprecipitation and DNA Tiling Microarray (ChIP-on-chip) (Hui Gao, Chunyan Zhao)....Pages 43-51 Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing (Mário A. F. Soares, Diogo S. Castro)....Pages 53-63 Chromatin RNA Immunoprecipitation (ChRIP) (Tanmoy Mondal, Santhilal Subhash, Chandrasekhar Kanduri)....Pages 65-76 DNA Accessibility by MNase Digestions (Ann-Kristin Östlund Farrants)....Pages 77-82 Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq) (Wieteke Anna Maria Hoeijmakers, Richárd Bártfai)....Pages 83-101 ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation (Timothy V. Beischlag, Gratien G. Prefontaine, Oliver Hankinson)....Pages 103-112 Sm-ChIPi: Single-Molecule Chromatin Immunoprecipitation Imaging (Roubina Tatavosian, Xiaojun Ren)....Pages 113-126 Chromatin Immunoprecipitation of Skeletal Muscle Tissue (Amarjit Saini, Carl Johan Sundberg)....Pages 127-138 Chromatin Immunoprecipitation Assay in the Hyperthermoacidophilic Crenarchaeon, Sulfolobus acidocaldarius (Kun Wang, Ann-Christin Lindås)....Pages 139-146 Using Intra-ChIP to Measure Protein–DNA Interactions in Intracellular Pathogens (Brett R. Hanson, Ming Tan)....Pages 147-155 Native Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) from Low Cell Numbers (Teodora Ribarska, Gregor D. Gilfillan)....Pages 157-166 MOBE-ChIP: Probing Cell Type-Specific Binding Through Large-Scale Chromatin Immunoprecipitation (Shenqi Wang, On Sun Lau)....Pages 167-176 Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis (Christophe D. Chabbert, Sophie H. Adjalley, Lars M. Steinmetz, Vicent Pelechano)....Pages 177-194 Analysis of ChIP-seq Data in R/Bioconductor (Ines de Santiago, Thomas Carroll)....Pages 195-226 Spike-In Normalization of ChIP Data Using DNA–DIG–Antibody Complex (Andrea B. Eberle)....Pages 227-238 Back Matter ....Pages 239-243