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?Genome methylation and folate intake
By daniellebourque, Section Biology Posted on Sun May 2nd, 2010 at 05:09:33 PM PST

The goal of this study is to view the effects of different diets on the methylation patterns of repetitive DNA sequences in mice.

Methylation of DNA is associated with genomic regions that are currently inactive (e.g. imprinted genes, repetitive elements). Loss of methylation can result in reactivation of genes/regions that should be inactive and gain of methylation can silence genes that should be expressed. Niacin has previously been shown to be required to keep DNA in an unmethylated state. In contrast, folate has been shown to act as a methyl donor and in turn can increase DNA methylation. I propose to feed mice diets varying in the quantity of niacin and folate (alone and in combination). I would then like to use pyrosequencing to examine the changes in DNA methylation at LINEs (LINE-1) and SINEs (B1, B2) in the mouse genome in this generation and their offspring. Alteration of genomic methylation can potentially lead to problems such as cancer and birth defects.

< Alternative Splicing QTL (6 comments) | A simple method for determining the target genes of transcription factors (0 comments) >

Genome methylation and folate intake | 4 comments (4 topical, 0 editorial)

[new] Accounting for multiple testing (none / 0) (#1)
by dfornika on Tue Mar 27th, 2007 at 01:47:14 PM PST
(User Info)

LINEs and SINEs are present in hundreds of thousands of copies in the genome. At a p0.05 threshold, one would expect to see thousands of positive hits by chance, even if niacin and folate have no effect on methylation status. How can you determine true positives from false positives?

[new] Pyrosequencing (none / 0) (#3)
by daniellebourque on Wed Mar 28th, 2007 at 08:30:55 PM PST
(User Info)

With PCR we can amplify all the LINES/SINES at once (using primers for LINE/SINE specific sequences) and then use pyrosequencing to get an average methylation value for all LINES/SINES that are amplified. That should remove the need for a Bonferroni correction of the p=0.05 threshhold. The goal here is just to get an idea of whole genome methylation, not to get specific methylation values for each LINE/SINE.

[ Parent ]

[new] Focus on specific candidate genes? (none / 0) (#2)
by awang on Tue Mar 27th, 2007 at 06:54:07 PM PST
(User Info)

Do you think it would be better to focus on the DNA methylation of specific candidate genes that may be involved, instead of looking at the entire genome?

[new] Comment (none / 0) (#4)
by LubaV on Thu Apr 12th, 2007 at 02:55:40 PM PST
(User Info)

It seems that the study has been done before by Randall Parker with synthetic form of folate. The result was change in gene Agouti, which among other things regulates coat color. The study mentioned that for know they don't know how to account for methylation timescale. Methylation at one stage unexpectedly may be a good thing , while later one it will be a negative thing. How are you going to account for different satges during the development?

Genome methylation and folate intake | 4 comments (4 topical, 0 editorial)

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