Up-regulation of ERE-close genes during reprogramming. (A) Using a twofold change cutoff and an adjusted P-value of <0.05, 3703 genes were found up-regulated in CD34+ cells at day 19 post-OKS transduction, compared with untransduced cells. (Left) Relative expression of HERVH (top) or HERVK (bottom) integrants situated close (<40 kb) or far (>80 kb) from these genes. No significant difference was detected (Wilcoxon test P = 0.14 for HERVK, 0.11 for HERVH). (Right) Reverse analysis, revealing that HERVH-close transcripts (n = 365 genes, or 695 transcripts) were more likely to be up-regulated than HERVH-distant transcripts (n = 18145 genes, or 30,053 transcripts). (NA) Not available due to insufficient numbers. (B) Expression levels of intragenic vs. intergenic HERVHs or HERVKs at d19 of CD34+ cells reprogramming showing no bias toward intragenic HERVs. In fact, the reverse trend was observed, with more intergenic than intragenic HERVs up-regulated at d19 of reprogramming.
