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Putative tumor suppressor promoter heavily methylated yet upregulated by DNA dam


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#1 darthvader

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Posted 22 April 2011 - 01:59 AM

Hi All,

Have a puzzle now bothering me. Hope someone can shed some light to help me please!

I am working on a putative tumor suppressor and found that its promoter is heavily methylated and expression silenced in a number of cancer cell lines. However what really baffles me is that take a few of these cell lines and treat it with DNA damage drugs like Adriamycin and also UV irradiation and this gene is up-regulated strongly after 24 hours (up to 6-fold increase in mRNA transcripts) with NO removal of its promoter DNA methylation. In addition, Fetal Bovine Serum (FBS) can strongly upregulate this gene by up to 60-fold after just 2 hours of adding new culture media to the cells and again with NO changes to the dense DNA methylation at its promoter.

Can anyone shed some light on this phenomenon? Also if there are any genes that exhibit such traits, please do point me to it. It is bothering the hell out of me!

Darth

#2 darthvader

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Posted 22 April 2011 - 05:17 PM

Anyone can help?? PCRMan??? Methylnick??? Anyone???

#3 pcrman

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Posted 02 May 2011 - 10:45 PM

I don't think this is a big surprise. Apart from DNA methylation, there are many other way for transcriptional regulation. Does the gene have a CpG island in its promoter? Although you observed heavy methylation of its promoter and the methylation correlates with reduced expression in some cell lines. This does not necessarily mean a cause-effect relationship. Not all methylation in promoters has an impact on gene transcription. Since your gene is upregulated so quickly after treatments, neither de novo methylation is the mechanism for silencing nor de-methylation is the mechanism for reactivation.

#4 darthvader

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Posted 13 May 2011 - 01:04 AM

I don't think this is a big surprise. Apart from DNA methylation, there are many other way for transcriptional regulation. Does the gene have a CpG island in its promoter? Although you observed heavy methylation of its promoter and the methylation correlates with reduced expression in some cell lines. This does not necessarily mean a cause-effect relationship. Not all methylation in promoters has an impact on gene transcription. Since your gene is upregulated so quickly after treatments, neither de novo methylation is the mechanism for silencing nor de-methylation is the mechanism for reactivation.


Hey pcrman! Thanks for your reply!!!

Yes the gene has a BIG CpG Island spanning something like 2000+ bp and covering the whole of exon 1, intron 1 and part of exon 2! Yes I observed that the CpG island is densely methylated in tumor cell lines but not in normal cell lines also and that the dense DNA methylation can be reversed by Aza treatment and re-expression is induced as a result.

Regarding this statement of yours can you please elaborate?

"Since your gene is upregulated so quickly after treatments, neither de novo methylation is the mechanism for silencing nor de-methylation is the mechanism for reactivation."

I checked through Pubmed and found that HIC1 is also regulated something like my gene. http://mcr.aacrjourn...6.full.pdf html




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