I have been trying to map out the H19/IGF2 locus and I am having difficulties in finding literature which either agrees or states the exact positioning of the DMR region containing 7 CTCF sites as used in many previous publications ( Takai et al. 2001, Vu et al. 2000 and Ollikainen et al. 2010 to name a few). As I understood the region falls within the ICR, roughly bp 2021000-2023000 (chromosome 11). However, Ollikainen et al. 2010 has a table in the supplementary information which states the bp as 1,977,544-1,977,869 which is a very different position! Has anyone worked on this region before and could point me roughly in the right direction? Any help or advice would be greatly appreciated!
Kristina,
If you use the genome browser (http://www.ncbi.nlm.nih.gov/epigenomics/view/genome/3481/?assembly=27&term=IGF2), you will see that the sequence between IGF2 and H19 includes the bp 2021000-2023000 position. My guess is that if you use a transcription factor browser you will find the CTCF sites within this region.
I'd concur with the response above. See the following UCSC browser (Feb. 2009 GRCh37/hg19) output showing CTCF ChIP annotation:
(http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:2018665-2025334&hgsid=342411819&wgEncodeBroadHistoneViewSignal=full)
It is also likely that different genome builds were used by each study. The genome assembly and co-ordinates for a given locus may vary between successive builds. The older studies would have used earlier builds which might explain the discrepancies you mention.
Thank you for your answers! My initial estimate within the 2021000-2023000 position was made on my initial preliminary searches using such websites but as I looked into the literature the conflicting data somewhat confused me. Too much mixed lingo and interpretations in some published papers! Lesson learnt to stick to my gut instinct. Thank you again.
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