There are hundreds of chromatin regulators (CRs) out there, and yet we know so little about them other than that they control chromatin structure and function through interactions with histone mods. To help tie down the CR rules of engagement, some handy scientists developed the ChIP-string assay to provide a snapshot of several CRs in action all at once.
Scientists at the Broad Institute created ChIP-string by combining multiple chromatin immunoprecipitations together to scan 487 loci and form a CR signature for a sample. Although it’s not quite high-throughput (they call it “meso-scale”), the resulting data creates a CR pattern that can then be used to compare tissue types and cell-lines, or get a better handle on which regulators are associated with each other or certain loci. So, what’s the payoff for using the ChIP-string method?
- Investigating several hundred regions is way less biased than picking and choosing just a few loci like most ChIP-PCR experiments.
- The data output forms a ‘‘signature’’ pattern that help determine specific CR associations with chromatin states.
- Signatures can be measured and analyzed faster and than a full genome- wide profiles, so it’s better suited to screening antibodies and finicky ChIP conditions, or even for RNAi or small molecule screens.
The team kicked things off by screening for antibodies that were most effective in the ChIP reactions, which as you might imagine is extremely critical. 145 antibodies were put through more challenges than a Japanese game-show contestant and the best ones were used to map the binding of 29 CRs in two cell types across the genome. Here are highlights from the initial ChIP-string runs:
- CRs form specific patterns at chromatin states, genes with similar functions, and regulatory elements.
- Certain groups of CRs stick together even though they may act on different loci in separate cell lines.
Co-author Alon Goren presented this work at the most recent CHI X-Gen Congress. Afterwards, we caught up with Sr. Product Manager – Epigenetics Michael Sturges and Epigenetics R&D Manager John Rosenfeld from EMD Millipore, who sponsored the talk, for their take on ChIP-string.
“The approach they have developed is a very creative method of screening and it provides a very interesting holistic approach to dissecting chromatin modifier function. We look forward to seeing if the organizational principles of these modules hold true in other cell and tissue models,” commented Rosenfeld.
“We were pleased that this team at the Broad Institute evaluated a number of our antibodies in ChIP-string and found that their results were consistent with our own in house characterization,” sharedSturges.
The authors say that one thing holding this technique back is the lack of available, quality, ChIP validated antibodies. The moderate success rate of the antibodies tested here suggests better reagents are needed, and the researchers hope their work will help encourage the development of different antibodies to CR epitopes, like the EMD Millipore program that cranks out the ChIP Ab+ Antibody products.
Now that the Broad group has proven their new ChIP-string tool works, they think it will enable researchers to explore and better understand the inner workings of chromatin regulation.
Get wrapped up in the rest of the ChIP-string data at Cell, December 2011