RNA DNA interaction

RNA-DNA interactions (with a little artistic licence) – tightly coiled DNA makes up the ‘dragon’, while interacting RNAs form the hairs / Victor O. Leshyk

Knowing the sequence of bases that make up a gene is just a small part of the overall picture. To understand how a gene works (and what happens when it doesn’t work) scientists need to get a handle on how gene sequence translates into gene function. Now bioengineers at the University of California San Diego have developed a new tool to identify interactions between RNA and DNA molecules.

Called ‘MARGI’ (Mapping RNA Genome Interactions), this approach is the first technology capable of providing a full account of all the RNA molecules that interact with a segment of DNA. 

“Most of the human genome sequence is now known, but we still don’t know what most of these sequences mean,” said Sheng Zhong, bioengineering professor at the UC San Diego Jacobs School of Engineering and the study’s lead author. “To better understand the functions of the genome, it would be useful to have the entire catalog of all the RNA molecules that interact with DNA, and what sequences they interact with. We’ve developed a tool that can give us that information.”

RNA molecules can attach to particular DNA sequences to help control how much protein these particular genes produce within a given time, and within a given cell. And by knowing what genes produce these regulatory RNAs, researchers can start to identify new functions and instructions encoded in the genome. Existing methods to study RNA-DNA interactions can only look at one RNA molecule at a time. MARGI has the edge in being able to analyse hundreds of RNAs in a single experiment. 

Zhong and his team published their findings in the Feb. issue of Current Biology.

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