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Chromatin

Completing the picture

Nature Reviews Genetics volume 10, page 151 (2009)Cite this article

Chromatin immunoprecipitation (ChIP) is a technique that is widely used to determine whether a protein of interest binds to a particular genomic region. But this method relies on antibodies to known DNA-binding proteins and does not provide a complete description of protein composition. To overcome these limitations PiCh uses a specific DNA probe to isolate proteins from fixed cells, which are then characterized using mass spectrometry (MS). Because MS analysis requires a relatively large quantity of protein (at least a picomole) Dejardin and Kingston, who developed PiCh, tested their approach using telomeres — the abundance of which necessitates less starting material than for single copy loci.

Using PiCh, the authors were able to identify most known telomeric factors. By comparing different cell lines that expressed mutant telomerase, they were also able to pinpoint differences in protein composition of telomeres maintained by the reverse transcriptase and alternative lengthening of telomeres (ALT) pathways. Importantly, they also discovered many novel telomeric associations; for example, between telomeres that are maintained by ALT and orphan receptors from the nuclear hormone receptor superfamily. Although further optimization will be required to study single copy genes in humans and other organisms with large genomes, PiCh could be immediately applied to other repeat sequences and to low copy sequences in organisms with small genomes.

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References

ORIGINAL RESEARCH PAPER

  1. Dejardin, J. & Kingston, R. E. Purification of proteins associated with specific genomic loci. Cell 136, 175–186 (2009).

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FURTHER READING

  1. Schones, D. E. & Zhao, K. Genome-wide approaches to studying chromatin modifications. Nature Rev. Genet. 9, 179–191 (2008).

    Article  CAS  Google Scholar 

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Authors
  1. Meera Swami
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Swami, M. Completing the picture. Nat Rev Genet 10, 151 (2009). https://doi.org/10.1038/nrg2542

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  • DOI: https://doi.org/10.1038/nrg2542

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