When it comes to studying chromatin structure and histone modifications, a new technique proves that sometime less really is more, ChIP-less that is.

Antibodies for individual histone post-translational modifications (PTMs) have long been the star of chromatin technology, but PTMs often act in concert to form a dynamic histone code whose combinations can interfere with antibodies attempting to bind a single mark in a sea of post-translational mods.

To better tackle the complex histone code, a crack team from the University of Wisconsin has developed and “efficient, quantitative, antibody-free, chromatin immunoprecipitation-less (ChIP-less)” technique that makes use of reader domains to decipher the combos that can elude classic ChIP analysis. Employing recombinant chromatin reader domains as affinity reagents to target unique combinations of PTMs, the researchers were able to isolate and investigate distinct chromatin states, rather than just one histone mark at a time.

With this new tool on their bench, the Badger team put it to use:

The scientists found, using specially designed histone peptide microarrays, that their three reader domains have a greater specificity towards PTM combos than their corresponding individual antibodies.

The chromatin reader-based affinity enrichment platform known as Matrix-assisted reader chromatin capture (MARCC) was born to take advantage of the readers ability to recognize specific PTM combos.

MARCC was employed to capture unique chromatin states that were then quantified/coerced by mass spec to reveal their intimate interconnections and found a novel signature associating with one of their readers.

The authors envision that their new technique will be a huge boon for the study of combinatorial histone PTM patterns that have in the past been difficult to probe using antibodies. Compatibility with a number of downstream analytics methods should also enable the interrogation of the PTM patterns in specific genomic loci, as well. When it comes down to it, this chromatin reader-based technique has a lot to offer to our understanding of how chromatin states and reader domains affect the regulation of gene expression.

Take a combinatorial crack at the histone code in Epigenetics and Chromatin, April 2014