Epigenetic adaptations of the masticatory mucosa to periodontal inflammation

Clinical Epigenetics

Table 6 Summary of significant differentially methylated regions

Chr:position (start–end) (hg19)	Gene symbol	Median TPM*	Regulatory features**	Paired analysis		Full analysis
Chr:position (start–end) (hg19)	Gene symbol	Median TPM*	Regulatory features**	p	FWER	p	FWER
chr1:224,544,384–224,544,535	CNIH4	723	TSS; DHS	< 10^–6	< 0.01	< 10^–6	< 0.01
chr16:3,220,475–3,221,355	tRNA pseudogene	NA	R, E, TSS***	< 10^–6	< 0.01	4.7 × 10^–4	0.04
chr1:23,857,884–23,858,301	E2F2	154	TSS; DHS	9.8 × 10^–5	0.01	n.s	n.s
chr11:8,986,449–8,986,674	TMEM9B	1020	TSS; DHS	9.8 × 10^–5	0.01	n.s	n.s
chr6:31,515,391–31,515,404	NFKBIL1	128	TSS; DHS	9.8 × 10^–5	0.01	1.2 × 10^–4	0.01
chr7:158,342,283–15,8342,600	PTPRN2	39	R, T, WE***; DHS	9.8 × 10^–5	0.01	5.9 × 10^–4	0.04
chr10:135,164,246–135,164,482	PRAP1	0	T	9.8 × 10^–5	0.01	5.9 × 10^–4	0.04
chr19:2,462,441–2,462,961	LMNB2	1103	R, E, TSS***	2.0 × 10^–4	0.02	5.9 × 10^–4	0.04
chr11:64,360,872–64,360,997	SLC22A12	0	R	2.9 × 10^–4	0.03	n.s	n.s
chr11:2,919,808–2,920,209	SLC22A18 (+ -AS)	53 (5)	TSS, E, WE***; DHS	3.9 × 10^–4	0.04	n.s	n.s
chr1:161,087,882–161,087,906	NIT1	238	TSS; DHS	3.9 × 10^–4	0.04	n.s	n.s

^*mRNA-sequencing in healthy keratinized oral mucosa with 16mio reads/sample [12]. **Based on ChIP-seq data from the ENCODE Consortium. ***depending on cell type. DNase hypersensitivity sites (DHS) with cluster score 1000 are listed. TPM = transcripts per million, FWER = family wise error rate, TSS = Predicted promoter region including transcription start site, E = Predicted enhancer, WE = Predicted weak enhancer or open chromatin cis regulatory element, T = Predicted transcribed region, R = Predicted repressed or low activity region, N.s. = not significant (p and FWER > 0.05, respectively)

ISSN: 1868-7083