Stanford researchers developed a way to pinpoint the exact location of DNA sequences bound by regulatory RNAs by finding where RNA molecules were binding on chromatin, according to dermatology professor and lead author Howard Chang in a press release.

Regulatory RNAs are a critical part of many cell processes, especially those related to regeneration and development. They are also a critical part of unlocking genes.

Messenger RNAs were first identified half a century ago, and over the years, the information flow from DNA to RNA to protein became a central tenet of molecular biology. The discovery of regulatory RNAs have challenged that view, since they bind to DNA and affect which genes lead to protein synthesis.

Given the propensity of these long intergenic non-coding RNAs, or “lincRNAs,” in chromatin, researchers wondered exactly where the binding sites were that regulate gene function.

“To capture this picture, you have to trap that interaction between lincRNAs and chromatin in living cells,” Chang said. “It was not at all obvious how to do that.”

Using their technique, the group was able to examine the binding of three lincRNAs, two from mammals and one from the fruit fly. Since they weren’t sure which part of the lincRNA bound to the chromatin, they created tagged “probes” that would bind to the lincRNA and ensure that, even if the RNA molecule started to fall apart during the test, they would still be able to isolate what was left on the chromatin.

“Taken together, our research shows that our technique is widely applicable and can vastly enrich our understanding of how regulatory RNAs unlock the genome in many very specific ways,” Chang said.