ChIPSequencing

ChIP-sequencing, commonly written as ChIP-seq, stands for chromatin immunoprecipitation sequencing. It is a method used to map protein-DNA interactions across the genome by combining chromatin immunoprecipitation with next-generation sequencing. It identifies where a specific protein or histone modification binds to DNA.

The workflow involves treating cells to crosslink proteins to DNA, fragmenting chromatin by sonication or digestion, and enriching DNA-protein complexes with an antibody against the target protein. Crosslinks are reversed, DNA is purified, sequencing libraries are prepared and sequenced, and the resulting reads are aligned to a reference genome. Enriched regions are identified as peaks, representing binding sites or modified chromatin.

ChIP-seq is used to study transcription factors, histone modifications, and other chromatin-associated proteins. Variants such as ChIP-exo or ChIP-nexus provide higher resolution mapping, while CUT&RUN is a related approach that uses targeted nuclease digestion.

Applications include genome-wide mapping of regulatory elements, understanding gene regulation in development and disease, comparing cell types, and annotating promoters and enhancers. It supports integrative analyses with other epigenomic data to infer regulatory networks and chromatin states.

Limitations include dependence on antibody quality, potential crosslinking biases, and background signal. It requires appropriate controls (input DNA or IgG) and biological replicates, and data analysis is computationally intensive. Data processing typically involves aligning reads to the genome, peak calling with tools such as MACS, and annotating peaks to genomic features.

History: ChIP techniques evolved from earlier chromatin immunoprecipitation methods, with genome-wide sequencing approaches becoming standard in the late 2000s, greatly expanding epigenomic profiling.