antibody to use for methylase chip - DNMT/MBD/MeCP2? (Oct/15/2008 )

i posted this here instead of the chip section because no one talks about dnmt in that section. i think it has more to do with methylation than the actual chip process anyways.

anyways, i want to do a chip using an antibody for a methylation associated protein. the cells i will be using are human adrenal and breast cells. i would like to use antibodies for dnmt1. this would be the transferase associated with methylation in these cell lines, right?

also, is anti-dnmt1 the best choice or is anti-methyl binding protein a better choice? i know MeCP2 won't bind all methylated dna, so i'm thinking the anti-dnmt1 would be better. what do you think?

thanks for the help,
matt

So your purpose is to chip protein associated with methylated DNA, right? I don't think DNMT1 is a good choice because DNMT1 is a maintaining methylase and it methylates DNA during DNA synthesis. Crosslinking only provides a snap shot of the chromosome. I really doubt that ChIP can catch its action at the scene

what is commonly used to chip methylation associated proteins? would i have to try one of the MBPs, MeCP2? any suggestions?

anti-5mC would be the method of choice though you would need single stranded DNA.

There are some exciting new antibodies that are in the pipeline I heard at a Cancer workshop here and involves MBD protein.