I'm doing a homework about finding the CpG islands within a gene of our interest. I picked the FXN gene and found 11 possible CpG islands using this website http://dbcat.cgm.ntu.edu.tw/.
I'm also supposed to find out what role do these regions may play in gene regulation and transcription however I'm lost at this point. I know that if there is a CpG island close to the promoter region, it has a role in gene silencing but all of the islands in this gene appear to be located in introns only so they don't overlap with exons either. What kind of a role CpG islands may play if they're on the non-coding sequences?
Hi Nursena
CpG island often take a role in methylation process, especially in cancer cases, up or down regulating the proximal gene.
you can choose to see at the UCSC database (http://genome.ucsc.edu) where the genome browser and its options will give you positions of these sites, methylation aspects and chip-see data.
all the best
fred
Hi Nursena Kayabasi ,
CpG's in islands located near promotors are usually methylated and play a role in gene regulation (as mentioned) while CpG's in gene regions like introns/exons tend to be unmethylated. Methylation at such sites is usually subject to persistent epigenetic remodeling as part of genome packaging and chromosome structure but tend to become globally hypomethylated with age. I would check if there is any literature on this gene having parental imprinting - a quick search I did found a few articles on the epigenetic silencing of this gene and its involvement in Friedreich's ataxia (Article Gene regulation and epigenetics in Friedreich's ataxia
) which might be relevant to what you're looking at.
If this is for a homework assignment, then check your class notes!
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