Refinements in methods to uncover the higher-order structure of the genome will allow functional insight into genomic architecture at high resolution.
The importance of the chromatin interactome for genome function has long been recognized. Techniques to unravel the complicated architecture of chromatin (genomic DNA looped around proteins), such as chromatin conformation capture (3C) and its higher-throughput derivatives 4C and 5C, provide long-range chromatin interactions but are not scalable to the entire chromatin interactome.
Late in 2009 two methods burst on the scene that promise such genome-wide interaction maps. Hi-C, a 3C-based method that captures global interactions, shows the higher-order folding principles of chromatin, independent of any particular protein, at 1-megabase resolution (Science 326, 289–293, 2009). ChIA-PET (chromatin interaction analysis using paired-end ditag sequencing) resolves protein-mediated functional interactions at base-pair resolution. Its developers have so far applied it to draw the organization of the genome in response to estrogen receptor activation (Nature 462, 58–64, 2009).
One could say that Hi-C and ChIA-PET approach the chromatin interactome from two opposite directions—one providing the bird's-eye view of how chromatin is folded in the nucleus, the other looking at the effect of a particular protein on genomic architecture. To increase their impact and provide a detailed, functional map of the chromatin interactome, both methods will have to move toward the center. Higher sequencing power, on the order of hundreds of millions of reads, and new analysis methods will increase the resolution of Hi-C, possibly to the 1-kilobase resolution ultimately desired by its creators. The application of ChiA-PET to proteins with more generic function, such as polymerases, will help to identify all chromatin interactions involved in processes such as transcription. Merging the maps will provide one with the best of both worlds—all possible genome-wide interactions independent of proteins paired with the functional maps induced by the activation of certain proteins.
These maps will provide the basis for understanding the structure of each chromosome during biological processes as well as in diseases such as cancer in which chromosomes often become scrambled and rearranged. Seeing how this rearrangement affects chromatin architecture, and what the functional implications are, may yield unique insights into what drives disease progression.
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Rusk, N. Mapping genomes in 3D. Nat Methods 7, 35 (2010). https://doi.org/10.1038/nmeth.f.286