Gamma rays can give super powers to scientific insight, whether it be PET scans, the Epigenetic Hulk, or nucleosome-nucleosome interactions. While we’ve seen a lot about the primary structure of single nucleosomes and the tertiary structure of large chromatin loops, it seems that the 1–3 nucleosome (50–500 bp) architecture known as secondary structure has been awaiting a technique powerful enough to SMASH out its mysteries.
Thankfully, the chromatin superheroes in the lab of William Greenleaf at Stanford University have belted DNA with gamma rays and turned it into the first human genome-wide chromatin conformation map of nucleosome-nucleosome interaction. They achieved this feat by upgrading a previous technique with the power of high-throughput sequencing, turning it into Radiation-Induced Spatially Correlated Cleavage of DNA with sequencing (RICC-seq).
Here’s how RICC-seq works:
- Live cells are irradiated with gamma rays that deposit their energy on water molecules and produce hydroxyl radicals.
- These hydroxyl radicals are dispersed throughout the cell but form highly localized clusters which result in base damage and strand breaks in nearby DNA (~3.5 nm radius).
- Any DNA in close physical proximity, as it’s wrapped around adjacent nucleosomes, will pass through a hydroxyl radical cluster more than once
- This results in a spatial pattern of breaks, which produce single stranded DNA that reveals local DNA-DNA contacts.
- Although uncorrelated breaks happen, they are random and tend to produce fragments larger than 1 Kb in size, so after ligation of the sequencing adapters, size selection can be used to remove the background.
By investigating human skin fibroblasts, the team found a regional enrichment for alternating, rather an adjacent, nucleosome interactions amongst the tri-nucleosome subunits of heterochromatin marked by H3K9me3. They also found differences in nucleosome-nucleosome contacts between heterochromatin marked with H3K27me3 or H3K9me3, as well as open chromatin, and gained insight into the chromatin structures formed. Overall, RICC-seq offers a novel method that provides the base-pair resolution of short-range chromatin contacts needed to unravel the mysteries of nucleosome-nucleosome structure.
RAGE on and learn how to SMASH your DNA of interest over at Nature, December 2016