What Do The Terms 'Strand' And 'Directionality' Mean?

Question

[roll]

Hi,

I have a very basic question in genetics. I don't have any biological science degree, so if you can please explain it to me in a very simple way I will be gratefull.

What does strand means and what is + and - strand means? are they the same as upstream and downstream? or does this also show the direction of the reads?

Answer 1

[Emily]

You know how the structure of DNA is the double helix, two strands, joined together by cross-bars, twisted around. The monomers that make up the DNA are non-symmetrical - they have a 5' and 3' end. This means each of the two strands has a direction and a 5' and 3' end, and they go in opposite directions to one another. Each chromosome is a single length of DNA, which means it has two strands running in opposite directions to one another; we label one of them as the positive, forward or + strand, and the other as the negative, reverse or - strand. We normally draw chromosomes with the + strand on top, going left to right, and the - strand underneath going right to left, and we count chromosomal position from left to right.

Genes have a direction too; they are always transcribed from 5' to 3'. Genes can occur on either strand, so will be transcribed left to right in our diagram if they're on the + strand, and right to left if they're on the - strand. + strand genes will have start position < end position, whereas - strand genes will have start position > end position.

Upstream and downstream are descriptors of other features in relation to another feature. We describe something as upstream if it's at the 5' end of a feature and downstream if it's at the 3' end. This will depend on the strand of the feature we're looking at. So an upstream feature of a + feature will have a lower number for its position and will appear to the left in our diagram. An upstream feature of a - strand feature will have a higher number for its position and will appear to the right in our diagram.

[roll]

Thanks Emily_Ensembl. this is great. As a follow up question i would like to find features that are 1000kb upstream of my positive strand genes. I am using bedtools windows for this. Do i need to use bedtools windows -l 1000 or bedtools windows -r 1000 -sw ?

[Emily]

I think you should probably post this as a separate question. I'm not familiar with bedtools, and you'll get more coverage if you post separately.

Answer 2

[Michael]

http://en.wikipedia.org/wiki/Sense_(molecular_biology)

[PoGibas]

Link is not working (parentheses missing)... Should be like this: Sense_(molecular_biology)

[Michael]

Thanx, auto formatting of URLs did not work correctly in this case