Question: How to find CpG island shore?
0
gravatar for achamess
6.0 years ago by
achamess50
United States
achamess50 wrote:

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.

methylation • 4.9k views
ADD COMMENTlink modified 3.3 years ago by EagleEye6.6k • written 6.0 years ago by achamess50
1

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

ADD REPLYlink written 4.9 years ago by Shicheng Guo8.2k
4
gravatar for Chirag Nepal
6.0 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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.

ADD COMMENTlink modified 4 months ago by RamRS27k • written 6.0 years ago by Chirag Nepal2.2k

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

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

ADD REPLYlink written 5.6 years ago by Chirag Nepal2.2k
0
gravatar for mark.ziemann
5.2 years ago by
mark.ziemann1.2k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.2k wrote:

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

 

ADD COMMENTlink written 5.2 years ago by mark.ziemann1.2k
0
gravatar for EagleEye
3.3 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

Here is one more solution,

ADD COMMENTlink modified 4 months ago by RamRS27k • written 3.3 years ago by EagleEye6.6k
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