Look in one of my recent reviews - Vinkers et al, Epigenomics 2015, 7(4),593-608, PMID:26111031. Copy available here:- https://www.researchgate.net/publication/279303256_Traumatic_stress_and_human_DNA_methylation_A_critical_review

Figure 1 shown the numbering and the sequence of promoter 1F from the different groups working on the 1F promoter.

Hope this helps

Jon

Article Traumatic stress and human DNA methylation: A critical review

There are fundamentally three numbering systems, from three key papers.

The first paper was our 2008 Nucleic Acids Research paper (PMID:19004867). Here we numbered the CpGs from the start to the end of the promoter 1F from 1 to 42.

The second set of numbers were from Oberlander et al in Epigenetics (PMID:18536531). They only amplified the last few nucleotides, and had their own numbering system, 1-3 that are physically the 40-42nd CpGs in the promoter.

The third was from McGowan et al in Nature Neurioscience from 2009 (PMID: 19234457) where they did most of the promoter, but missed off the first 4 CpGs. Their number 1 is physically the 5th CpG in the promoter.

All subsequent studies have used one of these three numbering systems. The example you give (bottom of page 596, reference 44, CpG 1 and 3) is from Tyrka et al, where they have used the Oberlander assay and numbering scheme. And, in your original question Yehuda et al (Table 3, reference 55) actually uses the assay and numbering from McGowan et al.

So, as I said in my original reply, if you look at Figure 1B, you see the sequence with the CpGs numbered from the start to the end. Below that, you have the grey bar with the McGowan numbering where they started a bit later in the promoter. Their number 1 is actually the 5th CpG in the promoter. In white bars, you then have the Oberlander numbering, where they only amplify the 3' end of the promoter, and 1, 2, and 3 correspond to the 30th-42nd CpG in the promoter, and CpGs 36-38 in the McGowan numbering.

Hope this helps

Jon

@Jonathan D Turner, Awesome Dr. Jonathan. Thank you very much indeed for this detailed clarification. You clarified everything for me.

Best Regards.