"coding strand" or " template strand" ? - (Sep/02/2012 )

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@paulcross: I'm sorry, but you should refresh your DNA basics.
If you have CG on one strand 5'->3', you have GC on the other strand, but 3'->5', that means CG 5'->3'. And that's the same on both strands.

Methylation is on both strands too, since it takes place in the cytosine of CpG site. After replication of DNA, the single stranded methylation marks are quickly recognised and methylated on the daughter strand, which leads to preservation of the methylation pattern through division.

-Trof-

Trof on Tue Sep 4 12:48:59 2012 said:

Methylation is on both strands too, since it takes place in the cytosine of CpG site. After replication of DNA, the single stranded methylation marks are quickly recognised and methylated on the daughter strand, which leads to preservation of the methylation pattern through division.

You got it all wrong！

I will explained it in a real gene sequence.

Human Gene SUMO1 (uc002uza.1) NM_001005782

The first several bases of SUMO1 Exon1.

...coding strand ---------------tgcgcgaaGCGGAAGTGACGCGAGG
template strand ---------------acgcgcttCGCCTTCACTGCGCTCC

You can see that coding strand sequence start from tgcgcg to GAGG(left to right) , like the mRNA sequence. We use this direction and sequence to search CpG island !

Template strand are about to bind with transcription factors to start the TRANSCRIBE! So its direction also start from left to right. That is the direction gene transcription goes on.

If the template strand start form right to left , SUMO1 gene wont get expressed. It make no sense.

-paulcross-

This is your SUMO1 mRNA sequence (same as coding sequence).
If you search in page for your "GCGGAAGTG" from your first line, you will find it.

Now select Show reverse complement from the right Customize view menu. This should be your template strand. Try to find there your "CGCCTTCAC" from your second line. You will not. Because that's a 3'->5' direction what you have.
You will only find it's reverse orientation "CACTTCCGC" there. Because all sequences are read 5'->3'.

5' tgcgcgaaGCGGAAGTGACGCGAGG 3' coding
3' acgcgcttCGCCTTCACTGCGCTCC 5' template

That's the reality of your sequence. If the coding strand separates the polymerase will create new strand also in the 5'->3' direction, so it will actually move on the template strand in the 3'->5' direction. This is because polymerase can add nucleotides to existing 3' end only and the strands have to be anti-parallel.

5' tgcgc3' polymerase-> 3' new strand
3' acgcgcttCGCCTTCACTGCGCTCC 5' template

I know it can be confusing, but you better check it out in some book before you make some serious mistakes in your work.

-Trof-

Trof on Tue Sep 4 14:04:24 2012 said:

That's the reality of your sequence. If the coding strand separates the polymerase will create new strand also in the 5'->3' direction, so it will actually move on the template strand in the 3'->5' direction. This is because polymerase can add nucleotides to existing 3' end only and the strands have to be anti-parallel.

5' tgcgc3' polymerase-> 3' new strand
3' acgcgcttCGCCTTCACTGCGCTCC 5' template

I know it can be confusing, but you better check it out in some book before you make some serious mistakes in your work.

I see ！

I paid too much attention on the actual mRNA transcribing direction, but its irrelevant to DNA methylation.

THANK YOU!

-paulcross-

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