Question

ChIP-seq is widely used to analyze the distribution of specific proteins throughout the genome. Which is NOT a requirement for doing ChIP-seq?
Group of answer choices
Next Generation Sequencing (ie Illumina sequencing) is required to analyze the sequence composition of the DNA recovered from the immunoprecipitate.
The sequence of the genome for the organism you are studying must be known.
An antibody must be available to immunoprecipitate the protein of interest.
The protein of interest must crosslink either directly or indirectly to the DNA.
Intact messenger RNA must be purified from the cells.

Answer 1

Answer: ChIP-Seq is a technique used to determine the protein-DNA interaction. This technique involves cross-linking of DNA to protein followed by shearing of DNA. The sheared DNA containing DNA-protein complex is subjected to immunoprecipitation using protein specific antibodies. After immunoprecipitation, the DNA is extracted from the complex and sequenced using Next Generation Sequencing technique. (llumina sequencing). The sequence reads are compared to genome of an organism to determine which regions of DNA are interacting with the protein. Hence, options 1, 2, 3 and 4 are the requirement of the ChIP-Seq and are incorrect options.

As ChIP-Seq is used to determine DNA-protein interactions, there is no need to extract or purify intact mRNA from the cells. Hence, option 5 is not a requirement of the ChIP-Seq and is the correct answer.