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Table 2 Validation of gene promoter methylation by pyrosequencing and gene expression by ddPCR in the perilesional cortex, thalamus and hippocampus. As negative controls, we also assessed the methylation and gene expression in the ipsilateral hippocampus and thalamus. Wdr26, Lrp1b, and Ppid genes had only one CpG site whereas Gpr12 gene had two CpG sites

From: Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury

   Wdr26 Lrp1b Ppid Gpr12
Perilesional Cx Gene expression
Log2FC −0.94944 − 0.17498 − 0.60015 −0.37159
p-value 0.007592 0.7756 0.03596 0.3277
Methylation
Average methylation (%) 85.31 67.28 59.52 CpG site1: 73.43 CpG site2: 76.57
Difference TBI - sham (%) 1.07 −0.17 2.39 CpG site1:0.43 CpG site2:0.35
p-value 0.1135 0.9546 0.3636 CpG site1: 0.8639 CpG site2: 1
Hippocampus Gene expression
Log2FC −0.6746 −0.6457 −1.3397 −0.3415
p-value 0.366 0.1375 0.366 0.366
Methylation
Average methylation (%) 87.22 59.92 57.25 CpG site1: 69.06 CpG site2: 73.48
Difference TBI - sham (%) 1.10 −2.73 2.65 CpG site1: 1.70 CpG site2: −0.59
p-value 0.366 0.2343 0.366 CpG site1: 0.5338 CpG site2: 1
Thalamus Gene expression
Log2FC −0.8936 −0.4964 −0.9309 −1.3735
p-value 0.181 0.3277 0.06633 0.001598
Methylation
Average methylation (%) 85.11 65.82 49.95 CpG site1: 74.23 CpG site2: 77.40
Difference TBI - sham (%) 1.07 −2.33 7.69 CpG site1: −0.95 CpG site2: −0.93
p-value 0.1469 0.5287 0.3884 CpG site1: 0.7756 CpG site2: 0.1135
  1. Abbreviations: Cx cortex, FC fold-change. Statistical significances: log2FC change and corresponding p-value (< 0.05) are shown in bolded font