Studying epigenetics of paternal or maternal allele - (Nov/12/2012 )
I have been wondering and searching but haven't found a method that enables distinguishing the paternal and maternal allele with all the modifications and proteins bound to DNA. This would be extremely helpful when studying imprinted genes and their regulatory proteins and modifications - now bisulfite seq and ChIP only give a mixed result.
Separating the alleles could be possible at the chromosome level, but how? Any ideas or comments? I have heard about some technique that uses mitosis as a starting point but the regulatory mechanisms cannot be studied with the same strategy. I have thought that artificial triplex structures in the area of many maternal/paternal SNPs could serve as a starting point for chromosome capture but applying this technique might be impossible.
Don't hesitate to share your ideas or comments, I'm looking forward to them!
We have a model, where we transfered single specific human chromosome into MEL cell line. But I'm not sure whether the modifications will be conserved along the cell divisions.
Thanks for the reply. Indeed, artificial biochemical microenvironments and cell divisions will affect the combination of regulatory factors. This cell line would at least help indentifying paternal/maternal SNPs. Have you published a paper about making this cell line?
We used similar approach as descirbed in this original paper, but used patients EBV-transformed lymphocytes instead of fetal cells.
Papayannopoulou T, Brice M, Stamatoyannopoulos G. Analysis of human hemoglobin switching in MEL x human fetal erythroid cell hybrids. Cell. 1986 Aug 1;46(3):469-76.