ChIP-sequencing

The ChIP -Seq (of English. Chromatin immunoprecipitation DNA sequencing ) is a biochemical method for the determination of protein-DNA interactions. The ChIP -on-chip is a combination of chromatin immunoprecipitation and DNA sequencing in high throughput. DNA -protein interactions occur in binding sequences for transcription factors, promoters, enhancers, repressors, silencers, insulators, as well as binding sequences for the DNA replication.

Properties

The purified recombinant protein was mixed with the DNA or attached in vivo, reversibly cross-linked with formaldehyde. This is followed by fragmentation using ultrasound and the immunoprecipitation of the cross-linked protein -DNA complexes with an antibody against the recombinant protein or protein tag. Finally, the thermal release of DNA and DNA sequencing in a high throughput.

An alternative method is the chip-on- chip connecting the chromatin immunoprecipitation with a hybridisation with a DNA microarray ( DNA chip synonymously ). Systematic errors of the methods can be partially offset by a parallel use of both methods. In contrast to ChIP -on-chip increase in the ChIP -Seq, the costs associated with an increase in sensitivity, as this more Sequenziervorgänge be required. A variant of the ChIP -Seq is the Competition ChIP -Seq.

Related methods are the DNAse -Seq and FAIRE -seq, which unfolded regions of the DNA sequence, in which there is a regulation of gene expression. Chirp is a chip - Seq Seq can be selectively detected in the DNA-binding RNA.

The combination of a nuclease protection assays with a ChIP -Seq is called ChIP - exo, with the uncovered proteins DNA regions by an exonuclease from bacteriophage λ digested, the remaining sequenced it.