Dinh 2011/NOTES/2011-7-8

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Correlation of DNA methylation with reprogramming efficiency and metabolic genes

Athanasia have found that the reprogramming efficiencies of different somatic cell types may be due to their differential use of metabolic pathways especially oxidative phosphorylation and glycolysis. Her study mainly focused on comparing Keratinocytes and fibroblasts with the addition of HUVECs. Although we did not used cells of the same lineages, we have methylation data for these cell types.

The question from reviewers were concerning whether we see differential methylation patterns associated with the genes involved in either of these pathways

The following analysis was done using the BSPP data for 
K-MMTA, KiPS4F8, HFF-XF, FiPS3F1, FiPS4F7, HUVEC, HUViPS4F1, and HUViPS4F3.
  • First, I did paired-wise calculation of DMS using Benjamini Hochberg's FDR 0.01. Only the sites available between pairs at 10x coverage were considered. Finally, I merged DMSs together, and obtained a set of "potential" DMS for Ker, Fib, and Huv lineages.
KiPS4F8 vs KMMTA
FiPS3F1 vs HFF-XF and FiPS4F7 vs HFF-XF (merged DMSs)
HUViPS4F1 vs HUVEC and HUViPS4F3 vs HUVEC (merged DMSs)
  • I uploaded the "potential" DMSs to GREAT, and obtained a list of possible Gene-CG site interactions based on distance regulation to known regulatory regions and TSS.
  • Next, I went to KEGG and downloaded the genes involved in oxidative phosphorylation, glycolysis, and in the citrate cycle.
  • Then I labeled the potential genes-DMS interaction list with either Glycolysis, Oxidative Phos, or TCA if the gene belongs to each pathway.

Note: A CG site may have interaction with more than one gene, but not in the same pathways.

  • Finally, a count of gene-DMS interactions involved in either glycolysis, oxidative phosphorylation, or citrate cycle over the count of the gene-DMS interactions which are not involved.
Oxidative - 
Fib = 300/(75,732+300) = 0.39%
Ker = 276/(60,742+276) = 0.45%
Huv = 317/(70,380+317) = 0.45%
In oxidative phosphorylation keratinocytes share similar amount of methylation changes as HUVEC
Glycolysis - 
Fib = 218/(75,816+218) = 0.29%
Ker = 237/(60,784+237) = 0.39%
Huv = 197/(70,503+197) = 0.28%
In glycolysis, keratinocytes share similar amount of methylation changes as fibroblasts
Citrate - 
Fib = 72/(75960+72) = 0.09%
Ker = 80/(60938+80) = 0.13%
Huv = 78/(70619+78) = 0.11%
  • Methylation levels heatmaps at DMSs near pathway genes [DMSs are binned in windows of CGs within 1kb]

File:Heat map binnedDMSs.pdf