The genome inside each of our cells is influenced by mechanical forces such as tension and torsion, largely due to the activity of proteins that compact, loop, wrap, and untwist DNA. However, scientists have limited knowledge of how these forces affect the transcription of genes. Transcription is the process by which a cell makes an RNA copy of a segment of DNA, specifically messenger RNA (mRNA) which encodes information to make proteins necessary for cell structure and function. RNA polymerase (RNAP) is responsible for producing mRNA by tracking along double helical DNA, untwisting it to read the sequence, and synthesizing the corresponding mRNA.
In a study led by Laura Finzi and David Dunlap at Clemson University, researchers used magnetic tweezers to pull RNAP along a DNA template to investigate the role of force in an alternative to canonical termination of transcription. They discovered that upon reaching a terminator, bacterial RNA polymerase may remain on the DNA template and slide backward to the same or forward to an adjacent promoter to initiate another cycle of transcription. The direction of force dictates whether a particular DNA segment may be transcribed multiple times or only once, potentially altering the relative abundance of adjacent genes.
The researchers also found that the C-terminal domain of the alpha subunit of RNAP plays a crucial role in recognizing promoters oriented in the opposite direction during sliding. Deleting these subunits prevented the enzyme from flipping around to grab the other strand of the DNA double helix where another promoter might be located. This force-directed recycling mechanism could have significant implications for understanding how transcriptional activity is regulated in the genome, potentially leading to therapeutic alternatives by modifying RNAP to suppress certain proteins and prevent disease.
Despite these findings, it is still unclear whether certain locations in the genome exhibit more frequent recycling of transcription than others. Laura Finzi expressed her hope that future research will yield a spatio-temporal map of forces acting on the genome at different times in various cell types within the organism’s life cycle. By highlighting the impact of forces on the probability of repetitive transcription, the research may aid in predicting and mapping the diverse levels of gene transcription in a heat map format.
Ultimately, a thorough comprehension of the molecular mechanisms controlling transcriptional activity in the genome could provide valuable insights for developing therapeutic interventions. Understanding how forces influence RNA polymerase behavior and gene transcription may offer new opportunities to manipulate gene expression and potentially address various disease processes. The research conducted by Finzi and Dunlap sheds light on the complex interplay between mechanical forces and gene transcription, paving the way for further exploration into the regulation of gene expression at a molecular level.