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The cost and accessibility of ChIP-seq is a major disadvantage, which has led to the more predominant use of ChIP-chip in laboratories across the world. [2] This photo compares the efficacy of the two experimental techniques, ChIP-seq and ChIP-chip. Table 1 Advantages and disadvantages of NChIP and XChIP
The performance of ChIP-seq was then compared to the alternative protein–DNA interaction methods of ChIP-PCR and ChIP-chip. [17] Nucleosome Architecture of Promoters: Using ChIP-seq, it was determined that Yeast genes seem to have a minimal nucleosome-free promoter region of 150bp in which RNA polymerase can initiate transcription. [18]
Recent advances in chromatin immunoprecipitation followed by sequencing have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. [ 1 ] [ 2 ] The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
The Carlson curve is a term to describe the rate of DNA sequencing or cost per sequenced base as a function of time. [1] It is the biotechnological equivalent of Moore's law. Carlson predicted that the doubling time of DNA sequencing technologies (measured by cost and performance) would be at least as fast as Moore's law. [2]
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 ideal size of DNA fragments for the sequencing library depends on the sequencing platform that will be used. [4] [16] DNA can first be sheared to fragments around 300–500 bp long using sonication. [4] [16] [17] Fragments of this size are suitable for high-throughput sequencing.
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The cost of the DNA microarrays is often a limiting factor to whether a laboratory should proceed with a ChIP-on-chip experiment. Another limitation is the size of DNA fragments that can be achieved. Most ChIP-on-chip protocols utilize sonication as a method of breaking up DNA into small pieces.
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