Hi all,

I've recently begun analyzing Northern blots, and I'm finding multiple bands when using a single probe. I understand that the different bands represent different lengths/species of transcript originating from the same promoter, but I am puzzled as to why the transcript appears to end in the middle of a gene (i.e. incomplete transcription). There are no putative rho-independent terminator sites, and S. mutans does not contain rho-dependent terminators. Any help would be appreciated.

Do you really know all transcripts have the same 5' end? I'm no expert in terminators, but I there could be other reasons for the bands than diff termination sites. Are you using a single stranded probe (and not detecting minus stranded transcripts too)? Is there a cross-hybridizing gene in S. mutans? What is known about RNA splicing in this species?
dan

There is as much (or greater) chance that you are seeing different promoter locations than different terminator locations in prokaryotic systems. You can also see transcriptional readthrough of an upstream terminator (another way of saying the same thing, for larger length differences).

It is possilbe that we are seeing read through of an upstream terminator, that is something that I will evaluate. Primer extension analysis indicated that the transcription start site for the gene of interest was in the region downstream of the terminator, but again I will look at the promoter of the upstream gene to see check the possibility of expression from another promoter. Thanks for all of your input!