Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

Villalba-Benito, Leticia; López-López, Daniel; Torroglosa, Ana; Casimiro-Soriguer, Carlos S.; Luzón-Toro, Berta; Fernández, Raquel María; Moya-Jiménez, María José; Antiñolo, Guillermo; Dopazo, Joaquín; Borrego, Salud

doi:10.1186/s13148-021-01040-6

Table 2 HSCR-susceptibility genes that showed an aberrant methylation level in HSCR patients versus controls

From: Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

	Gene	Seqnames	Start	End	Width	Beta	Pval	Annot,strand	1to5kb	5UTRs	Promoters	Firstexons	Exons	Introns	3UTRs
1	*ABO*	chr9	133,259,941	133,260,919	979	− 0.858	0.004	−						X
2	ACTN4	chr19	38,647,739	38,647,796	58	0.119	0.033	+		X	X	X	X
3	ADORA2A	chr22	24,427,450	24,427,589	140	0.378	0.036	+	X	X	X	X	X	X
4	*AES*	chr19	3,057,417	3,059,794	2378	− 0.885	0.001	−	X	X	X	X	X	X
5	*AFAP1-AS1*	chr4	7,768,658	7,771,115	2458	− 0.647	0.047	+						X
6	*AHNAK*	chr11	62,538,664	62,539,087	424	− 0.987	0.042	−	X					X
7	*AP3B2*	chr15	82,703,145	82,703,810	666	− 0.526	0.027	−	X					X
8	*ARNT2*	chr15	80,435,195	80,437,732	2538	− 0.544	0.047	+	X					X
9	ASCL1	chr12	102,958,457	102,958,690	234	0.124	0.023	+				X	X
10	BCL11B	chr14	99,271,192	99,272,182	991	0.123	0.031	−		X	X	X	X
11	*CA3*	chr8	85,423,540	85,424,639	1100	− 0.669	0.040	+						X
12	*CACNA1C*	chr12	2,230,284	2,230,376	93	− 1.031	0.003	+						X
13	CAPN10	chr2	240,589,510	240,589,844	335	0.692	0.039	+	X		X		X	X
14	*CHRNA7*	chr15	32,060,846	32,060,974	129	− 0.645	0.022	+						X
15	*COL6A1*	chr21	45,992,053	45,994,972	2920	− 0.258	0.046	+	X				X	X
16	*CREBBP*	chr16	3,773,849	3,774,877	1029	− 0.530	0.043	−	X		X	X	X	X
17	CTNS	chr17	3,635,527	3,637,759	2233	0.345	0.014	+	X	X	X	X	X	X
18	*DBH*	chr9	133,642,000	133,642,886	887	− 0.636	0.039	+					X	X
19	DHCR7	chr11	71,440,414	71,442,189	1776	0.413	0.026	−	X		X	X	X	X
20	*DSCAM*	chr21	40,197,142	40,198,150	1009	− 0.805	0.001	−						X
21	ECE1	chr1	21,290,149	21,290,245	97	0.090	0.039	−		X		X	X	X
22	*FAT3*	chr11	92,451,580	92,452,675	1096	− 0.605	0.008	+						X
23	*FGD2*	chr6	37,025,970	37,026,290	321	− 0.411	0.050	+						X
24	*GDNF*	chr5	37,834,936	37,835,683	748	− 0.649	0.012	−		X	X	X	X	X
25	*GFRA1*	chr10	116,112,901	116,113,661	761	− 0.479	0.043	−						X
26	GLI2	chr2	120,987,959	120,988,503	545	0.176	0.039	+					X	X	X
27	*IHH*	chr2	219,055,465	219,055,534	70	− 0.558	0.038	−					X
28	IRS1	chr2	226,796,575	226,797,233	659	0.983	0.019	−	X			X	X
29	*ITGB2*	chr21	44,886,345	44,888,733	2389	− 0.637	0.006	−				X	X	X	X
30	*ITIH5*	chr10	7,602,000	7,602,962	963	− 0.737	0.023	−						X
31	*KCNH2*	chr7	150,958,459	150,958,537	79	− 0.615	0.019	−	X				X	X
32	*KCNN3*	chr1	154,790,536	154,791,444	909	− 0.735	0.025	−						X
33	*LAMA1*	chr18	7,109,731	7,109,954	224	− 0.413	0.044	−						X
34	*MEG3*	chr14	100,824,290	100,824,355	66	− 1.330	0.001	+	X					X
35	*MUC4*	chr3	195,778,818	195,778,991	174	− 0.499	0.016	−					X	X
36	*NLRP12*	chr19	53,809,751	53,810,198	448	− 0.729	0.025	−	X				X
37	*NLRP3*	chr1	247,430,893	247,431,526	634	− 1.075	0.001	+						X
38	*NOTCH1*	chr9	136,507,039	136,507,083	45	− 0.598	0.038	−	X					X
39	*NR2F1*	chr5	93,588,640	93,588,660	21	− 1.076	0.004	+	X					X
40	*NTF3*	chr12	5,452,375	5,453,552	1178	− 0.547	0.017	+	X					X
41	*NTRK3*	chr15	88,059,303	88,061,553	2251	− 0.788	0.031	−						X
42	*PCDHA9*	chr5	140,877,089	140,877,155	67	− 0.548	0.016	+						X
43	PTCH1	chr9	95,504,586	95,505,498	913	0.835	0.041	−	X					X
44	RARB	chr3	25,380,243	25,380,308	66	0.959	0.007	+						X
45	*RBP3*	chr10	47,348,275	47,349,153	879	− 0.821	0.006	+		X	X	X	X
46	*RBPMS*	chr8	30,441,141	30,441,979	839	− 0.696	0.039	+	X		X			X
47	*RPS6KA3*	chrX	20,265,270	20,265,640	371	− 0.488	0.007	−						X
48	SH2B1	chr16	28,862,077	28,862,273	197	0.647	0.046	+	X		X			X
49	*SIX2*	chr2	45,012,355	45,013,494	1140	− 0.739	0.006	−	X			X	X
50	SLC2A1	chr1	42,940,264	42,941,301	1038	0.528	0.043	−						X
51	*SOX8*	chr16	978,998	980,273	1276	− 0.789	0.008	+	X
52	*TERT*	chr5	1,292,813	1,293,293	481	− 0.639	0.032	−						X
53	*TNC*	chr9	115,085,688	115,086,564	877	− 0.600	0.014	−					X	X
54	*TST*	chr22	37,024,548	37,024,766	219	− 0.305	0.038	−	X
55	ZFHX3	chr16	72,947,027	72,948,255	1229	0.937	0.041	−						X

Genes in bold were hypomethylated (ß < 0), whereas the remaining genes were hypermethylated (ß > 0)

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ISSN: 1868-7083

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