Dear all, we have a mutant with a T-DNA inserted in a gene encoding one ubiquitin system component. In this mutant, a number of genes are highly downregulated at the transcript levels, which looks like relevant to the observed phenotypes. We are trying to PCR-amplify those downregulated genes from genomic DNA of the mutant, however, we encountered difficulty to amplify those genes. It may well be possible the PCR failure is due to additional T-DNAs inserted into those genes. However, after mutant complementation by corresponding wild-type gene, those downregulated genes can now be amplified. We suspect, in the mutant, those genes are hypermethylated and hypermethylation may affect PCR amplification drastically. Is this possible, do you aware of this? Any published report regarding hypermethylation affects PCR amplification? Of course we are currently trying to analyze the methylation status for these downregulated genes. Thank you for your help in advance. Best regards! Hong!
Institute of Plant and Microbial Biology,