title: High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states.
abstract: Dynamic protein binding to DNA elements regulates genome function and cell fate. Although methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect of genomic research, they are laborious and costly, thereby limiting progress. Here we present a protocol for mapping in vivo protein-DNA interactions using a high-throughput chromatin immunoprecipitation (HT-ChIP) approach. By using paramagnetic beads, we streamline the entire ChIP and indexed library construction process: sample transfer and loss is minimized and the need for manually labor-intensive procedures such as washes, gel extraction and DNA precipitation is eliminated. All of this allows for fully automated, cost effective and highly sensitive 96-well ChIP sequencing (ChIP-seq). Sample preparation takes 3 d from cultured cells to pooled libraries. Compared with previous methods, HT-ChIP is more suitable for large-scale in vivo studies, specifically those measuring the dynamics of a large number of different chromatin modifications/transcription factors or multiple perturbations.
authors: Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
authors: Ronnie
authors: R
authors: Blecher-Gonen
authors: Zohar
authors: Z
authors: Barnett-Itzhaki
authors: Diego
authors: D
authors: Jaitin
authors: Daniela
authors: D
authors: Amann-Zalcenstein
authors: David
authors: D
authors: Lara-Astiaso
authors: Ido
authors: I
authors: Amit
mesh_terms: D001666:Binding Sites, Antibody; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods; D004268:DNA-Binding Proteins / Q000737:chemistry*; D044127:Epigenesis, Genetic; D015698:Genomic Library; D050835:Interferon Regulatory Factors / Q000737:chemistry*; D000099185:Interferon Regulatory Factor-8
chemical_list: D004268:DNA-Binding Proteins; D050835:Interferon Regulatory Factors; D000099185:Interferon Regulatory Factor-8