For researchers tackling the epigenome, there are two key tools: bisulphite conversion kits and ChIP-grade antibodies.

Getting complete conversion of unmethylated cytosine to uracil has been one of the main challenges for the bisulphite treatment of DNA, not least because the reaction conditions can cause the DNA to degrade. A number of companies have tackled the problem.

“There are incredibly good kits for bisulphite conversion,” says Achim Plum, senior vice-president for corporate development at Epigenomics in Berlin. “If you use home brews you can make many mistakes, but with kits this is no longer an issue.” QIAGEN of Venlo, the Netherlands, sells EpiTect, a kit based on Epigenomics' technology that Plum says offers nearly 100% conversion without DNA degradation. In June, QIAGEN expanded the EpiTect product line to include a standardized workflow for methylation analysis from sample collection, stabilization and purification to bisulphite conversion, and real-time endpoint PCR methylation analysis or sequencing.

Epigentek in Brooklyn, New York, also sells epigenetic products and kits for DNA methylation and histone modification. Its Methylamp DNA modification kit takes two hours to convert cytosine to uracil with more than 99% accuracy and requires only 50 picograms of starting DNA, according to Adam Li, the company's chief scientific officer. The sample can then be applied for methylation-specific PCR or a methylation array.

Epigentek's Methylamp kit takes two hours to convert cytosines to uracil. Credit: EPIGENTEK

In June last year, Sigma-Aldrich of St Louis, Missouri, launched a number of products for epigenetic research based on Epigentek's technologies. Other providers of bisulphite conversion kits and related epigenetics products include Human Genetic Signatures in Sydney, Australia; Invitrogen of Carlsbad, California; Promega of Madison, Wisconsin; and Zymo Research of Orange, California.

When it comes to antibodies that can be used in ChIP experiments, a fresh set of problems presents itself. “For most transcription factors there are not that many antibodies,” says Kevin Struhl, a ChIP pioneer at Harvard Medical School in Boston, Massachusetts. “And a lot of antibodies don't work well on ChIP.”

ChIP-on-chip requires highly specific antibodies that recognize a protein's epitope in free solution and under fixed conditions. “Because an antibody that works well in ChIP must recognize the target while it is bound to DNA, the epitope that the antibody recognizes must be available in a spatial conformation that is not obscured by the shape the protein takes while bound to DNA,” explains Dana Meents, a product manager at Active Motif in Carlsbad, California. Active Motif is one of several companies now selling products that have been ChIP validated.

Abcam in Cambridge, UK, sells just over 200 ChIP-grade antibodies, many of them specific to histone post-translational modifications.

As an alternative to antibodies, the HaloCHIP system developed by Promega allows researchers to perform ChIP-on-chip experiments by cross-linking DNA to a protein of interest fused to a modified haloalkane dehalogenase tag (HaloTag). The protein–DNA complex can then be captured on a resin that recognizes the HaloTag for further microarray analysis.

L.B.