no DNA fragment pull down in the first CpG island (MBD-seq)
Posted 13 September 2012 - 06:28 PM
I performed a methyl-CpG binding doman (MBD) protein capture and genome-wide sequencing.
To see any methylation level changes in those gene I am interest in.
After I got the data, using IGV to see the reads, I found that most of the gene's first CpG island (start from TSS) has almost no reads!
Same situation in this journal:
Dnmt3a-Dependent Nonprmoter DNA Methylation Facilitates Transcription of Neurogenic Genes Science 329,444 (2010) fig2D
My question is:
1) Suppose MBD will capture the methylated DNA fragments, why most of the genes have no reads in the first CpG island?
2) Why only happen in the first CpG island of the genes but not the second or third even last one?
3) Is that any method can come over this problem? ( If this situation is a problem or bias)
Thanks in advance!
Posted 13 September 2012 - 07:22 PM
Posted 13 September 2012 - 07:48 PM
That means if the proximal promoter CpG island have methylation level changes, those genes I have to pay attention on it as it was activated by the oncogene?