What does 'distance to cpg' mean? And what is it used for?

Question

[aishsiva03]

Hi, I'm a bioinformatics intern and I have a data set that shows deferentially methylated DNA genes. I have the index number, gene name, level of methylation...etc.

I have also been provided the transcription start site (TSS) (a co-ordinate), the strand (+ or -), CPG ID (cpg island ID) and something called 'Dist2CPG' which I believe is the distance to CPG island.

I don't know if this dist2cpg means it is the distance between the CPG and the TSS or the distance of the methylation from the CPG island. I would be grateful if someone could answer this and explain its significance.

Answer 1

[R. Taylor Raborn]

I think h.mon provided the likely correct answer for what the 'Dist2CPG' value signifies. I'll just add that the association between the TSS and CpG Island is valuable because a prominent number of mammalian promoters are located near CpG Islands. This class of promoter (CpG Island Promoters) isn't as well characterized as the canonical 'TATA-containing' class. Lenhard et al. (2012) is an excellent review on the topic.

As recent work by Piero Carninci, Boris Lenhard (both FANTOM) and Roger Hoskins (modENCODE) (and many, many others) has shown that the distribution of TSSs at a promoter reflects the underlying promoter architecture, knowledge of the proximity of a given TSS (ideally TSS distribution from a CAGE experiment) to CpG islands is valuable, especially on a genome scale. The methylation status (and dynamics, depending on the experiment you have) will be informative and should be consistent with the proximity to a given CpG Island.

The above may be more background than you were looking for, but I hope you (and potentially others) find this additional context informative.

[aishsiva03]

Thank you so much for the information you provided Taylor! I really appreciate it!

[R. Taylor Raborn]

You're welcome! If it was helpful give it a 'thumbs up' so others can (possibly) evaluate it down the road.

Answer 2

[h.mon]

This paper defines dist2cpg as:

dist2CpG is defined as the distance between the nearest point of a given site and the nearest CpG island; dist2CpG = 0 when a site overlaps any CpG island.

[aishsiva03]

Hello h.mon,

Thank you so much for your reply!

I apologize for the silly question but could you please clarify what you mean by 'site'. Do you mean the methylation site on the DNA?

[h.mon]

Any site, in case one refers to a methylation site, yes.

[aishsiva03]

Thank you for your help h.mon!

Do you know if I would be able to find out whether the site is upstream or downstream from the CpG island? I have been given a column titled 'strand' which tells me whether it is the plus or minus strand. Do I need to use that information or do I always assume its downstream of that CpG island?