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

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

		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

Abbreviations: Cx cortex, FC fold-change. Statistical significances: log2FC change and corresponding p-value (< 0.05) are shown in bolded font

ISSN: 2051-5960