The DNA within our cells experiences tension and twisting, influenced by proteins that compact, loop, wrap, and untwist it. However, scientists are still learning how these physical forces impact gene transcription.
Laura Finzi, the Dr. Waenard L. Miller, Jr. ’69 and Sheila M. Miller Endowed Chair in Medical Biophysics at Clemson University, noted, “There are many mechanical forces constantly at work that we often overlook and understand very little about, and these topics aren’t usually covered in textbooks.”
Transcription is the mechanism through which a cell creates an RNA copy from a segment of DNA. One form of RNA, called messenger RNA (mRNA), carries information necessary for producing proteins that are essential for the structure and function of cells or tissues.
RNA polymerase (RNAP) is a protein responsible for synthesizing mRNA. It moves along the double-helix DNA, unwinding it to read the base pair sequence on one strand and producing a corresponding mRNA. The transcription process starts when RNAP attaches to a “promoter” sequence in the DNA and concludes at a “terminator” site, where the mRNA is released. Traditionally, it is believed that once the mRNA is released, RNAP detaches from the DNA.
A research team led by Finzi and including David Dunlap, a research professor in Clemson’s Department of Physics and Astronomy, has revealed for the first time how mechanical forces can influence an alternative method of termination.
Utilizing magnetic tweezers to pull RNAP along a DNA strand, the researchers demonstrated that upon reaching a terminator, bacterial RNA polymerase can actually stay on the DNA and may move backward or forward to another promoter to initiate a new round of transcription. Therefore, the direction of the force impacts whether a portion of DNA can be transcribed multiple times or just once. Finzi and Dunlap found that this force-driven recycling mechanism can alter the abundance of neighboring genes.
Additionally, they discovered that for RNAP to slide effectively, it relies on the C-terminal domain of its alpha subunit to identify a promoter that is oriented against the direction of movement. These subunits help it stay aligned, allowing it to pivot and attach to the opposite strand of the DNA where another promoter may be located, as Finzi explained. Indeed, without the alpha subunits, RNAP could not pivot toward oppositely arranged promoters.
Gaining a comprehensive understanding of the molecular processes that manage transcriptional activity within the genome could lead to new therapeutic strategies where RNAP may be altered to inhibit specific proteins and help prevent diseases.
Finzi mentioned that there may be specific regions in the genome where recycling occurs more often than in others, although that is not yet confirmed.
“I hope that one day we will create a spatial and temporal map of the forces acting on the genome during various stages of different cell types in our body. Our research, which emphasizes the impact of forces on the likelihood of repetitive transcription, may eventually assist in forecasting and visually representing the diverse levels of transcription for different genes,” Finzi stated.
