Why do RNAseq reads align to non-gene regions of the bacterial genome?

Question

[Texx]

I played a bit around with visualizing the RNA reads from the sequencing of the bacterial transcriptome and see that a lot of reads align to the regions in the genome that are not annotated as genes.

Of course, the explanation could be contamination with the bacterial DNA during sequencing, but since the samples were subjected to DNase treatment this is a less likely explanation. Another possibility is that those non-annotated regions are actual genes, but this is even less likely.

I'm wondering whether the real reason is actually that the RNA polymerase during the transcription doesn't stop immediately at the end of the protein encoded by the gene, but continues until it falls off the strand in either rho-dependent or independent way.

What do you think?

Answer 1

[Mensur Dlakic]

I'm wondering whether the real reason is actually that the RNA polymerase during the transcription doesn't stop immediately at the end of the protein encoded by the gene, but continues until it falls off the strand in either rho-dependent or independent way.

This is certainly a possible reason. Others:

• 5' and 3' untranslated regions
• non-coding RNAs
• polycistronic transcripts

Answer 2

[i.sudbery]

As Mensur Dlakic noted, bacteria have 3 and 5' untranslated regions like any other organism. The polymerase absolutely doesn't stop at the end of the protein coding regions. This is well known. Note, its not just that this sometimes happens, but it is the norm.

Its also that case that bacterial genes are transcribed as cistons (again, as noted by Mensur). Cistrons are single transcripts that contain the coding sequence for multiple proteins. Again, this is the rule, rather than the exception in bacteria.

However, its also worth noting some other explainations.

Firstly you dismess genomic contaimination, but you shouldn't - no DNase treatment is 100% effective, and your intergenic signal is much weaker than, say, the signal at the gene at the left of the plot you show.

Secondly, polymerase binding and transcription initiation is a stochastic process. It happens at all points in the genome at some low level. If you sequence deeply enough you will find transcription from any part of a genome.