All You Need to Know About ChIP-Seq

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June 10, 2019





ChIP-sequencing is a way to study protein interactions with DNA. It combines chromatin immunoprecipitation or ChIP with parallel DNA sequencing, which makes it possible to identify the binding sites of the proteins associated with the DNA. The main benefit is being able to precisely map global binding sites for any protein of interest. It essentially replaced the ChIP-ChIP method as the most common technique of analysing DNA relations.

Benefits of ChIP-sequencing

ChIP is mainly used to identify how various transcription factors and other chromatin-related proteins play a role in influencing phenotype mechanisms. It gives researchers a better view of the many biological processes and disease states, by determining how the proteins react with DNA to mitigate gene expression.

Today, ChIP-seq is the primary alternative to the ChIP-ChIP method, which requires a hybridization array, unnecessarily introducing a bias. By having a hybridization array, you are limited to only a certain number of probes.

On the other hand, ChIP-seq’s sequencing has less bias, though there are still a lot of mystery that has yet to be uncovered about the technique.

Chromatin immunoprecipitation makes it possible to isolate various DNA sties directly interacting with other proteins and transcription factors. What this does is it produces a wide variety of target DNA sites bound to a protein. Through massively parallel sequence analysis and in conjunction with whole-genome sequence databases, you can analyse the interaction pattern of any protein that’s within the DNA. You can also identify and analyse any pattern of epigenetic chromatin modifications.

The method is very effective when applied to a set of ChIP proteins and modifications, including but not limited to DNA modifications, polymerases and transcriptional machinery, structural proteins, and more. Furthermore, different techniques have risen to find the superset of all nucleosome-depleted regulatory regions of the genome. This includes DNase-seq and FAIRE-seq, both alternatives to the dependence on specific antibodies.

How it Works

ChIP. Chromatin immunoprecipitation is a great technique to selectively enrich DNA sequences, which are bound by cellular proteins. But the use of this method is not widespread, mainly because it has been limited by the lack of robust techniques to correctly identify the DNA sequences that has been enriched. This ChIP process targets specific crosslinked DNA-protein to enrich, using an antibody. Then, oligonucleotide adaptors are added to the DNA stretches which are bound to the protein of interest, enabling the sequencing process.