Who/What Determines The Sense And Antisense Strand

Question

[John]

Hello everyone!

So a pretty simple question - but when you sequence a chromosome does it have any innate strandedness? Or did someone just decide when DNA came off the sequencer that primer X was binding to the sense strand and primer Y was binding to the antisense strand, and so long as everything else thats mapped is mapped to the right strand, it doesn't really matter what you call sense and antisense?

The reason I ask is that there are gaps in every organisms genome, and surely as soon as you have a gap you don't know if the 'sense' DNA either side of the gap are actually on the same strand. Perhaps in the future when that gap gets filled, you'll find your sense's don't match up.

Does my question make sense? ;-)

~ John

[Istvan Albert]

In general I think that it is safe to assume that there are checks and balances in place to ensure that sequences separated by gaps are on the same strand.

[John]

Without understanding how it could be theoretically possible, I would avoid assuming anything :P

[Neilfws]

I think one issue here is that "sense strand" and "antisense strand" are confusing terms and not especially helpful.

[Istvan Albert]

indeed, this is a terminology that I also find to be both unfortunate and inappropriate. Same with calling them "top" and "bottom" strands.

Answer 1

[swbarnes2]

No. DNA doesn't have strandedness in a biological sense.

However, reference sequences are simple strings, not double-stranded, so a read can either be going in the same direction as that reference, or in the opposite direction. Which way the reference runs is kind of an arbitrary decision, based on conventions. For instance, in bacteria, you tend to start at the place where DNA replication starts, and that direction that replication happens in is "forward". For an acro-centric chromosome, "forward" tends to run away from the centromere, towards the telomere.

As far as your question, I think it is safe to assume that both pieces of DNA flanking a gap are in the appropriate orientation with respect to each other, until such time as you have compelling evidence that they are not.

[John]

I see, so if you sequenced the DNA going towards a telomere at one end, and away from the telomere at the other, those sequences are on the same strand even though you have the 'gap' of the unsequenced centromere in the middle. Same would be true for DNA going towards/away from the centromere.

I guess this is only a problem when you don't have a genetic landmark and your DNA is just a small fragment. But the strandedness also determines the orientation and thus order of the genes, so you could use FISH or whatever you to see if Gene A before the gap is closer to Gene B (at one end of the fragment) or Gene C (other end of the fragment).

Man.... i don't envy people doing de novo assembly one bit :P Thanks guys!