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ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.
The term was coined by The Economist [3] and is named after author Rob Carlson. [1]Carlson curves illustrate the rapid (in some cases above exponential growth) decreases in cost, and increases in performance, of a variety of technologies, including DNA sequencing, DNA synthesis and a range of physical and computational tools used in protein production and in determining protein structures.
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Quick and quantitative ChIP (Q 2 ChIP): The assay uses 100,000 cells as starting material and is suitable for up to 1,000 histone ChIPs or 100 transcription factor ChIPs. Thus many chromatin samples can be prepared in parallel and stored, and Q 2 ChIP can be undertaken in a day. [20]
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
The appetite for genomic data continues to rise in the field of biotech and pharmaceutical research, but cost is still a factor -- even sequencing a full genome now costs as little as $1,000.
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Wilbanks and colleagues [3] is a survey of the ChIP-seq peak callers, and Bailey et al. [4] is a description of practical guidelines for peak calling in ChIP-seq data. Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq [ 5 ] or m6Aseq [ 6 ] for detection of post-transcriptional RNA ...