DNA bioinformatic search and methylation analysis by qMSP

Question

Im quoting the methods which was used

We performed a bioinformatics analysis to identify potential CpG islands in the genomic sequences of RANKL and OPG genes. The USCS Human Genome Browser public database (genome.ucsc.edu), the Primer Express software (available from Applied Biosystems), and CpG Island Explorer software (cpgie.sourceforge.net) were used to explore the nucleo- tide sequences surrounding de transcription start site (TSS) of RANKL isoforms I and II (NG_008990.1 Ref Seq Gene), and OPG (NG_012202.1 Ref Seq Gene). A (C + G)/total bases ratio

0.5 and CpG observed/CpG expected ratio >0.6 were used as criteria.

Im looking for the region which they have used

This is the paper

"Role of DNA methylation in the regulation of the
RANKL-OPG system in human bone"

I tried using ucsc to check the region but didn't get much. The idea is to find the region to design the primer for the same

How can i get the region from ucsc ,the CpG island around the TSS of the above mentioned genes which are RANKL and OPG

Any suggestion or help would be highly appreciated

Answer 1

It's likely that they accomplished this by using the UCSC Table Browser to:

1. Find the loci of the two isoforms you mention
2. Finding CpG islands (Group = Regulation, Track = CpG Islands) near those transcription start sites
3. Design primers using Applied Biosystem's software

Alternatively, they list the exact primers used in Table 1.

They don't detail exactly how they did it, so if you have specific questions it might be worth it to email the corresponding author