When reading publications doing transcriptomics studies in bacteria (microarray or qPCR on e.g. L. lactis, B. subtilis, E. coli), I often see that only a subset of genes on the same operon are up-regulated by some condition. Some explicitly state that no change in expression was observed in genes downstream or upstream of one gene. Anyone know the primary mechanisms involved here?
There are a variety of ways that you can get differential expression of genes in an operon. You could have more than one promoter so that the entire operon is expressed from one but an internal promoter, regulated independently, expresses only a subset of genes. Or you could have an internal terminator so that transcription only covers a subset of genes (and termination could be regulated). The Trp operon attenuator is an example but there are many others. There could also be mRNA processing occurring, although this is more rate in bacteria. Obviously translation can also be differential but you specifically only mention transcriptomic experiments.
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