Chromatin Immunoprecipitation Assays Methods and Protocols

Over the past twenty years, the development of chromatin immunoprecipitation, or ChIP, assays has immensely enhanced the biological significance of the multifaceted DNA-binding proteins. In Chromatin Immunoprecipitation Assays: Methods and Protocols, researchers deeply involved in the development and improvement of the field provide cutting-edge protocols devoted to the most recent progress in ChIP and related subjects. The thorough chapters involve topics such as the characterization of ChIP antibodies, ChIP methods for small cell numbers, fast ChIP protocols, assays adapted to various species and cell types, as well as several strategies for the analysis of genome-wide datasets, while also extending a bit beyond ChIP assays to cover immunoprecipitation-based DNA methylation analyses, determination of spatial chromatin organization of large genomic regions, and RNA immunoprecipitation. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easy-to-use, Chromatin Immunoprecipitation Assays: Methods and Protocols is a timely guide for all those who wish to further the development of this powerful tool and continue delving into the incredible complexity of the cell’s biology.

The State-of-the-Art of Chromatin Immunoprecipitation.- Characterization and Quality Control of Antibodies Used in ChIP Assays.- The Fast Chromatin Immunoprecipitation Method.- ?ChIP: Chromatin Immunoprecipitation for Small Cell Numbers.- Fish’n ChIPs: Chromatin Immunoprecipitation in the Zebrafish Embryo.- Epitope Tagging of Endogenous Proteins for Genome-Wide Chromatin Immunoprecipitation Analysis.- Flow Cytometric and Laser Scanning Microscopic Approaches in Epigenetics Research.- Serial Analysis of Binding Elements for Transcription Factors.- Modeling and Analysis of ChIP-Chip Experiments.- Use of SNP-Arrays for ChIP Assays: Computational Aspects.- DamID: A Methylation-Based Chromatin Profiling Approach.- Chromosome Conformation Capture (from 3C to 5C) and Its ChIP-Based Modification.- Determining Spatial Chromatin Organization of Large Genomic Regions Using 5C Technology.- Analysis of Nascent RNA Transcripts by Chromatin RNA Immunoprecipitation.- Methyl DNA Immunoprecipitation.- Immunoprecipitation of Methylated DNA.- Erratum to: Chromosome Conformation Capture (from 3C to 5C) and Its ChIP-Based Modification.