Studies measuring mRNA abundance, such as those using microarrays, have often been used as a proxy for transcriptional control of gene expression. However, the quantity of a given mRNA at any time is a balance between its production and degradation. In an article recently published in Genome Biology, Oliver Rando and colleagues at the University of Massachusetts have shown that mRNA abundance does not always correlate with the quantity of RNA polymerase on a gene, and thus mRNA abundance is not always a good indicator of transcriptional activity.
Rando and colleagues exposed yeast cells to two different stresses. They then measured mRNA abundance using microarrays and PolII localization using chromatin immunoprecipitation. In general, PolII abundance did explain mRNA abundance, but there were genes which showed an excess or dearth of mRNA per PolII molecule. Interestingly, in many cases those genes were also those showing non-productive transcription – transcription of non-coding genes overlapping the coding genes. Rando concludes that genes not involved in normal growth show non-productive transcription, but that when the cells are stressed the polymerase shifts to the 5′ end of the genes to transcribe as they are needed.
Thus, not only has this study shed light on how mRNA levels correlate with PolII activity, it has also revealed a potential new way to regulated gene expression via non-productive transcription.