D-peaks: A visual tool to display ChIP-seq peaks along the genome (original) (raw)

These very last years, researchers have been challenged by the development of novel techniques derived from high-throughput sequencing (e.g., genome, RNA or exome sequencing and epigenetic sequencing approaches). Among those, a very popular approach is ChIP-sequencing (ChIP-seq), which is currently widely used to analyze protein interactions (e.g., transcription factors and chromatin modifying enzymes) with DNA. ChIPseq replaces now ChIP-chip as the method of choice allowing the exhaustive discovery of precise global DNA binding sites for a protein of interest. Briefly, ChIP-seq consists in chemically cross-linking DNA to proteins (among which is the protein of interest) to DNA with a chemical agent, then fragmenting the DNA into pieces of about 50 to 500 bp. The DNA pieces linked to the protein of interest are then immunoprecipitated using an antibody directed against this protein. Finally, the DNA pieces, enriched in the binding sites of the protein of interest, are sequenced .