Confused on strandedness, what are antisense transcripts?

Question

[coboyfan12]

Hello, I am trying to wrap my head around anti-sense transcripts.

When looking at refseq's annotations on IGV you can see a (-) or a (+) for each transcript.

From reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664467/#sec-2title I understand that transcription from the antisense strand is most common and primarily comprises protein coding genes. However, it mentions there can be transcription from the sense strand? Referring to the image below and what I think I know about RNA polymerase is that it only acts on the antisense (-) strand because it builds from 5' -> 3'.

So how can it be the case that there can be sense (+) or antisense (-) transcripts if RNA polymerase builds in one direction? I understand the from this image you could simultaneously transcribe from the other strand, but then the naming scheme would flip, no? Then they would both be considered (-) right?

Answer 1

[dsull]

Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" transcript. If the mRNA made is the reverse complement of the "sense" DNA strand, it is "antisense" RNA.

In the picture, simply flip the RNA pol so that it points left and put it on the bottom DNA strand. Realize that now your resulting transcript is the reverse complement sequence of the "sense" (green) transcript so we call the transcript "antisense".

One strand is designated sense and the other strand is designated antisense. The "sense" is the orientation where you make proteins (i.e. you start from the ATG start codon and end with a TAA/TGA/TAG stop codon).

Better explanations here: Forward And Reverse Strand Conventions