Question

Describe a ChIP-chip experiment. How were ChIP-chip experiments used to study the regulation of target genes by Dorsal? This ChIP-chip approach is a bit dated. Today one would likely conduct ChIP-seq analysis. What is ChIP-seq and how does it differ from ChIP-chip?

Answer 1

CHIP-chip experiments is a special technique which allows us for studying DNA-protein interactions and applies the combination of chromatin immunoprecipitation with DNA microarray. It allows us the determination functional elements present in the genome by locating binding sites for protein.

ChIP-chip experiments used to study the regulation of target genes by Dorsal.The experiment was carried out with antibodies raised against the Dorsal.The whole genome CHIP-chip assays lead to the result that strong binding clusters of Dorsal are present which are several hundred in number.It lead to the identification of known enhancers of Dorsal.

ChIP- seq assays are performed for the analysis of interactions of protein with DNA.It uses the combination of chromatin immunoprecipitation and DNA sequencing.

Differences:

• CHIP-chip assays involve hybridization arrays but ChIP -seq do not.
• ChIP -seq allows us the determination of mechanisms as to how transcription factors affect a phenotype.
• ChIP -seq assays result in production of profiles where signal-to-noise ratio is much better as compared to CHIP-chip assays.