Method Developed to Sequence Backtracked RNA

A team led by researchers from NYU Grossman School of Medicine has developed  a technique called Long Range Cleavage sequencing (LORAX-seq) that can determine how frequently, and exactly where, a molecular event called backtracking occurs throughout the genome of any species.

Published in Molecular Cell, the team’s findings support the theory that backtracking represents a widespread form of gene regulation, which influences thousands of human genes, including many involved in basic life processes like cell division and development.

More than 15 years ago it was shown that RNA polymerase can sometimes slip backward along the chain it is reading, or backtrack. Studies since then have shown that backtracking occasionally takes place in living cells soon after RNA polymerase begins RNA synthesis or when it encounters damaged DNA to make room for incoming repair enzymes. Subsequent work suggested that the backsliding and repair machinery had to work quickly and dissipate, or it might collide with DNA polymerase to cause cell-death-inducing breaks in DNA chains.

LORAX-seq can directly detect where backtracking events begin and end. By complementing past approaches that were indirect or limited, the new method reveals that many such events move backward further than once thought, and in doing so, last longer. The results also suggest that persistent backtracking occurs frequently throughout genomes, happens more often near certain gene types, and has functions well beyond DNA repair.

“The surprising stability of backtracking at longer distances makes it likely that it represents a ubiquitous form of genetic regulation in species from bacteria to humans,” says Evgeny Nudler, the study’s senior author. “If further work expands our findings to different developmental programs and pathological conditions, backtracking may be akin to epigenetics, the discovery of which revealed a surprising new layer of gene regulation without changing the DNA code.”