Transcription is the process by which a cell makes an RNA copy of a segment of DNA. One type of RNA, called messenger RNA (mRNA), encodes information to make proteins required for the structure and functions of cells or tissues. RNA polymerase (RNAP) is a type of protein that produces mRNA. It tracks processively along double helical DNA, untwists it to read the base pair sequence of only one strand and synthesizes a matching mRNA. Such "transcription" of a gene begins when RNAP binds to a "promoter" DNA sequence and ends at a "terminator" sequence where the mRNA copy is released. The canonical view of termination holds that after releasing the mRNA, RNAP dissociates from the DNA.

 

A team of researchers led by Finzi and including David Dunlap, research professor in the Clemson Department of Physics and Astronomy, have, for the first time, demonstrated how force plays a role in an alternative to canonical termination. Using magnetic tweezers to pull RNAP polymerase along a DNA template, the researchers were able to show that upon reaching a terminator, bacterial RNA polymerase may remain on the DNA template and be pulled to slide backward to the same or forward to an adjacent promoter to start a subsequent cycle of transcription. Thus, the direction of force determines whether a segment of DNA may be transcribed multiple times or only once. Furthermore, they found that the ability of a sliding RNAP requires the C-terminal domain of the alpha subunit to recognize a promoter oriented opposite to the direction of sliding.

 

A thorough understanding of the molecular mechanisms that regulate transcriptional activity in the genome may identify therapeutic alternatives in which RNAP might be modified to suppress certain proteins and prevent disease. Finzi said there might be locations in the genome where recycling is more frequent than others, but that is still unknown. The research highlighting the effect of forces on the probability of repetitive transcription may then help predicting and plotting, in a heat map sort of way, the different levels of transcription of different genes.