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Genomics

Complete coverage?

Nature Reviews Cancer volume 6, page 173 (2006)Cite this article

Chromatin immunoprecipitation (ChIP) is a technique that extracts DNA fragments to which a transcription factor is bound. Having done this, these fragments need to be identified. One approach is to hybridize them to microarrays (ChIP on chip); this has been used successfully in yeast but mammalian genomes have proved too large. Alternatively, the fragments can be sequenced, but this has also proved unwieldy for mammalian genomes and only a few chromosomes have been studied in any one screen.

These authors have recently developed a new sequencing approach that is sufficiently efficient to screen the entire human genome — paired-end ditag (PET) sequencing. In this method, after cloning the precipitated fragments, the 5′ and 3′ ends of several clones are concatenated for efficient sequencing. Each pair of ends is then mapped to the genome to identify a potential binding site.

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References

ORIGINAL RESEARCH PAPER

  1. Wei, C. -L. et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 124, 207–219 (2006)

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FURTHER READING

  1. Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2, 105–111 (2005)

    Article  CAS  Google Scholar 

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Authors
  1. Patrick Goymer
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Goymer, P. Complete coverage?. Nat Rev Cancer 6, 173 (2006). https://doi.org/10.1038/nrc1823

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