Researchers are divided over whether RNA polymerase tracks down genes that are ready to be transcribed or whether the enzyme remains in place. Xu and Cook add to the evidence that a gene has to relocate to one of a few sites in the nucleus to be transcribed.

One possibility is that the RNA polymerase, the DNA-reading enzyme, moves from gene to gene, transcribing each in situ. The alternative is that active RNA polymerase molecules remain stationary in “factories,” which genes visit to be transcribed. Some results support the existence of these factories, but the issue remains controversial.

Xu and Cook tackled the question by inserting two plasmids that carried different promoters and identifier genes into monkey cells. The plasmid DNA fused to form minichromosomes that the host's RNA polymerase can read. The researchers then tracked these minichromosomes to determine where they were being transcribed. Instead of spreading around the nucleus, they clumped at only about 20 sites, the team found. Minichromosomes with the same promoter ended up in the same location, even though their genes differed. But minichromosomes with different promoters separated. Intron-carrying and inton-lacking minichromosomes went to different locations, although the reason for this separation is mysterious.

The findings offer further backing for the presence of transcription factories, the team says, and suggest that the factories specialize to handle certain types of genes. The researchers now want to determine how many kinds of transcription factories a cell contains and what directs genes to particular ones.

Xu, M., and P.R. Cook.
J. Cell Biol.