Conventions For Designating Forward And Reverse Strands

Question

[Bio_X2Y]

I always assumed the designations of "forward" and "reverse" strand on DNA were chosen arbitrarily (i.e. the strands could just as easily have been named the other way around).

However, a quick browse of the chromosome maps for Human on the NCBI map viewer seems to imply that in all cases, base numbering starts on the side closest to the centromere. Assuming that this numbering applies to the "forward" strands of the reference genome, does this mean that, for humans at least, there is a policy whereby the forward strand is always the one which contains the centromere at the lowest numerical index?

Also, if this is the case, does anybody know if this convention would apply outside humans?

Thanks for your time.

Answer 1

[Casey Bergman]

...does this mean that, for humans at least, there is a policy whereby the forward strand is always the one which contains the centromere at the lowest numerical index?

Yes, in humans the centromere is always closest to the start coordinate of each chromosome, since human chromosomes are oriented based on their p (for "petit") and q arms. The p and q designation comes from the size of the chromosomes arms observed classically during mitotic cytogenetic preparations.

Also, if this is the case, does anybody know if this convention would apply outside humans?

No, this convention does not apply generally outside of humans. For example, the yeast Saccharomyces cerevisae has sixteen chromosomes, 9 of which have the centromere closer to the start of the chromosome than the end.

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D sacCer1 -e 'select sgdOther.chrom as "chrom.", size as "chrom. size", sgdOther.chromStart as "left arm", size-chromStart as "right arm", chromStart/(size-chromStart) as "left/right ratio"  from sgdOther, chromInfo  where name like "CEN%" and sgdOther.chrom=chromInfo.chrom order by size/(size-chromStart);'
+--------+-------------+----------+-----------+------------------+
| chrom. | chrom. size | left arm | right arm | left/right ratio |
+--------+-------------+----------+-----------+------------------+
| chr12  |     1078173 |   150826 |    927347 |           0.1626 | 
| chr8   |      562639 |   105578 |    457061 |           0.2310 | 
| chr5   |      576869 |   151959 |    424910 |           0.3576 | 
| chr13  |      924430 |   268030 |    656400 |           0.4083 | 
| chr2   |      813136 |   238167 |    574969 |           0.4142 | 
| chr4   |     1531914 |   449706 |   1082208 |           0.4155 | 
| chr15  |     1091285 |   326583 |    764702 |           0.4271 | 
| chr3   |      316613 |   114378 |    202235 |           0.5656 | 
| chr7   |     1090944 |   496920 |    594024 |           0.8365 | 
| chr6   |      270148 |   148503 |    121645 |           1.2208 | 
| chr10  |      745446 |   436001 |    309445 |           1.4090 | 
| chr16  |      948060 |   555951 |    392109 |           1.4178 | 
| chr1   |      230208 |   151456 |     78752 |           1.9232 | 
| chr11  |      666445 |   439773 |    226672 |           1.9401 | 
| chr14  |      784328 |   628756 |    155572 |           4.0416 | 
| chr9   |      439885 |   355625 |     84260 |           4.2206 | 
+--------+-------------+----------+-----------+------------------+

Answer 2

[Fred Fleche]

http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation

You can also have a look at the last edition of the International System for Human Cytogenetic Nomenclature. http://www.amazon.com/ISCN-2009-International-Nomenclature-Recommendations/dp/3805589859/

[Andrea_Bio]

I don't why it is this way but I can confirm this is what i was taught in 1999 and i believe it applies to all organisms

Answer 3

[Jorge Amigo]

although I'm not able to explain the coincidence that the forward strand may be the one containing the centromere at the lowest numerical index, I should point out that the orientation of a DNA strand is a basic molecular genetics convention that just has to do with the synthesis of the RNA, which proceeds in the 5' → 3' direction. this convention states that a DNA sequence read in 5' → 3' direction is referred as "forward" or "+", and a DNA sequence read in 3' → 5' direction is referred as "reverse" or "-".

PS: of course this applies to all organisms, as long as they are DNA based ;)

[Bio_X2Y]

Hi Jorge, I think you're hitting on a different meaning of forward/reverse here than the one I mean. You're referring to the forward/reverse "reading directions", which, I agree, depends on the chemistry. However, I'm referring to the fact that in any annotation, one of the two strands of a chromosome is designated the "forward strand" and the other is designated the "reverse strand" (even though both strands have can read in the "forward direction (5-3)" or the "reverse direction (3-5)", depending on what we're doing).

[Jorge Amigo]

I think I get your point, but the forward and the reverse strand are always the same ones, and they are labeled following this convention for the mentioned normalizing reason: to try avoiding anyone to have the doubt you are having. of course you can read the forward strand in reverse direction if you want to, but it will still be the forward strand.