Every now and then, a study appears that reminds us how little we know about some of the most basic subjects in molecular biology, while at the same time expanding the connotations associated with these seemingly simple mechanisms. A recent paper in Science by a multinational collaborative team was a perfect example of one such moment for me. The problem statement is relatively simple: how does RNA polymerase recognize the orientation of DNA; in other words, how does it know towards which direction it should be heading? The answer as I knew it, was two parts: (i) there are certain promoter elements that are in of themselves directional, meaning the transcription complex specifically recognizes one strand and not the other (e.g. the world famous lac promoter is one such example). (ii) in cases where there is no directionality coded in the DNA or the epigenome, the polymerase in fact does go the wrong way, which produces the myriad anti-sense RNAs in the cell. Granted, there might be functionalities associated with these anti-sense RNAs, however, established examples are few and far between.
The more important observation, however, is the fact that there are genetic components to when the anti-sense RNA is transcribed and when it isn’t. The aforementioned study starts from one such mutant (ssu72) and goes on to dissect the mechanism through which Ssu27 establishes directionality of the RNA polymerase complex. The results are very simple and elegant: Ssu27 is a part of a bridging complex that demarcates the start and end of the gene, and consequently the correct direction for transcription (below you can see the figure from the main paper).
Ssu72-mediated loop formation
Now one might be wondering why all promoters are not directional at the sequence level? The short answer, I think, is “regulation”. There are a variety molecular mechanisms through which promoter directionality can be used in gene regulation, both for the downstream gene as well as the upstream ones. For the immediate gene, losing half of initiation complexes to the wrong direction ensures lower expression, a fraction that can very well be modulated (e.g. through regulating ssu72 in this example). And for the upstream of genes (as well as the downstream one), the presence of anti-sense RNA spells some form of doom or desist.