How to find CpG island shore?

Question

[achamess]

Hi,

I'm interested in analyzing the methylation of the TRPV1 gene. I need to find CpG islands as well as CpG island shores, since I've read these these shores can also be differentially methylated, even when the CpG islands aren't.

Could anyone point me to some web based or desktop tools to find CpG island shores? Or, if there aren't any tools off-the-shelf, could you describe a method for finding these shore regions?

Thanks.

[Shicheng Guo]

I tried to write a perl code to subtract 2000bp and add 2000 to the CpG island region to get CpG shore regions (55436 CpG shores) [Note: I removed chrUn, random and hap regions from hg19 genomes]. and then use bedtools subtract to remove CpG shores overlapped with CpG island (48790) and then merge the CpG shores which are overlapped within CpG shore regions (46817 CpG shore). 

Eventually, 46817 CpG shore region were obtained. and you can download this annotation: hg19.cpgshoreExt.txt

You can find the code in Perl Script for Bed file preparation for CpGI, CpG Shore, CpG shelf regions

Answer 1

[Chirag Nepal]

https://www.ncbi.nlm.nih.gov/pubmed/19151715

Here we show that most methylation alterations in colon cancer occur not in promoters, and also not in CpG islands, but in sequences up to 2 kb distant, which we term 'CpG island shores'.

It it is so, it is very st forward to get shores, using one liner in awk.

[Chirag Nepal]

Now there is CpG "ravines", inaddition to CoG island and CpG shores

http://www.epigeneticsandchromatin.com/content/7/1/28/abstract

Answer 2

[mark.ziemann]

You can find CpG shores by looking firstly at where the CpG islands are on your gene at the UCSC browser under "regulation" and then work in a 2 kbp window.

If you need to identify them across the whole genome, just follow my blog post.

http://genomespot.blogspot.com.au/2015/04/what-is-cpg-shore-and-how-to-i-get-them.html

Answer 3

[EagleEye]

Here is one more solution,