"coding strand" or " template strand" ? - (Sep/02/2012 )
Most papers I read analysised "coding strand" methylation status. I am very confusing about that.
Since transcription always happened in “template strand”, so coding strand methylation has nothing to do with transcription.
Am I wrong?
I thought we should use template strand sequence to design the MSP/BSP primers instead of coding strand sequence.
The coding strand is the one with the gene sequence that then is transcribed to make the mRNA... I don't get your question.
bob1 on Mon Sep 3 01:09:32 2012 said:
The coding strand is the one with the gene sequence that then is transcribed to make the mRNA... I don't get your question.
Its the non-coding strand that is used for the template for the mRNA, not the coding strand.
So I think what paulcross is asking is does (and how?) the methylation on the coding strand have any effect on the transcription of the template strand into mRNA. (is that what you mean, paul?
) leelee on Mon Sep 3 06:45:08 2012 said:
bob1 on Mon Sep 3 01:09:32 2012 said:
The coding strand is the one with the gene sequence that then is transcribed to make the mRNA... I don't get your question.
Its the non-coding strand that is used for the template for the mRNA, not the coding strand.
So I think what paulcross is asking is does (and how?) the methylation on the coding strand have any effect on the transcription of the template strand into mRNA. (is that what you mean, paul?
)YES！That‘s what I mean.
And I also want to ask some thing related to this: Why we search CpG islands in coding strand ? Coding strand never get transcribed. Why we always stick to it?
Actually if you imagine it on a double-helix CpG islands are on both strands 
Trof on Tue Sep 4 08:14:58 2012 said:
Actually if you imagine it on a double-helix CpG islands are on both strands
coding strand 5'----gcgcgcgcgcgc--........--cgcgcgcgcgcg---
template strand 5'----cgcgcgcgcgcg--........--gcgcgcgcgcgc---
One CpG island or TWO CpG islands?
Your example would be two, separated by an elipsis. Ones on complementary strands would not be considered separate islands.
Doesn't methylation lead to histone modification and formation of chromatin... inhibiting separation and hence transcription.
@paulcross: I don't understand what you ask. CpG island should be at 200bp long with high percentage of GC and CpG sequence. Your example is not. It can be within one island or not, still I don't see a point of counting them unless you want to compare between different organisms or whatever.
You asked why people search for them in coding strand, when it's not transcribed. Since CpG is a palindrome, it's always on both strands, so you can search whatever one, coding strands are mostly in the databases.
Trof on Tue Sep 4 09:23:34 2012 said:
@paulcross: I don't understand what you ask. CpG island should be at 200bp long with high percentage of GC and CpG sequence. Your example is not. It can be within one island or not, still I don't see a point of counting them unless you want to compare between different organisms or whatever.
You asked why people search for them in coding strand, when it's not transcribed. Since CpG is a palindrome, it's always on both strands, so you can search whatever one, coding strands are mostly in the databases.
Its just a schematic. I dont think I need to type 200 CG twice!
What you said "Since CpG is a palindrome, it's always on both strands" is wrong. CpG island in one strand, doesn't mean it would appear in another strand. One example is that if coding strand are consisted of 200 CGs , there would be 200 GCs in another strand. Since their transcribe direction are the same( no need to explain ) , there would be no CpG island in template strand at all.
bob1 on Tue Sep 4 09:10:48 2012 said:
Your example would be two, separated by an elipsis. Ones on complementary strands would not be considered separate islands.
Doesn't methylation lead to histone modification and formation of chromatin... inhibiting separation and hence transcription.
Methylation iinterrupted the transcription factors binds to DNA , then lead to mRNA treanscription decrease. That‘s why we focused on the TFBS methylation status in promoter region, in methylation study.