Making sense out of the visual representation of transcription

Question

Most people are familiar with the following diagram. Some genomic DNA with a promoter region, exons and introns. This is transcribed into RNA that is then translated into a polypeptide.

When we look closer at the strand that is being transcribed we can distinguish between the two as the sense and anti-sense strands.

So the transcription factors and RNA polymerase bind and begins transcribing mRNA in the 5' to 3' direction and thus reading the anti-sense strand in the 3' to 5' direction and have the same sequence as the sense DNA strand, substituting U for T in the mRNA.

My question would be, shouldn't the exons be numbered in the reverse order as shown in the first picture I provided. So instead of Promoter -> Exon1 -> Intron -> Exon 2, should it be, Promoter -> Exon N -> Intron -> Exon N-1?

Also, in bioinformatic sites are the gene sequences listed in the sense or anti-sense strand? I have noticed in some bioinformatic tools, to determine what polypeptide will result from a DNA sequence, one must input the sense strand in 5'to 3' orientation and not the anti-sense strand.

Answer 1

Gene sequences are annotated in the sense strand. So, these diagrams are correct.

Answer 2

In the top diagram, the ATG start is on the left, and the stop codon is on the right. Exon one is the left most exon. That's all correctly illustrated. If you look up a transcript sequence in, say, ensembl, it will be the same way, the start sequence will be in the beginning, the stop codon at the end. That's the convention.

Answer 3

All visual representations and nearly all coordinate systems are based on the sense strand. The polymerase machinery has no clue about what is sense and what is antisense, because each is the antisense of the other.

For visual representation this makes much more sense and relays more information as it removes the extra complicated layer of information. And, in most cases the gene structures are declared in the order of the reference genome which is always the positive or sense strand.

Next coming to the bioinformatics part, most of your databases such as UCSC, Ensemble and NCBI maintain gene coordinates on the reference genome, But, there's a catch, when reporting the information through a bed file,

Negative stranded genes are reported as chromosome stop start by NCBI (last I used it was a one a half years ago), UCSC will provide the chromosome start stop and both will report the strandedness, UCSC expects that you the bioinformatician will create the reverse complement when you find the strand information, while NCBI expects that your program will fail a sanity check because stop - start will come as negative, implying that you cannot make a mistake while parsing NCBI bed files. Furthermore, UCSC indexes are maintained as 0 based, while NCBI is maintained as 1 based.

I would urge you to validate this information

But why not just keep a negative strand as well? while keeping the gene coordinates and elements for the antisense in the format you just mentioned.

Because speaking from a Computational point of view it just makes more sense, this system would consume more storage (please remember the entire system was formulated before storage became as cheap as it is today) it would consume more memory during tasks (exactly double of what it is consuming today). So it's just better to have a positive strand reference genome and all genes and elements based on that.

Just an example of how alignment of sequencing reads works,

1. You align your read to the reference genome
2. Aligns? If yes it has mapped to the positive strand
3. No? Reverse complement the read and align back
4. Aligns? If yes it has mapped to the negative strand
5. No? Possibly an erroneous read or other artefacts.