Strengths and weaknesses of ChIP-on-chip

Strengths and weaknesses of ChIP-on-chip
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  • Using tiled arrays, ChIP-on-chip allows for excessive resolution of genome-huge maps. These maps can decide the binding web sites of many DNA-binding proteins like transcription factors and also chromatin changes.
  • Although ChIP-on-chip can be a powerful approach in the vicinity of genomics, it’s far very pricey. Most published research the usage of ChIP-on-chip repeat their experiments at least 3 times to make certain biologically significant maps. The fee of the DNA microarrays is often a restricting issue to whether a laboratory must continue with a ChIP-on-chip experiment. Another hassle is the size of DNA fragments that can be performed. Most ChIP-on-chip protocols make use of sonication as a method of breaking apart DNA into small portions. However, sonication is confined to a minimal fragment size of 200 bp. For higher resolution maps, this drawback have to be overcome to reap smaller fragments, preferably to single nucleosome resolution. As noted previously, the statistical analysis of the large quantity of facts generated from arrays is a venture and normalization tactics have to purpose to minimize artifacts and determine what’s truly biologically tremendous. So a ways, utility to mammalian genomes has been a primary issue, for example, due to the great percentage of the genome that is occupied by repeats. However, as ChIP-on-chip era advances, high decision entire mammalian genome maps ought to end up practicable.
  • Antibodies used for ChIP-on-chip can be an important proscribing component. ChIP-on-chip calls for relatively particular antibodies that have to apprehend its epitope in unfastened answer and additionally underneath fixed conditions. If it’s miles validated to successfully immunoprecipitate go-connected chromatin, it’s miles termed “ChIP-grade”. Companies that offer ChIP-grade antibodies encompass Abcam, Cell Signaling Technology, Santa Cruz, and Upstate. To triumph over the hassle of specificity, the protein of hobby may be fused to a tag like FLAG or HA which might be diagnosed by way of antibodies. An opportunity to ChIP-on-chip that doesn’t require antibodies is DamID.
  • Also available are antibodies towards a selected histone amendment like H3 tri methyl K4. As noted before, the combination of those antibodies and ChIP-on-chip has turn out to be extraordinarily powerful in determining complete genome evaluation of histone change styles and could contribute notably to our knowledge of the histone code and epigenetics.
  • A have a look at demonstrating the non-particular nature of DNA binding proteins has been published in PLoS Biology. This suggests that exchange confirmation of practical relevancy is a vital step in any ChIP-chip test.

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