Human genomes are diploid. So, is the methylation pattern in one homologous chromosome the same as the methylation pattern in the other homologous chromosome?
One more question is that when CpG is methylated in one site, is CpG always methylated on both strands of the DNA or only one strand, as there are two strands of opposing directions in every DNA.
Very appreciated.
No. Both chromosomes are different in methylation paterns. It depends a lot in which gene you're looking for. For example, if you double the mother genes and put them in an oocyte, (2n=46, all mother's) the fetus will develop partially, the embrionary anexus will not have a good development at all and both will eventually stop, and the opposite (2n=46 all father's) the fetus will have a poor development and the anexus will have a better one (compared with (2n=46 all mother's) and both will eventually stop. This aspect is observed in embrionary development, and is cause by the genomic imprinting, which is the different methylation patern of the strands. In most cases, when leading with development genes, one chromosome will be methylated and the other will not be, but that is not a rule and methylation patern can change with age and because of external agents.
When talking about strands, once you have two strands and one is read and the other is not, known as coding strand and template strand (not a rule either), That makes no sense to have the same patern of methylation in both. Think like this -> 5'CTGACTGA3' is not the same as 3'GACTGACT5'
There are some exceptions, though (e.g. have a look at http://www.jbc.org/content/280/15/14413.full)
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