Can these CpG islands be representative? - (Jul/11/2005 )
I get the DNA sequence 5kb upstream from exon1 and exon1 to predicate CpG islands.
I use CpG Island Explorer to predicate CpG islands,but in one gene I did not get CpG island in the promoter region adjacent to exon1 , I only get one CpG island about 4kb upstream the ATG codon, does the CpG region could be representative for study? If it is not appropriate,should I discard this gene?
Another question, if a 200bp fragment of CpG island across part of promoter and part of exon1, does its' methylation state could be representative the methylation state of the whole promter CpG islands(more than 1000bp long)? Does it necessary to detect methylation state of the whole promoter CpG islands? If not, which region is the best representative? And how to find it? For MSP method,how long fragment is appropriate for detection?
Thanks for any advice!
If the CpG island is far away from the promoter or transcriptional start site, it is hard to say whether its methylation has any impact on transcription.
Some CpG islands extend into exon 1. To know methylation of which area affects transcription, you have to do a high resolution mapping using bisulfite sequencing. There is no way of predicting it.
MSP usually amplifies a region around 200 bp.