ChIP-Seq: technique to discover protein-DNA interactions

Scientific India|March - April 2020

ChIP-Seq: technique to discover protein-DNA interactions
ChIP-Seq or ChIPSequencing is a powerful technique to study protein-DNA interactions.
Swati Saxena and Tanvi Kaila

ChIP-Seq is a combination of chromatin immunoprecipitation (ChIP) with massively parallel next-generation DNA sequencing. It allows identification of DNA binding proteins mainly transcription factors, chromatin-modifying proteins and histones associated proteins influencing phenotype in a genome-wide manner. Identification of how proteins interact with DNA to regulate gene expression is highly significant and informative for a better understanding of various biological processes and diseases. ChIP-Seq is primarily evolved from ChIPchip assay which requires hybridization assay. In the past years, the rapid advancements in next-generation sequencing (NGS) techniques have allowed researchers to sequence millions of short DNA fragments in a single run. ChIP-Seq was one of the early applications of NGS and the technique was first described in 2007. In comparison to ChIP-chip (microarray) assay, ChIP- Seq provides superior quality data owing to its various attributes such as high resolution, greater genomic coverage, fewer artifacts and broad dynamic range.

How do ChIP-Seq works?

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March - April 2020