Innovative method reveals additional human gene regulation layer

A new study, published online on February 9, 2024, in Molecular Cell, demonstrates a technique capable of finding the frequency and locations of "backtracking" molecular events across any species' genome. These findings support the theory that backtracking serves as a widespread mechanism of gene regulation, impacting numerous human genes crucial for fundamental life processes such as cell division and embryonic development.

The work revolved around genes, the stretches of DNA molecular "letters" arranged in a certain order (sequence) to encode the blueprints for most organisms. In both humans and bacteria, the first step in a gene's expression, transcription, proceeds as a protein "machine" called RNA polymerase II ticks down the DNA chain, reading genetic instructions in one direction. As RNA polymerase II backtracks, it forces out (extrudes) from its interior channel the tip of the RNA chain it has been building based on the DNA code.

The study led by Evgeny A. Nudler and his team at NYU Langone Health reveals that the new technique called Long Range Cleavage sequencing (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 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 Nudler, the study's senior author, and the Julie Wilson Anderson Professor in the Department of Biochemistry and Molecular Pharmacology at NYU Langone. "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."

The findings suggest that persistent backtracking occurs frequently throughout genomes and occurs more often near certain gene types, and has functions well beyond DNA repair.

Reference: Kevin B. Yang, Aviram Rasouly, Vitaly Epshtein, Criseyda Martinez, Thao Nguyen, Ilya Shamovsky, Evgeny Nudler. Persistence of backtracking by human RNA polymerase II. Molecular Cell, 2024; DOI: 10.1016/j.molcel.2024.01.019