Dna Methylation Of Cpg Sites Near Gene Of Interest

Question

[qliu2011]

Do we currently have any information (research studies, models, ...etc) on how far away a CpG site is from a specific gene of interest where methylation of that site has an impact on the gene of interest's expression. For example, if I'm interested in CFTR (cystic_fibrosis_transmembrane_conductance_regulator) which is located from 117105838 bp to 117308719 bp on chromosome 7, do we know if a CpG site at 1000 bp may or may not affect this gene's expression.

My gut instinct is that no, we don't have any information on whether a distantly located CpG has any effect on a particular gene's expression, but any current research information on location of methylated sites and their effect on gene expression would be very helpful.

Thanks! Wishing everyone a nice holiday.

Answer 1

[Devon Ryan]

There will be no single answer that will apply to every gene. Enhancer sites, for example, can be quite distal (have a look at some of the Hi-C or similar papers), so one could imagine that altered methylation there could have a similar effect to that right by the TSS. So yeah, your gut is right on this one.

Answer 2

[Charles Warden]

I would recommend checking the UCSC CpG islands track. This is the design for the Illumina methylation arrays and the Agilent targeted BS-Seq kit.

For a handful of genes, you can just use the UCSC Genome Browser:

http://genome.ucsc.edu/cgi-bin/hgGateway

1) Search for your gene

2) Go to Regulation --> CpG Islands, and switch setting from "hide" to anything else (I would recommend "dense"). Then click "refresh". You might also need to hide some other tracks to make the CpG islands easier to visualize

In the case of CFTR, it seems like the nearest UCSC CpG island is fairly far away (overlapping another gene):

http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=354152077&db=hg19&position=chr7%3A117067404-117067666